Starting phenix.real_space_refine on Thu Jul 2 11:17:54 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8eu2_28602/07_2026/8eu2_28602_neut.cif Found real_map, /net/cci-nas-00/data/ceres_data/8eu2_28602/07_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_28602/07_2026/8eu2_28602.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8eu2_28602/07_2026/8eu2_28602.map" model { file = "/net/cci-nas-00/data/ceres_data/8eu2_28602/07_2026/8eu2_28602_neut.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8eu2_28602/07_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-dev-6108/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: 1.93, per 1000 atoms: 0.22 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: 0.70 Conformation dependent library (CDL) restraints added in 259.1 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: 1.04 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: 1.48 Time building geometry restraints manager: 0.94 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: 12478 1.83 - 3.67: 919 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: 0.010 Normalize map: mean=0, sd=1: 6.990 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: 0.180 Check model and map are aligned: 0.030 Set scattering table: 0.030 Process input model: 9.490 Find NCS groups from input model: 0.070 Set up NCS constraints: 0.010 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:6.440 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 23.270 ------------------------------------------------------------------------------- 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= 0.598 Angle : 0.957 9.165 13477 Z= 0.774 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 0.95701 / 0.77 (13477) hydrogen bonds : bond 0.11358 / 12.57 ( 561) hydrogen bonds : angle 3.72919 / 4.80 ( 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 : 0.218 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: L 45 ARG cc_start: 0.7928 (mmm-85) cc_final: 0.7603 (mtp-110) 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: 0.6028 time to fit residues: 122.7071 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 : 0.214 ------------------------------------------------------------------------------- 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: 0.0050 overall best weight: 0.3994 ------------------------------------------------------------------------------- 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 = 0.131763 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3585 r_free = 0.3585 target = 0.105743 restraints weight = 15841.685| |-----------------------------------------------------------------------------| r_work (start): 0.3559 rms_B_bonded: 1.55 r_work: 0.3420 rms_B_bonded: 2.72 restraints_weight: 0.5000 r_work: 0.3276 rms_B_bonded: 4.59 restraints_weight: 0.2500 r_work (final): 0.3276 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8443 moved from start: 0.1009 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 9282 Z= 0.185 Angle : 0.686 8.289 13477 Z= 0.409 Chirality : 0.047 0.202 1536 Planarity : 0.005 0.070 944 Dihedral : 31.128 171.203 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 : 18.76 % Favored : 78.72 % 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 : -0.54 (0.53), residues: 126 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG O 63 TYR 0.015 0.001 TYR M 57 PHE 0.006 0.001 PHE K 104 HIS 0.001 0.001 HIS P 75 Details of bonding type rmsd/Z covalent geometry : bond 0.00303 / 0.19 ( 9282) covalent geometry : angle 0.68588 / 0.41 (13477) hydrogen bonds : bond 0.05835 / 6.42 ( 561) hydrogen bonds : angle 2.96418 / 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 208 residues out of total 437 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 197 time to evaluate : 0.143 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: K 85 GLN cc_start: 0.8394 (mt0) cc_final: 0.8141 (mt0) REVERT: K 131 ARG cc_start: 0.8731 (ttt180) cc_final: 0.8438 (mtt-85) REVERT: M 61 GLU cc_start: 0.8030 (mp0) cc_final: 0.7686 (mp0) REVERT: M 64 GLU cc_start: 0.8234 (tp30) cc_final: 0.7854 (tp30) REVERT: M 68 ASN cc_start: 0.8475 (m-40) cc_final: 0.7186 (m110) REVERT: N 64 ASN cc_start: 0.8788 (m-40) cc_final: 0.8527 (m-40) REVERT: N 73 GLU cc_start: 0.8449 (tp30) cc_final: 0.8101 (tp30) REVERT: O 120 MET cc_start: 0.7904 (mtt) cc_final: 0.7557 (mtm) REVERT: O 129 ARG cc_start: 0.8627 (mmm-85) cc_final: 0.8255 (tmm-80) REVERT: O 130 ILE cc_start: 0.9004 (mm) cc_final: 0.8790 (mt) outliers start: 11 outliers final: 9 residues processed: 198 average time/residue: 0.5814 time to fit residues: 121.2861 Evaluate side-chains 203 residues out of total 437 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 194 time to evaluate : 0.142 ------------------------------------------------------------------------------- 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: 0.5980 chunk 3 optimal weight: 3.9990 chunk 56 optimal weight: 0.9990 chunk 13 optimal weight: 3.9990 chunk 24 optimal weight: 0.9980 chunk 65 optimal weight: 0.9990 chunk 1 optimal weight: 3.9990 chunk 29 optimal weight: 0.3980 chunk 21 optimal weight: 3.9990 chunk 33 optimal weight: 0.3980 chunk 37 optimal weight: 0.7980 overall best weight: 0.6380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... M 89 ASN M 94 ASN M 112 GLN N 44 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: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3939 r_free = 0.3939 target = 0.130287 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3560 r_free = 0.3560 target = 0.104240 restraints weight = 15696.188| |-----------------------------------------------------------------------------| r_work (start): 0.3533 rms_B_bonded: 1.53 r_work: 0.3395 rms_B_bonded: 2.70 restraints_weight: 0.5000 r_work: 0.3253 rms_B_bonded: 4.52 restraints_weight: 0.2500 r_work (final): 0.3253 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8470 moved from start: 0.1330 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 : 0.669 6.961 13477 Z= 0.399 Chirality : 0.046 0.203 1536 Planarity : 0.005 0.063 944 Dihedral : 31.094 170.430 2968 Min Nonbonded Distance : 2.453 Molprobity Statistics. All-atom Clashscore : 7.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.17 % Favored : 98.83 % Rotamer: Outliers : 4.35 % Allowed : 22.20 % Favored : 73.46 % 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: 1.89 (0.38), residues: 512 helix: 1.85 (0.27), residues: 387 sheet: None (None), residues: 0 loop : -0.59 (0.52), residues: 125 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG O 63 TYR 0.020 0.002 TYR P 88 PHE 0.010 0.001 PHE K 104 HIS 0.003 0.001 HIS M 31 Details of bonding type rmsd/Z covalent geometry : bond 0.00357 / 0.20 ( 9282) covalent geometry : angle 0.66929 / 0.40 (13477) hydrogen bonds : bond 0.05807 / 6.41 ( 561) hydrogen bonds : angle 2.86256 / 3.80 ( 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 222 residues out of total 437 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 203 time to evaluate : 0.160 Fit side-chains revert: symmetry clash REVERT: K 85 GLN cc_start: 0.8494 (mt0) cc_final: 0.8280 (mt0) REVERT: K 131 ARG cc_start: 0.8730 (OUTLIER) cc_final: 0.8438 (mtt-85) REVERT: L 45 ARG cc_start: 0.8293 (mmm-85) cc_final: 0.7886 (mtp-110) REVERT: L 88 TYR cc_start: 0.8824 (m-10) cc_final: 0.8615 (m-10) REVERT: M 61 GLU cc_start: 0.8057 (mp0) cc_final: 0.7590 (mp0) REVERT: M 64 GLU cc_start: 0.8228 (tp30) cc_final: 0.7640 (tp30) REVERT: M 68 ASN cc_start: 0.8498 (m-40) cc_final: 0.6996 (m-40) REVERT: N 39 TYR cc_start: 0.8671 (t80) cc_final: 0.8415 (t80) REVERT: N 64 ASN cc_start: 0.8806 (m-40) cc_final: 0.8535 (m-40) REVERT: O 70 LEU cc_start: 0.8873 (tp) cc_final: 0.8590 (tm) REVERT: O 116 ARG cc_start: 0.8666 (ttp80) cc_final: 0.8417 (ttp80) REVERT: O 120 MET cc_start: 0.7906 (mtt) cc_final: 0.7545 (mtm) outliers start: 19 outliers final: 12 residues processed: 205 average time/residue: 0.5807 time to fit residues: 124.9464 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 : 0.137 ------------------------------------------------------------------------------- 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 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 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: 0.7980 chunk 12 optimal weight: 6.9990 chunk 45 optimal weight: 0.9980 chunk 16 optimal weight: 2.9990 chunk 7 optimal weight: 3.9990 chunk 26 optimal weight: 0.8980 chunk 4 optimal weight: 2.9990 chunk 22 optimal weight: 0.3980 chunk 8 optimal weight: 2.9990 chunk 60 optimal weight: 0.5980 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... K 108 ASN ** L 75 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** L 93 GLN O 55 GLN O 68 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 = 0.3915 r_free = 0.3915 target = 0.128641 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3532 r_free = 0.3532 target = 0.102449 restraints weight = 15927.588| |-----------------------------------------------------------------------------| r_work (start): 0.3507 rms_B_bonded: 1.54 r_work: 0.3366 rms_B_bonded: 2.72 restraints_weight: 0.5000 r_work: 0.3223 rms_B_bonded: 4.56 restraints_weight: 0.2500 r_work (final): 0.3223 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8500 moved from start: 0.1696 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= 0.222 Angle : 0.687 7.792 13477 Z= 0.404 Chirality : 0.047 0.208 1536 Planarity : 0.006 0.060 944 Dihedral : 31.099 167.182 2968 Min Nonbonded Distance : 2.465 Molprobity Statistics. All-atom Clashscore : 7.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.15 % Favored : 97.85 % Rotamer: Outliers : 5.49 % Allowed : 24.03 % Favored : 70.48 % 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: 2.12 (0.37), residues: 512 helix: 2.05 (0.27), residues: 387 sheet: None (None), residues: 0 loop : -0.66 (0.51), residues: 125 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG M 71 TYR 0.018 0.002 TYR P 88 PHE 0.016 0.002 PHE K 78 HIS 0.004 0.001 HIS M 31 Details of bonding type rmsd/Z covalent geometry : bond 0.00403 / 0.22 ( 9282) covalent geometry : angle 0.68688 / 0.40 (13477) hydrogen bonds : bond 0.05972 / 6.57 ( 561) hydrogen bonds : angle 2.83290 / 3.78 ( 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 221 residues out of total 437 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 197 time to evaluate : 0.150 Fit side-chains revert: symmetry clash REVERT: K 125 GLN cc_start: 0.8786 (OUTLIER) cc_final: 0.7874 (mp10) REVERT: K 131 ARG cc_start: 0.8697 (OUTLIER) cc_final: 0.8414 (mtt-85) REVERT: M 61 GLU cc_start: 0.8080 (mp0) cc_final: 0.7784 (mp0) REVERT: M 64 GLU cc_start: 0.8247 (tp30) cc_final: 0.7767 (tp30) REVERT: M 68 ASN cc_start: 0.8482 (m-40) cc_final: 0.7191 (m-40) REVERT: N 39 TYR cc_start: 0.8679 (t80) cc_final: 0.8402 (t80) REVERT: N 64 ASN cc_start: 0.8839 (m-40) cc_final: 0.8551 (m-40) REVERT: N 73 GLU cc_start: 0.8464 (tp30) cc_final: 0.8203 (tp30) REVERT: O 70 LEU cc_start: 0.8896 (tp) cc_final: 0.8545 (tm) REVERT: O 116 ARG cc_start: 0.8726 (ttp80) cc_final: 0.8491 (ttp80) REVERT: O 120 MET cc_start: 0.7950 (mtt) cc_final: 0.7578 (mtm) REVERT: P 31 LYS cc_start: 0.9007 (OUTLIER) cc_final: 0.8470 (tptm) REVERT: P 91 LYS cc_start: 0.8835 (ttmt) cc_final: 0.8610 (ttmt) outliers start: 24 outliers final: 16 residues processed: 200 average time/residue: 0.5990 time to fit residues: 125.9840 Evaluate side-chains 215 residues out of total 437 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 196 time to evaluate : 0.214 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 Chi-restraints excluded: chain P residue 88 TYR 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: 0.5980 chunk 70 optimal weight: 0.3980 chunk 32 optimal weight: 0.0270 chunk 69 optimal weight: 0.7980 chunk 16 optimal weight: 2.9990 chunk 43 optimal weight: 1.9990 chunk 11 optimal weight: 30.0000 chunk 42 optimal weight: 0.5980 chunk 60 optimal weight: 0.3980 chunk 3 optimal weight: 3.9990 overall best weight: 0.4038 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** O 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3941 r_free = 0.3941 target = 0.130337 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3564 r_free = 0.3564 target = 0.104380 restraints weight = 15815.184| |-----------------------------------------------------------------------------| r_work (start): 0.3539 rms_B_bonded: 1.56 r_work: 0.3401 rms_B_bonded: 2.73 restraints_weight: 0.5000 r_work: 0.3258 rms_B_bonded: 4.59 restraints_weight: 0.2500 r_work (final): 0.3258 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8471 moved from start: 0.1767 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 9282 Z= 0.165 Angle : 0.639 6.723 13477 Z= 0.381 Chirality : 0.045 0.196 1536 Planarity : 0.005 0.065 944 Dihedral : 31.054 167.573 2968 Min Nonbonded Distance : 2.468 Molprobity Statistics. All-atom Clashscore : 7.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.17 % Favored : 98.83 % Rotamer: Outliers : 5.03 % Allowed : 25.86 % Favored : 69.11 % 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 (0.37), residues: 512 helix: 2.36 (0.27), residues: 386 sheet: None (None), residues: 0 loop : -0.60 (0.51), residues: 126 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG M 20 TYR 0.020 0.002 TYR P 88 PHE 0.012 0.001 PHE K 78 HIS 0.006 0.001 HIS M 31 Details of bonding type rmsd/Z covalent geometry : bond 0.00275 / 0.16 ( 9282) covalent geometry : angle 0.63900 / 0.38 (13477) hydrogen bonds : bond 0.05229 / 5.80 ( 561) hydrogen bonds : angle 2.70845 / 3.63 ( 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 220 residues out of total 437 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 198 time to evaluate : 0.216 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: K 125 GLN cc_start: 0.8747 (OUTLIER) cc_final: 0.7817 (mp10) REVERT: K 131 ARG cc_start: 0.8685 (OUTLIER) cc_final: 0.8397 (mtt-85) REVERT: M 61 GLU cc_start: 0.8051 (mp0) cc_final: 0.7800 (mp0) REVERT: M 64 GLU cc_start: 0.8182 (tp30) cc_final: 0.7742 (tp30) REVERT: M 68 ASN cc_start: 0.8432 (m-40) cc_final: 0.7420 (m-40) REVERT: N 64 ASN cc_start: 0.8835 (m-40) cc_final: 0.8551 (m-40) REVERT: N 73 GLU cc_start: 0.8507 (tp30) cc_final: 0.8245 (tp30) REVERT: O 70 LEU cc_start: 0.8868 (tp) cc_final: 0.8514 (tm) REVERT: O 116 ARG cc_start: 0.8668 (ttp80) cc_final: 0.8435 (ttp80) REVERT: O 120 MET cc_start: 0.7943 (mtt) cc_final: 0.7560 (mtm) REVERT: P 91 LYS cc_start: 0.8798 (ttmt) cc_final: 0.8559 (ttmt) outliers start: 22 outliers final: 15 residues processed: 202 average time/residue: 0.6361 time to fit residues: 135.4415 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 : 0.234 ------------------------------------------------------------------------------- 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 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 98 LEU 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 88 TYR 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: 0.0570 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: 1.4104 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... K 108 ASN ** L 75 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 81 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** O 55 GLN P 93 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3864 r_free = 0.3864 target = 0.125095 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3474 r_free = 0.3474 target = 0.098963 restraints weight = 15789.582| |-----------------------------------------------------------------------------| r_work (start): 0.3451 rms_B_bonded: 1.62 r_work: 0.3310 rms_B_bonded: 2.75 restraints_weight: 0.5000 r_work: 0.3166 rms_B_bonded: 4.62 restraints_weight: 0.2500 r_work (final): 0.3166 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8553 moved from start: 0.2139 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.058 9282 Z= 0.369 Angle : 0.810 10.855 13477 Z= 0.456 Chirality : 0.054 0.225 1536 Planarity : 0.007 0.069 944 Dihedral : 31.203 158.955 2968 Min Nonbonded Distance : 2.476 Molprobity Statistics. All-atom Clashscore : 8.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.54 % Favored : 97.46 % Rotamer: Outliers : 5.72 % Allowed : 25.40 % Favored : 68.88 % 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: 1.78 (0.36), residues: 512 helix: 1.86 (0.26), residues: 380 sheet: None (None), residues: 0 loop : -0.81 (0.49), residues: 132 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.001 ARG K 72 TYR 0.041 0.003 TYR P 88 PHE 0.020 0.002 PHE K 78 HIS 0.007 0.002 HIS K 113 Details of bonding type rmsd/Z covalent geometry : bond 0.00715 / 0.37 ( 9282) covalent geometry : angle 0.80985 / 0.46 (13477) hydrogen bonds : bond 0.07714 / 8.39 ( 561) hydrogen bonds : angle 3.18020 / 4.30 ( 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 232 residues out of total 437 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 207 time to evaluate : 0.137 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: K 125 GLN cc_start: 0.8848 (OUTLIER) cc_final: 0.7959 (mp10) REVERT: K 131 ARG cc_start: 0.8694 (OUTLIER) cc_final: 0.8431 (mtt-85) REVERT: L 57 VAL cc_start: 0.9279 (m) cc_final: 0.9076 (t) REVERT: M 61 GLU cc_start: 0.8134 (mp0) cc_final: 0.7864 (mp0) REVERT: M 64 GLU cc_start: 0.8212 (tp30) cc_final: 0.7701 (tp30) REVERT: M 68 ASN cc_start: 0.8514 (m-40) cc_final: 0.7558 (m-40) REVERT: N 64 ASN cc_start: 0.8869 (m-40) cc_final: 0.8599 (m-40) REVERT: N 76 ARG cc_start: 0.8549 (OUTLIER) cc_final: 0.7963 (mtp180) REVERT: O 70 LEU cc_start: 0.8955 (tp) cc_final: 0.8628 (tm) REVERT: O 97 GLU cc_start: 0.8386 (mm-30) cc_final: 0.8156 (mm-30) REVERT: O 120 MET cc_start: 0.8035 (mtt) cc_final: 0.7603 (mtm) outliers start: 25 outliers final: 18 residues processed: 210 average time/residue: 0.6270 time to fit residues: 138.5834 Evaluate side-chains 228 residues out of total 437 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 207 time to evaluate : 0.217 ------------------------------------------------------------------------------- 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 101 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 57 SER 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 Chi-restraints excluded: chain P residue 88 TYR 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: 0.4980 chunk 57 optimal weight: 0.0870 chunk 6 optimal weight: 3.9990 chunk 36 optimal weight: 1.9990 chunk 4 optimal weight: 2.9990 chunk 56 optimal weight: 0.3980 chunk 28 optimal weight: 0.6980 chunk 29 optimal weight: 0.9980 chunk 3 optimal weight: 2.9990 overall best weight: 0.5358 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** M 31 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** M 110 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3912 r_free = 0.3912 target = 0.128354 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3532 r_free = 0.3532 target = 0.102487 restraints weight = 15957.211| |-----------------------------------------------------------------------------| r_work (start): 0.3503 rms_B_bonded: 1.54 r_work: 0.3363 rms_B_bonded: 2.72 restraints_weight: 0.5000 r_work: 0.3217 rms_B_bonded: 4.58 restraints_weight: 0.2500 r_work (final): 0.3217 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8510 moved from start: 0.2095 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= 0.185 Angle : 0.687 8.169 13477 Z= 0.399 Chirality : 0.048 0.209 1536 Planarity : 0.005 0.058 944 Dihedral : 31.108 161.394 2968 Min Nonbonded Distance : 2.479 Molprobity Statistics. All-atom Clashscore : 8.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.98 % Favored : 99.02 % Rotamer: Outliers : 5.03 % Allowed : 28.60 % 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: 2.40 (0.37), residues: 512 helix: 2.30 (0.26), residues: 384 sheet: None (None), residues: 0 loop : -0.66 (0.51), residues: 128 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG M 35 TYR 0.033 0.002 TYR P 88 PHE 0.014 0.001 PHE K 78 HIS 0.005 0.001 HIS M 31 Details of bonding type rmsd/Z covalent geometry : bond 0.00324 / 0.18 ( 9282) covalent geometry : angle 0.68695 / 0.40 (13477) hydrogen bonds : bond 0.05741 / 6.39 ( 561) hydrogen bonds : angle 2.86222 / 3.87 ( 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 220 residues out of total 437 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 198 time to evaluate : 0.173 Fit side-chains REVERT: K 125 GLN cc_start: 0.8736 (OUTLIER) cc_final: 0.7821 (mp10) REVERT: K 131 ARG cc_start: 0.8658 (OUTLIER) cc_final: 0.8402 (mtt-85) REVERT: M 61 GLU cc_start: 0.8075 (mp0) cc_final: 0.7792 (mp0) REVERT: M 64 GLU cc_start: 0.8160 (tp30) cc_final: 0.7664 (tp30) REVERT: M 68 ASN cc_start: 0.8458 (m-40) cc_final: 0.7441 (m-40) REVERT: N 64 ASN cc_start: 0.8835 (m-40) cc_final: 0.8570 (m-40) REVERT: N 73 GLU cc_start: 0.8515 (tp30) cc_final: 0.8212 (tp30) REVERT: O 97 GLU cc_start: 0.8388 (mm-30) cc_final: 0.8096 (mm-30) REVERT: O 120 MET cc_start: 0.7967 (mtt) cc_final: 0.7683 (mtm) REVERT: P 31 LYS cc_start: 0.9053 (OUTLIER) cc_final: 0.8450 (tptm) REVERT: P 84 MET cc_start: 0.8184 (tpt) cc_final: 0.7329 (tpt) outliers start: 22 outliers final: 12 residues processed: 202 average time/residue: 0.5230 time to fit residues: 111.5888 Evaluate side-chains 212 residues out of total 437 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 197 time to evaluate : 0.144 ------------------------------------------------------------------------------- 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 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: 0.6980 chunk 67 optimal weight: 0.5980 chunk 45 optimal weight: 0.6980 chunk 49 optimal weight: 0.9990 chunk 22 optimal weight: 0.3980 chunk 63 optimal weight: 0.0980 chunk 34 optimal weight: 0.8980 chunk 60 optimal weight: 0.9990 chunk 42 optimal weight: 0.6980 chunk 1 optimal weight: 3.9990 chunk 5 optimal weight: 3.9990 overall best weight: 0.4980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... K 108 ASN ** M 31 HIS ** 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 = 0.3916 r_free = 0.3916 target = 0.128548 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3536 r_free = 0.3536 target = 0.102721 restraints weight = 15712.274| |-----------------------------------------------------------------------------| r_work (start): 0.3509 rms_B_bonded: 1.54 r_work: 0.3370 rms_B_bonded: 2.71 restraints_weight: 0.5000 r_work: 0.3226 rms_B_bonded: 4.57 restraints_weight: 0.2500 r_work (final): 0.3226 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8501 moved from start: 0.2101 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 9282 Z= 0.183 Angle : 0.681 9.965 13477 Z= 0.396 Chirality : 0.046 0.224 1536 Planarity : 0.006 0.072 944 Dihedral : 31.070 163.195 2968 Min Nonbonded Distance : 2.480 Molprobity Statistics. All-atom Clashscore : 8.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.54 % Favored : 97.46 % Rotamer: Outliers : 4.35 % Allowed : 28.38 % Favored : 67.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.45 (0.37), residues: 512 helix: 2.35 (0.26), residues: 384 sheet: None (None), residues: 0 loop : -0.68 (0.50), residues: 128 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG K 72 TYR 0.020 0.002 TYR P 88 PHE 0.011 0.001 PHE K 78 HIS 0.004 0.001 HIS M 31 Details of bonding type rmsd/Z covalent geometry : bond 0.00323 / 0.18 ( 9282) covalent geometry : angle 0.68073 / 0.40 (13477) hydrogen bonds : bond 0.05605 / 6.17 ( 561) hydrogen bonds : angle 2.84724 / 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 219 residues out of total 437 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 200 time to evaluate : 0.217 Fit side-chains revert: symmetry clash REVERT: K 72 ARG cc_start: 0.9031 (mtt-85) cc_final: 0.8753 (mtt-85) REVERT: K 125 GLN cc_start: 0.8735 (OUTLIER) cc_final: 0.7849 (mp10) REVERT: K 131 ARG cc_start: 0.8665 (OUTLIER) cc_final: 0.8394 (mtt-85) REVERT: M 20 ARG cc_start: 0.8600 (ttm-80) cc_final: 0.8396 (ttm110) REVERT: M 61 GLU cc_start: 0.8076 (mp0) cc_final: 0.7799 (mp0) REVERT: M 64 GLU cc_start: 0.8154 (tp30) cc_final: 0.7601 (tp30) REVERT: M 68 ASN cc_start: 0.8435 (m-40) cc_final: 0.7441 (m-40) REVERT: N 64 ASN cc_start: 0.8833 (m-40) cc_final: 0.8582 (m-40) REVERT: N 73 GLU cc_start: 0.8513 (tp30) cc_final: 0.8248 (tp30) REVERT: O 70 LEU cc_start: 0.8917 (tp) cc_final: 0.8572 (tm) REVERT: O 97 GLU cc_start: 0.8396 (mm-30) cc_final: 0.8138 (mm-30) REVERT: O 120 MET cc_start: 0.8027 (mtt) cc_final: 0.7750 (mtp) REVERT: P 31 LYS cc_start: 0.9069 (OUTLIER) cc_final: 0.8492 (tptm) outliers start: 19 outliers final: 13 residues processed: 203 average time/residue: 0.6296 time to fit residues: 134.7418 Evaluate side-chains 217 residues out of total 437 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 201 time to evaluate : 0.232 ------------------------------------------------------------------------------- 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 33 SER Chi-restraints excluded: chain N residue 57 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 90 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 71 random chunks: chunk 42 optimal weight: 0.4980 chunk 37 optimal weight: 0.3980 chunk 43 optimal weight: 0.5980 chunk 8 optimal weight: 2.9990 chunk 40 optimal weight: 0.5980 chunk 23 optimal weight: 0.8980 chunk 29 optimal weight: 0.7980 chunk 67 optimal weight: 0.6980 chunk 22 optimal weight: 0.1980 chunk 48 optimal weight: 0.6980 chunk 53 optimal weight: 0.0000 overall best weight: 0.3384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... K 108 ASN O 55 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3936 r_free = 0.3936 target = 0.129966 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3560 r_free = 0.3560 target = 0.104187 restraints weight = 15738.283| |-----------------------------------------------------------------------------| r_work (start): 0.3533 rms_B_bonded: 1.53 r_work: 0.3398 rms_B_bonded: 2.70 restraints_weight: 0.5000 r_work: 0.3256 rms_B_bonded: 4.55 restraints_weight: 0.2500 r_work (final): 0.3256 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8470 moved from start: 0.2106 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 9282 Z= 0.157 Angle : 0.662 8.580 13477 Z= 0.386 Chirality : 0.045 0.200 1536 Planarity : 0.005 0.063 944 Dihedral : 31.021 165.800 2968 Min Nonbonded Distance : 2.479 Molprobity Statistics. All-atom Clashscore : 8.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.37 % Favored : 98.63 % Rotamer: Outliers : 3.20 % Allowed : 30.66 % 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: 2.60 (0.37), residues: 512 helix: 2.44 (0.26), residues: 385 sheet: None (None), residues: 0 loop : -0.60 (0.50), residues: 127 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG M 20 TYR 0.031 0.002 TYR P 88 PHE 0.011 0.001 PHE K 78 HIS 0.003 0.000 HIS M 31 Details of bonding type rmsd/Z covalent geometry : bond 0.00261 / 0.16 ( 9282) covalent geometry : angle 0.66161 / 0.39 (13477) hydrogen bonds : bond 0.05096 / 5.62 ( 561) hydrogen bonds : angle 2.78236 / 3.82 ( 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 215 residues out of total 437 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 201 time to evaluate : 0.217 Fit side-chains REVERT: K 125 GLN cc_start: 0.8710 (OUTLIER) cc_final: 0.7796 (mp10) REVERT: K 131 ARG cc_start: 0.8675 (OUTLIER) cc_final: 0.8408 (mtt-85) REVERT: L 45 ARG cc_start: 0.8265 (mmm-85) cc_final: 0.7971 (mtp-110) REVERT: M 20 ARG cc_start: 0.8614 (ttm-80) cc_final: 0.8397 (ttm110) REVERT: M 61 GLU cc_start: 0.8052 (mp0) cc_final: 0.7790 (mp0) REVERT: M 64 GLU cc_start: 0.8103 (tp30) cc_final: 0.7578 (tp30) REVERT: M 68 ASN cc_start: 0.8368 (m-40) cc_final: 0.7388 (m-40) REVERT: N 64 ASN cc_start: 0.8818 (m-40) cc_final: 0.8563 (m-40) REVERT: N 73 GLU cc_start: 0.8521 (tp30) cc_final: 0.8317 (tp30) REVERT: O 97 GLU cc_start: 0.8350 (mm-30) cc_final: 0.8096 (mm-30) REVERT: O 120 MET cc_start: 0.7942 (mtt) cc_final: 0.7701 (mtm) REVERT: P 31 LYS cc_start: 0.9040 (OUTLIER) cc_final: 0.8570 (tptp) REVERT: P 84 MET cc_start: 0.8048 (tpt) cc_final: 0.7259 (tpt) outliers start: 14 outliers final: 11 residues processed: 203 average time/residue: 0.6321 time to fit residues: 135.1798 Evaluate side-chains 213 residues out of total 437 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 199 time to evaluate : 0.203 ------------------------------------------------------------------------------- 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 23 LEU 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 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 71 random chunks: chunk 48 optimal weight: 0.0980 chunk 33 optimal weight: 0.7980 chunk 5 optimal weight: 3.9990 chunk 42 optimal weight: 0.7980 chunk 16 optimal weight: 2.9990 chunk 18 optimal weight: 3.9990 chunk 50 optimal weight: 0.7980 chunk 69 optimal weight: 0.5980 chunk 62 optimal weight: 0.7980 chunk 4 optimal weight: 2.9990 chunk 28 optimal weight: 0.9980 overall best weight: 0.6180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... K 108 ASN O 55 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3917 r_free = 0.3917 target = 0.128665 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3540 r_free = 0.3540 target = 0.102931 restraints weight = 15791.594| |-----------------------------------------------------------------------------| r_work (start): 0.3515 rms_B_bonded: 1.54 r_work: 0.3376 rms_B_bonded: 2.71 restraints_weight: 0.5000 r_work: 0.3231 rms_B_bonded: 4.57 restraints_weight: 0.2500 r_work (final): 0.3231 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8496 moved from start: 0.2165 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= 0.203 Angle : 0.710 12.177 13477 Z= 0.404 Chirality : 0.046 0.204 1536 Planarity : 0.005 0.063 944 Dihedral : 31.042 164.508 2968 Min Nonbonded Distance : 2.479 Molprobity Statistics. All-atom Clashscore : 9.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.34 % Favored : 97.66 % Rotamer: Outliers : 2.97 % Allowed : 30.21 % 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: 2.50 (0.37), residues: 512 helix: 2.41 (0.26), residues: 381 sheet: None (None), residues: 0 loop : -0.69 (0.49), residues: 131 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG M 20 TYR 0.045 0.002 TYR P 88 PHE 0.012 0.001 PHE K 78 HIS 0.003 0.001 HIS M 31 Details of bonding type rmsd/Z covalent geometry : bond 0.00373 / 0.20 ( 9282) covalent geometry : angle 0.70957 / 0.40 (13477) hydrogen bonds : bond 0.05585 / 6.11 ( 561) hydrogen bonds : angle 2.88067 / 4.02 ( 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 : 0.362 Fit side-chains revert: symmetry clash REVERT: K 125 GLN cc_start: 0.8750 (OUTLIER) cc_final: 0.7835 (mp10) REVERT: K 131 ARG cc_start: 0.8691 (OUTLIER) cc_final: 0.8416 (mtt-85) REVERT: M 61 GLU cc_start: 0.8066 (mp0) cc_final: 0.7796 (mp0) REVERT: M 64 GLU cc_start: 0.8152 (tp30) cc_final: 0.7633 (tp30) REVERT: M 68 ASN cc_start: 0.8395 (m-40) cc_final: 0.7423 (m-40) REVERT: N 64 ASN cc_start: 0.8832 (m-40) cc_final: 0.8575 (m-40) REVERT: N 73 GLU cc_start: 0.8525 (tp30) cc_final: 0.8311 (tp30) REVERT: N 96 ARG cc_start: 0.8349 (ttm-80) cc_final: 0.8107 (ttm-80) REVERT: O 70 LEU cc_start: 0.8950 (tp) cc_final: 0.8574 (tm) REVERT: O 97 GLU cc_start: 0.8375 (mm-30) cc_final: 0.8135 (mm-30) REVERT: O 120 MET cc_start: 0.8003 (mtt) cc_final: 0.7779 (mtp) REVERT: P 31 LYS cc_start: 0.9076 (OUTLIER) cc_final: 0.8483 (tptm) outliers start: 13 outliers final: 10 residues processed: 204 average time/residue: 0.6350 time to fit residues: 136.3718 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 : 0.246 ------------------------------------------------------------------------------- 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 23 LEU 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 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: 0.9980 chunk 60 optimal weight: 0.5980 chunk 50 optimal weight: 0.4980 chunk 51 optimal weight: 1.9990 chunk 44 optimal weight: 0.0060 chunk 59 optimal weight: 0.9980 chunk 43 optimal weight: 0.8980 chunk 11 optimal weight: 30.0000 chunk 33 optimal weight: 0.5980 chunk 56 optimal weight: 0.9980 chunk 16 optimal weight: 2.9990 overall best weight: 0.5196 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... K 108 ASN ** M 31 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** O 55 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3924 r_free = 0.3924 target = 0.129086 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3546 r_free = 0.3546 target = 0.103262 restraints weight = 15840.432| |-----------------------------------------------------------------------------| r_work (start): 0.3520 rms_B_bonded: 1.53 r_work: 0.3380 rms_B_bonded: 2.73 restraints_weight: 0.5000 r_work: 0.3236 rms_B_bonded: 4.59 restraints_weight: 0.2500 r_work (final): 0.3236 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8490 moved from start: 0.2169 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= 0.184 Angle : 0.699 11.692 13477 Z= 0.401 Chirality : 0.046 0.203 1536 Planarity : 0.006 0.067 944 Dihedral : 31.030 164.450 2968 Min Nonbonded Distance : 2.479 Molprobity Statistics. All-atom Clashscore : 9.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.34 % Favored : 97.66 % Rotamer: Outliers : 2.75 % Allowed : 31.58 % 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: 2.54 (0.37), residues: 512 helix: 2.47 (0.26), residues: 379 sheet: None (None), residues: 0 loop : -0.70 (0.48), residues: 133 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.015 0.001 ARG M 20 TYR 0.032 0.002 TYR P 88 PHE 0.011 0.001 PHE K 78 HIS 0.001 0.000 HIS M 31 Details of bonding type rmsd/Z covalent geometry : bond 0.00328 / 0.18 ( 9282) covalent geometry : angle 0.69933 / 0.40 (13477) hydrogen bonds : bond 0.05442 / 5.95 ( 561) hydrogen bonds : angle 2.85878 / 3.98 ( 1382) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3854.84 seconds wall clock time: 66 minutes 4.48 seconds (3964.48 seconds total)