Starting phenix.real_space_refine on Fri Aug 22 23:11:06 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8eu2_28602/08_2025/8eu2_28602_neut.cif Found real_map, /net/cci-nas-00/data/ceres_data/8eu2_28602/08_2025/8eu2_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 { model { file = "/net/cci-nas-00/data/ceres_data/8eu2_28602/08_2025/8eu2_28602_neut.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8eu2_28602/08_2025/8eu2_28602_neut.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8eu2_28602/08_2025/8eu2_28602.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8eu2_28602/08_2025/8eu2_28602.map" } 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-2.0-5787/lib/python3.9/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: 1.60, per 1000 atoms: 0.18 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: 0.64 Conformation dependent library (CDL) restraints added in 202.3 milliseconds Enol-peptide restraints added in 476.8 nanoseconds 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: 1.23 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: 1.20 Time building geometry restraints manager: 0.87 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=" N ASP L 24 " pdb=" CA ASP L 24 " ideal model delta sigma weight residual 1.457 1.485 -0.027 1.29e-02 6.01e+03 4.46e+00 bond pdb=" C3' DG J 20 " pdb=" O3' DG J 20 " ideal model delta sigma weight residual 1.422 1.484 -0.062 3.00e-02 1.11e+03 4.28e+00 bond pdb=" CB PRO O 43 " pdb=" CG PRO O 43 " ideal model delta sigma weight residual 1.492 1.592 -0.100 5.00e-02 4.00e+02 4.02e+00 bond pdb=" C3' DT J -17 " pdb=" O3' DT J -17 " ideal model delta sigma weight residual 1.422 1.477 -0.055 3.00e-02 1.11e+03 3.35e+00 bond pdb=" CG PRO O 43 " pdb=" CD PRO O 43 " ideal model delta sigma weight residual 1.503 1.564 -0.061 3.40e-02 8.65e+02 3.17e+00 ... (remaining 9277 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.83: 12875 1.83 - 3.67: 531 3.67 - 5.50: 49 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=" C ARG L 23 " pdb=" N ASP L 24 " pdb=" CA ASP L 24 " ideal model delta sigma weight residual 121.54 129.30 -7.76 1.91e+00 2.74e-01 1.65e+01 angle pdb=" CG ARG N 96 " pdb=" CD ARG N 96 " pdb=" NE ARG N 96 " ideal model delta sigma weight residual 112.00 119.73 -7.73 2.20e+00 2.07e-01 1.24e+01 angle pdb=" C3' DG J 20 " pdb=" O3' DG J 20 " pdb=" P DG J 21 " ideal model delta sigma weight residual 120.20 124.98 -4.78 1.50e+00 4.44e-01 1.02e+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: 1234 0.053 - 0.105: 243 0.105 - 0.158: 48 0.158 - 0.211: 7 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: 8.360 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.000 Extract box with map and model: 0.100 Check model and map are aligned: 0.020 Set scattering table: 0.010 Process input model: 8.340 Find NCS groups from input model: 0.030 Set up NCS constraints: 0.010 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:7.750 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 24.620 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7762 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 : 0.005 0.100 9282 Z= 0.234 Angle : 0.823 9.165 13477 Z= 0.475 Chirality : 0.046 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 aren 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 covalent geometry : bond 0.00507 ( 9282) covalent geometry : angle 0.82278 (13477) hydrogen bonds : bond 0.11358 ( 561) hydrogen bonds : angle 3.72919 ( 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 : 0.228 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: 0.8027 (m-40) REVERT: N 73 GLU cc_start: 0.7708 (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: 0.5447 time to fit residues: 110.6013 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 : 0.165 ------------------------------------------------------------------------------- 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: 0.9990 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: 0.9980 overall best weight: 0.5780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: L 27 GLN ** L 75 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** M 68 ASN ** M 84 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 89 ASN 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 = 0.3937 r_free = 0.3937 target = 0.130222 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3560 r_free = 0.3560 target = 0.104410 restraints weight = 15866.885| |-----------------------------------------------------------------------------| r_work (start): 0.3531 rms_B_bonded: 1.55 r_work: 0.3393 rms_B_bonded: 2.71 restraints_weight: 0.5000 r_work: 0.3250 rms_B_bonded: 4.55 restraints_weight: 0.2500 r_work (final): 0.3250 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8228 moved from start: 0.1364 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.034 9282 Z= 0.237 Angle : 0.622 8.191 13477 Z= 0.372 Chirality : 0.037 0.151 1536 Planarity : 0.005 0.066 944 Dihedral : 30.617 172.939 2971 Min Nonbonded Distance : 2.496 Molprobity Statistics. All-atom Clashscore : 7.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.17 % Favored : 98.83 % Rotamer: Outliers : 2.52 % Allowed : 19.68 % Favored : 77.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.45 (0.37), residues: 512 helix: 1.48 (0.27), residues: 387 sheet: None (None), residues: 0 loop : -0.55 (0.52), residues: 125 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 0.010 0.001 PHE K 104 HIS 0.002 0.001 HIS M 31 Details of bonding type rmsd covalent geometry : bond 0.00517 ( 9282) covalent geometry : angle 0.62193 (13477) hydrogen bonds : bond 0.05266 ( 561) hydrogen bonds : angle 2.78058 ( 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 211 residues out of total 437 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 200 time to evaluate : 0.212 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: K 131 ARG cc_start: 0.8741 (OUTLIER) cc_final: 0.8514 (mtt-85) REVERT: M 61 GLU cc_start: 0.7893 (mp0) cc_final: 0.7649 (mp0) REVERT: M 64 GLU cc_start: 0.8221 (tp30) cc_final: 0.7761 (tp30) REVERT: M 68 ASN cc_start: 0.8481 (m-40) cc_final: 0.6993 (m-40) REVERT: N 64 ASN cc_start: 0.8826 (m-40) cc_final: 0.8565 (m-40) REVERT: N 73 GLU cc_start: 0.8486 (tp30) cc_final: 0.8253 (tp30) REVERT: O 120 MET cc_start: 0.7936 (mtt) cc_final: 0.7597 (mtm) outliers start: 11 outliers final: 6 residues processed: 202 average time/residue: 0.5115 time to fit residues: 108.6501 Evaluate side-chains 204 residues out of total 437 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 197 time to evaluate : 0.131 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain K residue 109 LEU Chi-restraints excluded: chain K residue 131 ARG 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 119 THR 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: 0.9990 chunk 56 optimal weight: 0.7980 chunk 13 optimal weight: 0.9990 chunk 24 optimal weight: 0.6980 chunk 65 optimal weight: 0.9980 chunk 1 optimal weight: 0.9990 chunk 29 optimal weight: 1.9990 chunk 21 optimal weight: 0.9990 chunk 33 optimal weight: 0.9980 chunk 37 optimal weight: 0.9980 overall best weight: 0.7980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: K 108 ASN ** L 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 94 ASN 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 = 0.3895 r_free = 0.3895 target = 0.127198 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3513 r_free = 0.3513 target = 0.101484 restraints weight = 15739.149| |-----------------------------------------------------------------------------| r_work (start): 0.3487 rms_B_bonded: 1.54 r_work: 0.3348 rms_B_bonded: 2.70 restraints_weight: 0.5000 r_work: 0.3205 rms_B_bonded: 4.52 restraints_weight: 0.2500 r_work (final): 0.3205 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8278 moved from start: 0.1986 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.042 9282 Z= 0.291 Angle : 0.649 8.545 13477 Z= 0.387 Chirality : 0.039 0.147 1536 Planarity : 0.005 0.060 944 Dihedral : 30.698 168.470 2968 Min Nonbonded Distance : 2.498 Molprobity Statistics. All-atom Clashscore : 7.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.56 % Favored : 98.44 % Rotamer: Outliers : 4.58 % Allowed : 23.57 % Favored : 71.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 2.04 (0.37), residues: 512 helix: 1.99 (0.27), residues: 384 sheet: None (None), residues: 0 loop : -0.60 (0.52), residues: 128 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG M 71 TYR 0.010 0.002 TYR L 72 PHE 0.017 0.002 PHE K 78 HIS 0.003 0.001 HIS K 113 Details of bonding type rmsd covalent geometry : bond 0.00641 ( 9282) covalent geometry : angle 0.64929 (13477) hydrogen bonds : bond 0.05842 ( 561) hydrogen bonds : angle 2.83939 ( 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: 20 poor density : 202 time to evaluate : 0.206 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: K 106 ASP cc_start: 0.8080 (m-30) cc_final: 0.7636 (m-30) REVERT: K 125 GLN cc_start: 0.8740 (OUTLIER) cc_final: 0.7894 (mp10) REVERT: K 131 ARG cc_start: 0.8702 (ttt180) cc_final: 0.8408 (mtt-85) REVERT: L 57 VAL cc_start: 0.9252 (m) cc_final: 0.9042 (t) REVERT: L 92 ARG cc_start: 0.8455 (OUTLIER) cc_final: 0.8146 (mmm-85) REVERT: M 61 GLU cc_start: 0.7931 (mp0) cc_final: 0.7650 (mp0) REVERT: M 64 GLU cc_start: 0.8172 (tp30) cc_final: 0.7777 (tp30) REVERT: M 68 ASN cc_start: 0.8424 (m-40) cc_final: 0.7446 (m-40) REVERT: N 64 ASN cc_start: 0.8843 (m-40) cc_final: 0.8580 (m-40) REVERT: N 73 GLU cc_start: 0.8495 (tp30) cc_final: 0.8085 (tp30) REVERT: O 70 LEU cc_start: 0.8919 (tp) cc_final: 0.8561 (tm) REVERT: O 97 GLU cc_start: 0.8382 (mm-30) cc_final: 0.8128 (mm-30) REVERT: O 116 ARG cc_start: 0.8713 (ttp80) cc_final: 0.8432 (ttp80) REVERT: O 120 MET cc_start: 0.7981 (mtt) cc_final: 0.7686 (mtp) outliers start: 20 outliers final: 11 residues processed: 204 average time/residue: 0.5209 time to fit residues: 111.8295 Evaluate side-chains 213 residues out of total 437 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 200 time to evaluate : 0.122 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain K residue 124 ILE Chi-restraints excluded: chain K residue 125 GLN Chi-restraints excluded: chain L residue 86 VAL Chi-restraints excluded: chain L residue 92 ARG 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 57 SER Chi-restraints excluded: chain N residue 68 GLU Chi-restraints excluded: chain N residue 75 SER Chi-restraints excluded: chain O residue 57 SER Chi-restraints excluded: chain P residue 86 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 71 random chunks: chunk 3 optimal weight: 0.9990 chunk 62 optimal weight: 0.3980 chunk 12 optimal weight: 1.9990 chunk 45 optimal weight: 0.9990 chunk 16 optimal weight: 0.9990 chunk 7 optimal weight: 0.9990 chunk 26 optimal weight: 0.6980 chunk 4 optimal weight: 0.9990 chunk 22 optimal weight: 0.9980 chunk 8 optimal weight: 0.9990 chunk 60 optimal weight: 0.9990 overall best weight: 0.8184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** L 75 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** L 93 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3889 r_free = 0.3889 target = 0.126865 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3511 r_free = 0.3511 target = 0.101303 restraints weight = 15923.002| |-----------------------------------------------------------------------------| r_work (start): 0.3484 rms_B_bonded: 1.54 r_work: 0.3344 rms_B_bonded: 2.70 restraints_weight: 0.5000 r_work: 0.3200 rms_B_bonded: 4.54 restraints_weight: 0.2500 r_work (final): 0.3200 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8287 moved from start: 0.2214 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.038 9282 Z= 0.298 Angle : 0.645 7.624 13477 Z= 0.385 Chirality : 0.040 0.146 1536 Planarity : 0.005 0.058 944 Dihedral : 30.591 168.041 2968 Min Nonbonded Distance : 2.500 Molprobity Statistics. All-atom Clashscore : 7.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.15 % Favored : 97.85 % Rotamer: Outliers : 5.26 % Allowed : 24.49 % Favored : 70.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 2.22 (0.37), residues: 512 helix: 2.18 (0.26), residues: 381 sheet: None (None), residues: 0 loop : -0.65 (0.51), residues: 131 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG M 20 TYR 0.009 0.001 TYR N 118 PHE 0.018 0.002 PHE K 78 HIS 0.003 0.001 HIS K 113 Details of bonding type rmsd covalent geometry : bond 0.00656 ( 9282) covalent geometry : angle 0.64505 (13477) hydrogen bonds : bond 0.05707 ( 561) hydrogen bonds : angle 2.82592 ( 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 230 residues out of total 437 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 207 time to evaluate : 0.131 Fit side-chains revert: symmetry clash REVERT: K 125 GLN cc_start: 0.8764 (OUTLIER) cc_final: 0.7894 (mp10) REVERT: K 131 ARG cc_start: 0.8700 (OUTLIER) cc_final: 0.8466 (mtt-85) REVERT: L 57 VAL cc_start: 0.9220 (m) cc_final: 0.9018 (t) REVERT: L 92 ARG cc_start: 0.8502 (OUTLIER) cc_final: 0.8115 (ttm-80) REVERT: M 64 GLU cc_start: 0.8158 (tp30) cc_final: 0.7705 (tp30) REVERT: M 68 ASN cc_start: 0.8403 (m-40) cc_final: 0.7536 (m-40) REVERT: N 39 TYR cc_start: 0.8662 (t80) cc_final: 0.8279 (t80) REVERT: N 43 LYS cc_start: 0.9139 (mmtp) cc_final: 0.8852 (mmtp) REVERT: N 44 GLN cc_start: 0.8815 (tt0) cc_final: 0.8592 (tt0) REVERT: N 64 ASN cc_start: 0.8853 (m-40) cc_final: 0.8605 (m-40) REVERT: N 73 GLU cc_start: 0.8528 (tp30) cc_final: 0.8250 (tp30) REVERT: O 70 LEU cc_start: 0.8943 (tp) cc_final: 0.8578 (tm) REVERT: O 90 MET cc_start: 0.8580 (mpp) cc_final: 0.8358 (mmt) REVERT: O 97 GLU cc_start: 0.8426 (mm-30) cc_final: 0.8175 (mm-30) REVERT: O 116 ARG cc_start: 0.8723 (ttp80) cc_final: 0.8385 (ttp80) REVERT: O 120 MET cc_start: 0.8009 (mtt) cc_final: 0.7588 (mtp) outliers start: 23 outliers final: 15 residues processed: 211 average time/residue: 0.5070 time to fit residues: 112.3947 Evaluate side-chains 223 residues out of total 437 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 205 time to evaluate : 0.164 ------------------------------------------------------------------------------- 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 130 ILE Chi-restraints excluded: chain K residue 131 ARG Chi-restraints excluded: chain L residue 86 VAL Chi-restraints excluded: chain L residue 92 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 68 GLU 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 100 LEU 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: 0.9990 chunk 31 optimal weight: 0.9990 chunk 70 optimal weight: 0.8980 chunk 32 optimal weight: 0.9990 chunk 69 optimal weight: 0.5980 chunk 16 optimal weight: 0.9990 chunk 43 optimal weight: 0.9990 chunk 11 optimal weight: 8.9990 chunk 42 optimal weight: 0.5980 chunk 60 optimal weight: 0.5980 chunk 3 optimal weight: 0.9990 overall best weight: 0.7382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: K 108 ASN ** L 75 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** N 106 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3892 r_free = 0.3892 target = 0.127102 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3516 r_free = 0.3516 target = 0.101639 restraints weight = 15756.444| |-----------------------------------------------------------------------------| r_work (start): 0.3492 rms_B_bonded: 1.52 r_work: 0.3352 rms_B_bonded: 2.68 restraints_weight: 0.5000 r_work: 0.3210 rms_B_bonded: 4.50 restraints_weight: 0.2500 r_work (final): 0.3210 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8278 moved from start: 0.2344 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.038 9282 Z= 0.276 Angle : 0.636 9.131 13477 Z= 0.379 Chirality : 0.039 0.143 1536 Planarity : 0.005 0.060 944 Dihedral : 30.556 168.586 2968 Min Nonbonded Distance : 2.502 Molprobity Statistics. All-atom Clashscore : 7.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.34 % Favored : 97.66 % Rotamer: Outliers : 6.41 % Allowed : 26.32 % 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 aren not related in a simple way. whole: 2.38 (0.37), residues: 512 helix: 2.30 (0.26), residues: 381 sheet: None (None), residues: 0 loop : -0.63 (0.50), residues: 131 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG O 63 TYR 0.011 0.001 TYR M 57 PHE 0.013 0.002 PHE K 78 HIS 0.002 0.001 HIS K 113 Details of bonding type rmsd covalent geometry : bond 0.00608 ( 9282) covalent geometry : angle 0.63634 (13477) hydrogen bonds : bond 0.05533 ( 561) hydrogen bonds : angle 2.80878 ( 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 237 residues out of total 437 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 209 time to evaluate : 0.137 Fit side-chains revert: symmetry clash REVERT: K 125 GLN cc_start: 0.8734 (OUTLIER) cc_final: 0.7857 (mp10) REVERT: K 131 ARG cc_start: 0.8700 (OUTLIER) cc_final: 0.8447 (mtt-85) REVERT: L 57 VAL cc_start: 0.9217 (m) cc_final: 0.9009 (t) REVERT: L 92 ARG cc_start: 0.8488 (OUTLIER) cc_final: 0.8000 (ttm-80) REVERT: M 61 GLU cc_start: 0.8273 (mp0) cc_final: 0.7877 (mp0) REVERT: M 64 GLU cc_start: 0.8113 (tp30) cc_final: 0.7696 (tp30) REVERT: M 68 ASN cc_start: 0.8389 (m-40) cc_final: 0.7568 (m-40) REVERT: N 39 TYR cc_start: 0.8617 (t80) cc_final: 0.8309 (t80) REVERT: N 43 LYS cc_start: 0.9160 (mmtp) cc_final: 0.8866 (mmtp) REVERT: N 44 GLN cc_start: 0.8817 (tt0) cc_final: 0.8611 (tt0) REVERT: N 64 ASN cc_start: 0.8843 (m-40) cc_final: 0.8590 (m-40) REVERT: N 73 GLU cc_start: 0.8506 (tp30) cc_final: 0.8223 (tp30) REVERT: N 76 ARG cc_start: 0.8497 (OUTLIER) cc_final: 0.7924 (mtp180) REVERT: O 70 LEU cc_start: 0.8931 (tp) cc_final: 0.8589 (tm) REVERT: O 97 GLU cc_start: 0.8401 (mm-30) cc_final: 0.8177 (mm-30) REVERT: O 116 ARG cc_start: 0.8702 (ttp80) cc_final: 0.8419 (ttp80) REVERT: O 120 MET cc_start: 0.7975 (mtt) cc_final: 0.7644 (mtm) REVERT: O 128 ARG cc_start: 0.8993 (mtp-110) cc_final: 0.8791 (mtm180) outliers start: 28 outliers final: 17 residues processed: 212 average time/residue: 0.5034 time to fit residues: 112.3128 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 : 0.126 ------------------------------------------------------------------------------- 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 L residue 92 ARG Chi-restraints excluded: chain L residue 93 GLN 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 68 GLU Chi-restraints excluded: chain N residue 75 SER Chi-restraints excluded: chain N residue 76 ARG 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 100 LEU Chi-restraints excluded: chain P residue 86 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 71 random chunks: chunk 7 optimal weight: 0.9990 chunk 6 optimal weight: 0.9990 chunk 36 optimal weight: 2.9990 chunk 1 optimal weight: 0.9990 chunk 34 optimal weight: 0.6980 chunk 2 optimal weight: 0.9990 chunk 51 optimal weight: 0.0070 chunk 53 optimal weight: 0.7980 chunk 14 optimal weight: 0.9990 chunk 16 optimal weight: 0.9990 chunk 25 optimal weight: 0.7980 overall best weight: 0.6600 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: K 108 ASN ** L 75 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** O 68 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3897 r_free = 0.3897 target = 0.127469 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3522 r_free = 0.3522 target = 0.101874 restraints weight = 15762.731| |-----------------------------------------------------------------------------| r_work (start): 0.3500 rms_B_bonded: 1.52 r_work: 0.3360 rms_B_bonded: 2.69 restraints_weight: 0.5000 r_work: 0.3217 rms_B_bonded: 4.51 restraints_weight: 0.2500 r_work (final): 0.3217 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8271 moved from start: 0.2380 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.033 9282 Z= 0.256 Angle : 0.635 10.029 13477 Z= 0.375 Chirality : 0.038 0.142 1536 Planarity : 0.005 0.061 944 Dihedral : 30.523 169.160 2968 Min Nonbonded Distance : 2.503 Molprobity Statistics. All-atom Clashscore : 7.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.34 % Favored : 97.66 % Rotamer: Outliers : 6.18 % Allowed : 28.83 % Favored : 64.99 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 2.50 (0.37), residues: 512 helix: 2.38 (0.26), residues: 383 sheet: None (None), residues: 0 loop : -0.64 (0.51), residues: 129 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG M 71 TYR 0.009 0.001 TYR M 57 PHE 0.017 0.001 PHE K 78 HIS 0.002 0.001 HIS K 113 Details of bonding type rmsd covalent geometry : bond 0.00563 ( 9282) covalent geometry : angle 0.63460 (13477) hydrogen bonds : bond 0.05337 ( 561) hydrogen bonds : angle 2.78864 ( 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 235 residues out of total 437 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 208 time to evaluate : 0.172 Fit side-chains revert: symmetry clash REVERT: K 125 GLN cc_start: 0.8720 (OUTLIER) cc_final: 0.7852 (mp10) REVERT: K 131 ARG cc_start: 0.8688 (OUTLIER) cc_final: 0.8435 (mtt-85) REVERT: L 57 VAL cc_start: 0.9216 (m) cc_final: 0.9002 (t) REVERT: L 92 ARG cc_start: 0.8490 (OUTLIER) cc_final: 0.8060 (ttm-80) REVERT: M 61 GLU cc_start: 0.8268 (mp0) cc_final: 0.7882 (mp0) REVERT: M 64 GLU cc_start: 0.8122 (tp30) cc_final: 0.7716 (tp30) REVERT: M 68 ASN cc_start: 0.8394 (m-40) cc_final: 0.7622 (m-40) REVERT: N 39 TYR cc_start: 0.8617 (t80) cc_final: 0.8348 (t80) REVERT: N 64 ASN cc_start: 0.8848 (m-40) cc_final: 0.8594 (m-40) REVERT: O 97 GLU cc_start: 0.8389 (mm-30) cc_final: 0.8161 (mm-30) REVERT: O 116 ARG cc_start: 0.8708 (ttp80) cc_final: 0.8436 (ttp80) REVERT: O 120 MET cc_start: 0.7984 (mtt) cc_final: 0.7682 (mtm) outliers start: 27 outliers final: 19 residues processed: 211 average time/residue: 0.5287 time to fit residues: 117.1376 Evaluate side-chains 229 residues out of total 437 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 207 time to evaluate : 0.142 ------------------------------------------------------------------------------- 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 L residue 47 SER Chi-restraints excluded: chain L residue 86 VAL Chi-restraints excluded: chain L residue 92 ARG Chi-restraints excluded: chain L residue 93 GLN 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 68 GLU 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 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: 0.9990 chunk 9 optimal weight: 0.9990 chunk 64 optimal weight: 0.0570 chunk 57 optimal weight: 0.7980 chunk 6 optimal weight: 0.9990 chunk 36 optimal weight: 1.9990 chunk 4 optimal weight: 0.9990 chunk 56 optimal weight: 0.6980 chunk 28 optimal weight: 0.9990 chunk 29 optimal weight: 0.9990 chunk 3 optimal weight: 0.9990 overall best weight: 0.7102 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: K 108 ASN ** L 75 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 = 0.3894 r_free = 0.3894 target = 0.127121 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3516 r_free = 0.3516 target = 0.101519 restraints weight = 15929.228| |-----------------------------------------------------------------------------| r_work (start): 0.3491 rms_B_bonded: 1.53 r_work: 0.3351 rms_B_bonded: 2.72 restraints_weight: 0.5000 r_work: 0.3206 rms_B_bonded: 4.55 restraints_weight: 0.2500 r_work (final): 0.3206 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8278 moved from start: 0.2491 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.035 9282 Z= 0.270 Angle : 0.645 8.624 13477 Z= 0.381 Chirality : 0.039 0.142 1536 Planarity : 0.005 0.061 944 Dihedral : 30.519 168.742 2968 Min Nonbonded Distance : 2.504 Molprobity Statistics. All-atom Clashscore : 8.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.15 % Favored : 97.85 % Rotamer: Outliers : 7.09 % Allowed : 27.00 % Favored : 65.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 2.49 (0.37), residues: 512 helix: 2.42 (0.26), residues: 381 sheet: None (None), residues: 0 loop : -0.72 (0.50), residues: 131 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG M 71 TYR 0.012 0.001 TYR P 51 PHE 0.014 0.002 PHE K 78 HIS 0.002 0.001 HIS K 113 Details of bonding type rmsd covalent geometry : bond 0.00596 ( 9282) covalent geometry : angle 0.64495 (13477) hydrogen bonds : bond 0.05462 ( 561) hydrogen bonds : angle 2.82778 ( 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 238 residues out of total 437 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 207 time to evaluate : 0.162 Fit side-chains revert: symmetry clash REVERT: K 125 GLN cc_start: 0.8725 (OUTLIER) cc_final: 0.7860 (mp10) REVERT: K 131 ARG cc_start: 0.8695 (OUTLIER) cc_final: 0.8445 (mtt-85) REVERT: L 57 VAL cc_start: 0.9216 (m) cc_final: 0.9006 (t) REVERT: L 92 ARG cc_start: 0.8530 (OUTLIER) cc_final: 0.7911 (ttm-80) REVERT: M 61 GLU cc_start: 0.8293 (OUTLIER) cc_final: 0.7909 (mp0) REVERT: M 64 GLU cc_start: 0.8134 (tp30) cc_final: 0.7685 (tp30) REVERT: M 68 ASN cc_start: 0.8410 (m-40) cc_final: 0.7567 (m-40) REVERT: N 39 TYR cc_start: 0.8578 (t80) cc_final: 0.8310 (t80) REVERT: N 64 ASN cc_start: 0.8858 (m-40) cc_final: 0.8604 (m-40) REVERT: N 76 ARG cc_start: 0.8485 (OUTLIER) cc_final: 0.7874 (mtp180) REVERT: O 97 GLU cc_start: 0.8399 (mm-30) cc_final: 0.8197 (mm-30) REVERT: O 116 ARG cc_start: 0.8722 (ttp80) cc_final: 0.8446 (ttp80) REVERT: O 120 MET cc_start: 0.7982 (mtt) cc_final: 0.7683 (mtm) REVERT: O 128 ARG cc_start: 0.9002 (mtp-110) cc_final: 0.8796 (mtm180) REVERT: P 31 LYS cc_start: 0.9083 (OUTLIER) cc_final: 0.8512 (tptm) outliers start: 31 outliers final: 19 residues processed: 213 average time/residue: 0.5465 time to fit residues: 122.0516 Evaluate side-chains 231 residues out of total 437 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 206 time to evaluate : 0.162 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain K residue 76 GLN 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 L residue 86 VAL Chi-restraints excluded: chain L residue 92 ARG Chi-restraints excluded: chain L residue 93 GLN Chi-restraints excluded: chain M residue 59 THR Chi-restraints excluded: chain M residue 61 GLU 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 68 GLU Chi-restraints excluded: chain N residue 75 SER Chi-restraints excluded: chain N residue 76 ARG 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 100 LEU Chi-restraints excluded: chain P residue 31 LYS Chi-restraints excluded: chain P residue 70 VAL 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: 0.0770 chunk 45 optimal weight: 0.6980 chunk 49 optimal weight: 0.3980 chunk 22 optimal weight: 0.1980 chunk 63 optimal weight: 0.1980 chunk 34 optimal weight: 0.0070 chunk 60 optimal weight: 0.6980 chunk 42 optimal weight: 0.4980 chunk 1 optimal weight: 0.9990 chunk 5 optimal weight: 0.9990 overall best weight: 0.1756 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: K 93 GLN K 108 ASN ** L 75 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** P 93 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3968 r_free = 0.3968 target = 0.132372 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3605 r_free = 0.3605 target = 0.107087 restraints weight = 15680.370| |-----------------------------------------------------------------------------| r_work (start): 0.3578 rms_B_bonded: 1.49 r_work: 0.3444 rms_B_bonded: 2.69 restraints_weight: 0.5000 r_work: 0.3305 rms_B_bonded: 4.52 restraints_weight: 0.2500 r_work (final): 0.3305 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8162 moved from start: 0.2480 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= 0.161 Angle : 0.604 12.148 13477 Z= 0.351 Chirality : 0.034 0.138 1536 Planarity : 0.005 0.064 944 Dihedral : 30.314 174.474 2968 Min Nonbonded Distance : 2.507 Molprobity Statistics. All-atom Clashscore : 8.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.37 % Favored : 98.63 % Rotamer: Outliers : 5.26 % Allowed : 28.38 % 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 aren not related in a simple way. whole: 2.91 (0.37), residues: 512 helix: 2.69 (0.26), residues: 384 sheet: None (None), residues: 0 loop : -0.54 (0.50), residues: 128 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.018 0.001 ARG M 20 TYR 0.014 0.001 TYR P 51 PHE 0.005 0.001 PHE K 78 HIS 0.001 0.000 HIS M 31 Details of bonding type rmsd covalent geometry : bond 0.00350 ( 9282) covalent geometry : angle 0.60367 (13477) hydrogen bonds : bond 0.03977 ( 561) hydrogen bonds : angle 2.60517 ( 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 220 residues out of total 437 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 197 time to evaluate : 0.152 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: K 125 GLN cc_start: 0.8650 (OUTLIER) cc_final: 0.7829 (mp10) REVERT: K 131 ARG cc_start: 0.8655 (OUTLIER) cc_final: 0.8376 (mtt-85) REVERT: L 92 ARG cc_start: 0.8448 (OUTLIER) cc_final: 0.7917 (ttm-80) REVERT: M 32 ARG cc_start: 0.8718 (tmm160) cc_final: 0.8492 (ttp80) REVERT: M 64 GLU cc_start: 0.8025 (tp30) cc_final: 0.7629 (tp30) REVERT: M 68 ASN cc_start: 0.8228 (m-40) cc_final: 0.7350 (m-40) REVERT: N 64 ASN cc_start: 0.8798 (m-40) cc_final: 0.8556 (m-40) REVERT: O 90 MET cc_start: 0.8368 (mpp) cc_final: 0.8159 (mmp) REVERT: O 97 GLU cc_start: 0.8266 (mm-30) cc_final: 0.8030 (mm-30) REVERT: O 120 MET cc_start: 0.7858 (mtt) cc_final: 0.7541 (mtm) REVERT: P 31 LYS cc_start: 0.9025 (OUTLIER) cc_final: 0.8515 (tptm) outliers start: 23 outliers final: 11 residues processed: 201 average time/residue: 0.5412 time to fit residues: 114.1563 Evaluate side-chains 210 residues out of total 437 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 195 time to evaluate : 0.166 ------------------------------------------------------------------------------- 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 92 ARG Chi-restraints excluded: chain L residue 93 GLN 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 N residue 68 GLU 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=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 71 random chunks: chunk 42 optimal weight: 0.7980 chunk 37 optimal weight: 0.6980 chunk 43 optimal weight: 0.6980 chunk 8 optimal weight: 0.9990 chunk 40 optimal weight: 0.6980 chunk 23 optimal weight: 0.8980 chunk 29 optimal weight: 1.9990 chunk 67 optimal weight: 0.0970 chunk 22 optimal weight: 0.4980 chunk 48 optimal weight: 0.8980 chunk 53 optimal weight: 1.9990 overall best weight: 0.5378 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: K 108 ASN ** L 75 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 31 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** M 104 GLN O 55 GLN O 68 GLN O 93 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3923 r_free = 0.3923 target = 0.129049 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3551 r_free = 0.3551 target = 0.103544 restraints weight = 15674.760| |-----------------------------------------------------------------------------| r_work (start): 0.3532 rms_B_bonded: 1.50 r_work: 0.3391 rms_B_bonded: 2.70 restraints_weight: 0.5000 r_work: 0.3247 rms_B_bonded: 4.53 restraints_weight: 0.2500 r_work (final): 0.3247 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8235 moved from start: 0.2526 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.034 9282 Z= 0.227 Angle : 0.646 12.482 13477 Z= 0.371 Chirality : 0.037 0.185 1536 Planarity : 0.005 0.060 944 Dihedral : 30.351 170.349 2968 Min Nonbonded Distance : 2.507 Molprobity Statistics. All-atom Clashscore : 8.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.34 % Favored : 97.66 % Rotamer: Outliers : 3.66 % Allowed : 31.81 % Favored : 64.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 2.67 (0.37), residues: 512 helix: 2.51 (0.26), residues: 385 sheet: None (None), residues: 0 loop : -0.62 (0.50), residues: 127 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG M 35 TYR 0.014 0.002 TYR N 39 PHE 0.014 0.001 PHE K 78 HIS 0.002 0.001 HIS K 113 Details of bonding type rmsd covalent geometry : bond 0.00500 ( 9282) covalent geometry : angle 0.64639 (13477) hydrogen bonds : bond 0.04932 ( 561) hydrogen bonds : angle 2.76704 ( 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 220 residues out of total 437 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 204 time to evaluate : 0.217 Fit side-chains revert: symmetry clash REVERT: K 125 GLN cc_start: 0.8733 (OUTLIER) cc_final: 0.7901 (mp10) REVERT: K 131 ARG cc_start: 0.8680 (OUTLIER) cc_final: 0.8426 (mtt-85) REVERT: L 45 ARG cc_start: 0.8226 (mmm-85) cc_final: 0.7864 (mtp-110) REVERT: L 92 ARG cc_start: 0.8487 (OUTLIER) cc_final: 0.7924 (ttm-80) REVERT: M 61 GLU cc_start: 0.8247 (OUTLIER) cc_final: 0.7920 (mp0) REVERT: M 64 GLU cc_start: 0.8118 (tp30) cc_final: 0.7663 (tp30) REVERT: M 68 ASN cc_start: 0.8365 (m-40) cc_final: 0.7512 (m-40) REVERT: N 64 ASN cc_start: 0.8828 (m-40) cc_final: 0.8570 (m-40) REVERT: O 120 MET cc_start: 0.8023 (mtt) cc_final: 0.7717 (mtm) REVERT: P 31 LYS cc_start: 0.9047 (OUTLIER) cc_final: 0.8588 (tptp) outliers start: 16 outliers final: 11 residues processed: 207 average time/residue: 0.5435 time to fit residues: 118.1025 Evaluate side-chains 219 residues out of total 437 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 203 time to evaluate : 0.128 ------------------------------------------------------------------------------- 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 92 ARG Chi-restraints excluded: chain L residue 93 GLN Chi-restraints excluded: chain M residue 59 THR Chi-restraints excluded: chain M residue 61 GLU 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 N residue 68 GLU 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: 0.3980 chunk 33 optimal weight: 0.8980 chunk 5 optimal weight: 0.9990 chunk 42 optimal weight: 0.9980 chunk 16 optimal weight: 0.9990 chunk 18 optimal weight: 0.9990 chunk 50 optimal weight: 0.4980 chunk 69 optimal weight: 0.0870 chunk 62 optimal weight: 0.4980 chunk 4 optimal weight: 0.9990 chunk 28 optimal weight: 0.5980 overall best weight: 0.4158 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: K 108 ASN ** L 75 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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 = 0.3936 r_free = 0.3936 target = 0.129990 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3565 r_free = 0.3565 target = 0.104445 restraints weight = 15669.027| |-----------------------------------------------------------------------------| r_work (start): 0.3545 rms_B_bonded: 1.50 r_work: 0.3405 rms_B_bonded: 2.70 restraints_weight: 0.5000 r_work: 0.3263 rms_B_bonded: 4.53 restraints_weight: 0.2500 r_work (final): 0.3263 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8213 moved from start: 0.2564 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= 0.200 Angle : 0.636 13.054 13477 Z= 0.365 Chirality : 0.036 0.208 1536 Planarity : 0.005 0.061 944 Dihedral : 30.292 171.484 2968 Min Nonbonded Distance : 2.503 Molprobity Statistics. All-atom Clashscore : 9.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.15 % Favored : 97.85 % Rotamer: Outliers : 4.12 % Allowed : 32.04 % Favored : 63.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 2.69 (0.37), residues: 512 helix: 2.52 (0.26), residues: 385 sheet: None (None), residues: 0 loop : -0.63 (0.50), residues: 127 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG M 35 TYR 0.011 0.001 TYR P 51 PHE 0.010 0.001 PHE K 78 HIS 0.002 0.000 HIS M 31 Details of bonding type rmsd covalent geometry : bond 0.00439 ( 9282) covalent geometry : angle 0.63627 (13477) hydrogen bonds : bond 0.04619 ( 561) hydrogen bonds : angle 2.72525 ( 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 222 residues out of total 437 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 204 time to evaluate : 0.192 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: K 125 GLN cc_start: 0.8705 (OUTLIER) cc_final: 0.7884 (mp10) REVERT: K 131 ARG cc_start: 0.8668 (OUTLIER) cc_final: 0.8406 (mtt-85) REVERT: L 92 ARG cc_start: 0.8493 (OUTLIER) cc_final: 0.7928 (ttm-80) REVERT: M 64 GLU cc_start: 0.8098 (tp30) cc_final: 0.7681 (tp30) REVERT: M 68 ASN cc_start: 0.8332 (m-40) cc_final: 0.7474 (m-40) REVERT: N 64 ASN cc_start: 0.8833 (m-40) cc_final: 0.8589 (m-40) REVERT: O 72 ARG cc_start: 0.8852 (tpp80) cc_final: 0.8619 (ttm-80) REVERT: O 128 ARG cc_start: 0.8919 (mtp-110) cc_final: 0.8668 (mtp180) REVERT: P 31 LYS cc_start: 0.9030 (OUTLIER) cc_final: 0.8449 (tptm) outliers start: 18 outliers final: 13 residues processed: 207 average time/residue: 0.5166 time to fit residues: 112.1419 Evaluate side-chains 221 residues out of total 437 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 204 time to evaluate : 0.123 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain K residue 76 GLN 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 92 ARG Chi-restraints excluded: chain L residue 93 GLN Chi-restraints excluded: chain M residue 59 THR Chi-restraints excluded: chain M residue 61 GLU 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 N residue 68 GLU 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: 0.1980 chunk 60 optimal weight: 1.9990 chunk 50 optimal weight: 0.6980 chunk 51 optimal weight: 0.2980 chunk 44 optimal weight: 0.0980 chunk 59 optimal weight: 1.9990 chunk 43 optimal weight: 0.5980 chunk 11 optimal weight: 8.9990 chunk 33 optimal weight: 0.3980 chunk 56 optimal weight: 0.9980 chunk 16 optimal weight: 0.9990 overall best weight: 0.3180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: K 108 ASN ** L 75 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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 = 0.3950 r_free = 0.3950 target = 0.131035 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3581 r_free = 0.3581 target = 0.105577 restraints weight = 15711.058| |-----------------------------------------------------------------------------| r_work (start): 0.3554 rms_B_bonded: 1.54 r_work: 0.3414 rms_B_bonded: 2.73 restraints_weight: 0.5000 r_work: 0.3272 rms_B_bonded: 4.57 restraints_weight: 0.2500 r_work (final): 0.3272 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8207 moved from start: 0.2595 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 9282 Z= 0.180 Angle : 0.639 12.972 13477 Z= 0.365 Chirality : 0.036 0.205 1536 Planarity : 0.005 0.061 944 Dihedral : 30.297 171.913 2968 Min Nonbonded Distance : 2.503 Molprobity Statistics. All-atom Clashscore : 9.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.76 % Favored : 98.24 % Rotamer: Outliers : 4.35 % Allowed : 32.95 % Favored : 62.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 2.71 (0.37), residues: 512 helix: 2.55 (0.26), residues: 385 sheet: None (None), residues: 0 loop : -0.64 (0.50), residues: 127 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG M 35 TYR 0.013 0.001 TYR P 51 PHE 0.013 0.001 PHE K 78 HIS 0.002 0.000 HIS M 31 Details of bonding type rmsd covalent geometry : bond 0.00393 ( 9282) covalent geometry : angle 0.63905 (13477) hydrogen bonds : bond 0.04474 ( 561) hydrogen bonds : angle 2.68109 ( 1382) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3298.21 seconds wall clock time: 56 minutes 30.67 seconds (3390.67 seconds total)