Starting phenix.real_space_refine on Fri Aug 22 15:51:34 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8eh5_28135/08_2025/8eh5_28135.cif Found real_map, /net/cci-nas-00/data/ceres_data/8eh5_28135/08_2025/8eh5_28135.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.36 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8eh5_28135/08_2025/8eh5_28135.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8eh5_28135/08_2025/8eh5_28135.map" model { file = "/net/cci-nas-00/data/ceres_data/8eh5_28135/08_2025/8eh5_28135.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8eh5_28135/08_2025/8eh5_28135.cif" } resolution = 3.36 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= 0.003 sd= 0.064 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: 4 Type Number sf(0) Gaussians S 24 5.16 5 C 3481 2.51 5 N 939 2.21 5 O 1059 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 34 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: 5503 Number of models: 1 Model: "" Number of chains: 7 Chain: "G" Number of atoms: 187 Number of conformers: 1 Conformer: "" Number of residues, atoms: 26, 187 Classifications: {'peptide': 26} Link IDs: {'PTRANS': 6, 'TRANS': 19} Chain: "H" Number of atoms: 940 Number of conformers: 1 Conformer: "" Number of residues, atoms: 119, 940 Classifications: {'peptide': 119} Link IDs: {'PTRANS': 3, 'TRANS': 115} Chain: "L" Number of atoms: 832 Number of conformers: 1 Conformer: "" Number of residues, atoms: 107, 832 Classifications: {'peptide': 107} Link IDs: {'PTRANS': 5, 'TRANS': 101} Chain: "M" Number of atoms: 940 Number of conformers: 1 Conformer: "" Number of residues, atoms: 119, 940 Classifications: {'peptide': 119} Link IDs: {'PTRANS': 3, 'TRANS': 115} Chain: "N" Number of atoms: 832 Number of conformers: 1 Conformer: "" Number of residues, atoms: 107, 832 Classifications: {'peptide': 107} Link IDs: {'PTRANS': 5, 'TRANS': 101} Chain: "O" Number of atoms: 940 Number of conformers: 1 Conformer: "" Number of residues, atoms: 119, 940 Classifications: {'peptide': 119} Link IDs: {'PTRANS': 3, 'TRANS': 115} Chain: "P" Number of atoms: 832 Number of conformers: 1 Conformer: "" Number of residues, atoms: 107, 832 Classifications: {'peptide': 107} Link IDs: {'PTRANS': 5, 'TRANS': 101} Time building chain proxies: 1.60, per 1000 atoms: 0.29 Number of scatterers: 5503 At special positions: 0 Unit cell: (60.61, 98.23, 109.725, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 24 16.00 O 1059 8.00 N 939 7.00 C 3481 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=6, symmetry=0 Simple disulfide: pdb=" SG CYS H 22 " - pdb=" SG CYS H 92 " distance=2.02 Simple disulfide: pdb=" SG CYS L 23 " - pdb=" SG CYS L 88 " distance=2.03 Simple disulfide: pdb=" SG CYS M 22 " - pdb=" SG CYS M 92 " distance=2.02 Simple disulfide: pdb=" SG CYS N 23 " - pdb=" SG CYS N 88 " distance=2.03 Simple disulfide: pdb=" SG CYS O 22 " - pdb=" SG CYS O 92 " distance=2.03 Simple disulfide: pdb=" SG CYS P 23 " - pdb=" SG CYS P 88 " distance=2.05 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: 0.44 Conformation dependent library (CDL) restraints added in 238.2 milliseconds Enol-peptide restraints added in 476.8 nanoseconds 1380 Ramachandran restraints generated. 690 Oldfield, 0 Emsley, 690 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1276 Finding SS restraints... Secondary structure from input PDB file: 10 helices and 18 sheets defined 6.5% alpha, 42.2% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.26 Creating SS restraints... Processing helix chain 'H' and resid 52 through 55 removed outlier: 3.964A pdb=" N SER H 55 " --> pdb=" O PHE H 52A" (cutoff:3.500A) Processing helix chain 'H' and resid 61 through 64 Processing helix chain 'H' and resid 83 through 87 Processing helix chain 'L' and resid 79 through 83 Processing helix chain 'M' and resid 53 through 55 No H-bonds generated for 'chain 'M' and resid 53 through 55' Processing helix chain 'M' and resid 61 through 64 Processing helix chain 'M' and resid 83 through 87 Processing helix chain 'N' and resid 79 through 83 Processing helix chain 'O' and resid 83 through 87 Processing helix chain 'P' and resid 79 through 83 Processing sheet with id=AA1, first strand: chain 'H' and resid 3 through 7 Processing sheet with id=AA2, first strand: chain 'H' and resid 10 through 11 removed outlier: 6.103A pdb=" N GLY H 10 " --> pdb=" O THR H 110 " (cutoff:3.500A) removed outlier: 6.453A pdb=" N MET H 34 " --> pdb=" O VAL H 50 " (cutoff:3.500A) removed outlier: 4.447A pdb=" N VAL H 50 " --> pdb=" O MET H 34 " (cutoff:3.500A) removed outlier: 6.577A pdb=" N TRP H 36 " --> pdb=" O VAL H 48 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'H' and resid 96 through 97 removed outlier: 3.589A pdb=" N PHE H 96 " --> pdb=" O PHE H 100C" (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'L' and resid 5 through 6 Processing sheet with id=AA5, first strand: chain 'L' and resid 10 through 13 removed outlier: 5.514A pdb=" N LEU L 33 " --> pdb=" O TYR L 49 " (cutoff:3.500A) removed outlier: 5.679A pdb=" N TYR L 49 " --> pdb=" O LEU L 33 " (cutoff:3.500A) removed outlier: 6.467A pdb=" N TRP L 35 " --> pdb=" O LEU L 47 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'L' and resid 10 through 13 Processing sheet with id=AA7, first strand: chain 'M' and resid 3 through 7 Processing sheet with id=AA8, first strand: chain 'M' and resid 10 through 11 removed outlier: 6.114A pdb=" N GLY M 10 " --> pdb=" O THR M 110 " (cutoff:3.500A) removed outlier: 6.572A pdb=" N MET M 34 " --> pdb=" O VAL M 50 " (cutoff:3.500A) removed outlier: 4.484A pdb=" N VAL M 50 " --> pdb=" O MET M 34 " (cutoff:3.500A) removed outlier: 6.665A pdb=" N TRP M 36 " --> pdb=" O VAL M 48 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'M' and resid 96 through 97 Processing sheet with id=AB1, first strand: chain 'N' and resid 4 through 5 Processing sheet with id=AB2, first strand: chain 'N' and resid 10 through 13 removed outlier: 5.307A pdb=" N LEU N 33 " --> pdb=" O TYR N 49 " (cutoff:3.500A) removed outlier: 5.446A pdb=" N TYR N 49 " --> pdb=" O LEU N 33 " (cutoff:3.500A) removed outlier: 6.486A pdb=" N TRP N 35 " --> pdb=" O LEU N 47 " (cutoff:3.500A) removed outlier: 3.576A pdb=" N LYS N 50 " --> pdb=" O SER N 53 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'N' and resid 10 through 13 Processing sheet with id=AB4, first strand: chain 'O' and resid 3 through 7 Processing sheet with id=AB5, first strand: chain 'O' and resid 10 through 12 removed outlier: 6.682A pdb=" N MET O 34 " --> pdb=" O VAL O 50 " (cutoff:3.500A) removed outlier: 4.484A pdb=" N VAL O 50 " --> pdb=" O MET O 34 " (cutoff:3.500A) removed outlier: 6.620A pdb=" N TRP O 36 " --> pdb=" O VAL O 48 " (cutoff:3.500A) removed outlier: 4.209A pdb=" N TRP O 52 " --> pdb=" O ASN O 56 " (cutoff:3.500A) removed outlier: 5.672A pdb=" N ASN O 56 " --> pdb=" O TRP O 52 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'O' and resid 96 through 98 Processing sheet with id=AB7, first strand: chain 'P' and resid 4 through 6 Processing sheet with id=AB8, first strand: chain 'P' and resid 10 through 13 removed outlier: 4.584A pdb=" N LEU P 33 " --> pdb=" O TYR P 49 " (cutoff:3.500A) removed outlier: 5.114A pdb=" N TYR P 49 " --> pdb=" O LEU P 33 " (cutoff:3.500A) removed outlier: 6.528A pdb=" N TRP P 35 " --> pdb=" O LEU P 47 " (cutoff:3.500A) removed outlier: 6.399A pdb=" N SER P 53 " --> pdb=" O TYR P 49 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'P' and resid 10 through 13 233 hydrogen bonds defined for protein. 516 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 0.90 Time building geometry restraints manager: 0.59 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.18 - 1.31: 950 1.31 - 1.44: 1715 1.44 - 1.57: 2910 1.57 - 1.70: 33 1.70 - 1.83: 35 Bond restraints: 5643 Sorted by residual: bond pdb=" CB HIS O 35 " pdb=" CG HIS O 35 " ideal model delta sigma weight residual 1.497 1.403 0.094 1.40e-02 5.10e+03 4.52e+01 bond pdb=" CB ARG O 38 " pdb=" CG ARG O 38 " ideal model delta sigma weight residual 1.520 1.353 0.167 3.00e-02 1.11e+03 3.10e+01 bond pdb=" CB ARG H 38 " pdb=" CG ARG H 38 " ideal model delta sigma weight residual 1.520 1.357 0.163 3.00e-02 1.11e+03 2.95e+01 bond pdb=" CB PHE O 52A" pdb=" CG PHE O 52A" ideal model delta sigma weight residual 1.502 1.379 0.123 2.30e-02 1.89e+03 2.86e+01 bond pdb=" CB HIS M 93 " pdb=" CG HIS M 93 " ideal model delta sigma weight residual 1.497 1.423 0.074 1.40e-02 5.10e+03 2.79e+01 ... (remaining 5638 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.60: 6661 2.60 - 5.21: 857 5.21 - 7.81: 128 7.81 - 10.41: 6 10.41 - 13.01: 1 Bond angle restraints: 7653 Sorted by residual: angle pdb=" C GLY M 100A" pdb=" N PRO M 100B" pdb=" CA PRO M 100B" ideal model delta sigma weight residual 120.31 127.92 -7.61 9.80e-01 1.04e+00 6.03e+01 angle pdb=" CA ASP O 98 " pdb=" CB ASP O 98 " pdb=" CG ASP O 98 " ideal model delta sigma weight residual 112.60 120.06 -7.46 1.00e+00 1.00e+00 5.57e+01 angle pdb=" C TYR H 32 " pdb=" CA TYR H 32 " pdb=" CB TYR H 32 " ideal model delta sigma weight residual 109.54 122.55 -13.01 1.84e+00 2.95e-01 5.00e+01 angle pdb=" N ILE N 29 " pdb=" CA ILE N 29 " pdb=" C ILE N 29 " ideal model delta sigma weight residual 111.81 106.23 5.58 8.60e-01 1.35e+00 4.22e+01 angle pdb=" C GLY O 100A" pdb=" N PRO O 100B" pdb=" CA PRO O 100B" ideal model delta sigma weight residual 120.14 126.48 -6.34 1.06e+00 8.90e-01 3.58e+01 ... (remaining 7648 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.98: 3168 17.98 - 35.96: 85 35.96 - 53.95: 27 53.95 - 71.93: 14 71.93 - 89.91: 4 Dihedral angle restraints: 3298 sinusoidal: 1286 harmonic: 2012 Sorted by residual: dihedral pdb=" CB CYS N 23 " pdb=" SG CYS N 23 " pdb=" SG CYS N 88 " pdb=" CB CYS N 88 " ideal model delta sinusoidal sigma weight residual 93.00 166.66 -73.66 1 1.00e+01 1.00e-02 6.90e+01 dihedral pdb=" C TYR H 32 " pdb=" N TYR H 32 " pdb=" CA TYR H 32 " pdb=" CB TYR H 32 " ideal model delta harmonic sigma weight residual -122.60 -140.96 18.36 0 2.50e+00 1.60e-01 5.40e+01 dihedral pdb=" N TYR H 32 " pdb=" C TYR H 32 " pdb=" CA TYR H 32 " pdb=" CB TYR H 32 " ideal model delta harmonic sigma weight residual 122.80 135.69 -12.89 0 2.50e+00 1.60e-01 2.66e+01 ... (remaining 3295 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.120: 670 0.120 - 0.239: 130 0.239 - 0.359: 10 0.359 - 0.478: 1 0.478 - 0.598: 1 Chirality restraints: 812 Sorted by residual: chirality pdb=" CA TYR H 32 " pdb=" N TYR H 32 " pdb=" C TYR H 32 " pdb=" CB TYR H 32 " both_signs ideal model delta sigma weight residual False 2.51 1.91 0.60 2.00e-01 2.50e+01 8.93e+00 chirality pdb=" CA ILE H 28 " pdb=" N ILE H 28 " pdb=" C ILE H 28 " pdb=" CB ILE H 28 " both_signs ideal model delta sigma weight residual False 2.43 2.82 -0.38 2.00e-01 2.50e+01 3.65e+00 chirality pdb=" CA ARG H 94 " pdb=" N ARG H 94 " pdb=" C ARG H 94 " pdb=" CB ARG H 94 " both_signs ideal model delta sigma weight residual False 2.51 2.87 -0.36 2.00e-01 2.50e+01 3.17e+00 ... (remaining 809 not shown) Planarity restraints: 983 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TRP N 35 " -0.049 2.00e-02 2.50e+03 2.61e-02 1.71e+01 pdb=" CG TRP N 35 " 0.010 2.00e-02 2.50e+03 pdb=" CD1 TRP N 35 " 0.008 2.00e-02 2.50e+03 pdb=" CD2 TRP N 35 " 0.029 2.00e-02 2.50e+03 pdb=" NE1 TRP N 35 " 0.005 2.00e-02 2.50e+03 pdb=" CE2 TRP N 35 " 0.011 2.00e-02 2.50e+03 pdb=" CE3 TRP N 35 " 0.039 2.00e-02 2.50e+03 pdb=" CZ2 TRP N 35 " -0.019 2.00e-02 2.50e+03 pdb=" CZ3 TRP N 35 " 0.003 2.00e-02 2.50e+03 pdb=" CH2 TRP N 35 " -0.038 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA GLY O 100A" 0.019 2.00e-02 2.50e+03 3.75e-02 1.41e+01 pdb=" C GLY O 100A" -0.065 2.00e-02 2.50e+03 pdb=" O GLY O 100A" 0.025 2.00e-02 2.50e+03 pdb=" N PRO O 100B" 0.021 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA PRO H 100B" 0.019 2.00e-02 2.50e+03 3.75e-02 1.40e+01 pdb=" C PRO H 100B" -0.065 2.00e-02 2.50e+03 pdb=" O PRO H 100B" 0.024 2.00e-02 2.50e+03 pdb=" N PHE H 100C" 0.022 2.00e-02 2.50e+03 ... (remaining 980 not shown) Histogram of nonbonded interaction distances: 2.24 - 2.77: 1134 2.77 - 3.30: 4662 3.30 - 3.83: 9543 3.83 - 4.37: 11595 4.37 - 4.90: 19224 Nonbonded interactions: 46158 Sorted by model distance: nonbonded pdb=" OH TYR H 102 " pdb=" OG SER P 67 " model vdw 2.236 3.040 nonbonded pdb=" N ASP H 101 " pdb=" OD1 ASP H 101 " model vdw 2.412 3.120 nonbonded pdb=" OD2 ASP O 72 " pdb=" NZ LYS O 75 " model vdw 2.424 3.120 nonbonded pdb=" OD2 ASP H 72 " pdb=" NZ LYS H 75 " model vdw 2.429 3.120 nonbonded pdb=" O TYR H 32 " pdb=" NH1 ARG H 94 " model vdw 2.432 3.120 ... (remaining 46153 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 'H' selection = chain 'M' selection = chain 'O' } ncs_group { reference = chain 'L' selection = chain 'N' selection = chain 'P' } 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: 0.420 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: 0.080 Check model and map are aligned: 0.020 Set scattering table: 0.010 Process input model: 7.110 Find NCS groups from input model: 0.080 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:1.300 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 9.040 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7462 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 : 0.023 0.167 5649 Z= 1.158 Angle : 1.812 13.013 7665 Z= 1.207 Chirality : 0.094 0.598 812 Planarity : 0.008 0.043 983 Dihedral : 10.683 89.909 2004 Min Nonbonded Distance : 2.236 Molprobity Statistics. All-atom Clashscore : 2.69 Ramachandran Plot: Outliers : 0.58 % Allowed : 3.91 % Favored : 95.51 % Rotamer: Outliers : 0.50 % Allowed : 0.84 % Favored : 98.66 % Cbeta Deviations : 0.16 % 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: 0.43 (0.32), residues: 690 helix: None (None), residues: 0 sheet: -0.35 (0.29), residues: 282 loop : 0.98 (0.33), residues: 408 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG O 38 TYR 0.043 0.006 TYR N 49 PHE 0.033 0.006 PHE N 98 TRP 0.049 0.009 TRP N 35 HIS 0.011 0.003 HIS H 93 Details of bonding type rmsd covalent geometry : bond 0.02253 ( 5643) covalent geometry : angle 1.80746 ( 7653) SS BOND : bond 0.00857 ( 6) SS BOND : angle 3.74495 ( 12) hydrogen bonds : bond 0.15722 ( 218) hydrogen bonds : angle 8.79862 ( 516) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1380 Ramachandran restraints generated. 690 Oldfield, 0 Emsley, 690 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1380 Ramachandran restraints generated. 690 Oldfield, 0 Emsley, 690 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 190 residues out of total 598 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 187 time to evaluate : 0.227 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: H 93 HIS cc_start: 0.6970 (OUTLIER) cc_final: 0.6346 (t70) REVERT: H 95 ASN cc_start: 0.7541 (OUTLIER) cc_final: 0.6998 (t0) REVERT: L 4 MET cc_start: 0.8205 (mmm) cc_final: 0.7943 (mmm) REVERT: M 68 THR cc_start: 0.7417 (m) cc_final: 0.7096 (p) REVERT: M 77 THR cc_start: 0.6485 (m) cc_final: 0.6100 (m) REVERT: N 24 ARG cc_start: 0.8107 (mtt-85) cc_final: 0.7473 (ttt90) REVERT: O 46 GLU cc_start: 0.7849 (tt0) cc_final: 0.7438 (mt-10) REVERT: P 72 THR cc_start: 0.8330 (m) cc_final: 0.8003 (p) outliers start: 3 outliers final: 0 residues processed: 189 average time/residue: 0.1024 time to fit residues: 23.9298 Evaluate side-chains 128 residues out of total 598 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 126 time to evaluate : 0.216 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 93 HIS Chi-restraints excluded: chain H residue 95 ASN Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 65 random chunks: chunk 49 optimal weight: 3.9990 chunk 53 optimal weight: 2.9990 chunk 5 optimal weight: 0.9990 chunk 33 optimal weight: 0.8980 chunk 62 optimal weight: 1.9990 chunk 51 optimal weight: 1.9990 chunk 38 optimal weight: 0.9980 chunk 61 optimal weight: 4.9990 chunk 45 optimal weight: 1.9990 chunk 27 optimal weight: 0.9990 chunk 64 optimal weight: 0.8980 overall best weight: 0.9584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** H 93 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** M 1 GLN M 76 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4123 r_free = 0.4123 target = 0.165365 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3806 r_free = 0.3806 target = 0.136915 restraints weight = 7534.407| |-----------------------------------------------------------------------------| r_work (start): 0.3845 rms_B_bonded: 2.59 r_work: 0.3729 rms_B_bonded: 3.13 restraints_weight: 0.5000 r_work (final): 0.3729 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7231 moved from start: 0.3515 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.072 5649 Z= 0.152 Angle : 0.691 9.079 7665 Z= 0.373 Chirality : 0.048 0.198 812 Planarity : 0.005 0.026 983 Dihedral : 5.664 45.229 776 Min Nonbonded Distance : 2.457 Molprobity Statistics. All-atom Clashscore : 10.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.48 % Favored : 96.52 % Rotamer: Outliers : 2.51 % Allowed : 8.86 % Favored : 88.63 % 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: 0.28 (0.34), residues: 690 helix: None (None), residues: 0 sheet: 0.10 (0.30), residues: 291 loop : 0.41 (0.35), residues: 399 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG M 19 TYR 0.025 0.002 TYR M 32 PHE 0.018 0.002 PHE O 100C TRP 0.022 0.001 TRP M 52 HIS 0.008 0.002 HIS H 93 Details of bonding type rmsd covalent geometry : bond 0.00350 ( 5643) covalent geometry : angle 0.68992 ( 7653) SS BOND : bond 0.00276 ( 6) SS BOND : angle 1.07668 ( 12) hydrogen bonds : bond 0.04040 ( 218) hydrogen bonds : angle 6.18058 ( 516) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1380 Ramachandran restraints generated. 690 Oldfield, 0 Emsley, 690 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1380 Ramachandran restraints generated. 690 Oldfield, 0 Emsley, 690 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 156 residues out of total 598 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 141 time to evaluate : 0.222 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: H 43 LYS cc_start: 0.7920 (mttp) cc_final: 0.7647 (mtmm) REVERT: H 80 MET cc_start: 0.8243 (ttp) cc_final: 0.7942 (ttp) REVERT: H 83 ARG cc_start: 0.7649 (tpt170) cc_final: 0.7055 (mmt-90) REVERT: H 93 HIS cc_start: 0.7079 (OUTLIER) cc_final: 0.6374 (t70) REVERT: H 101 ASP cc_start: 0.7742 (p0) cc_final: 0.7319 (p0) REVERT: N 24 ARG cc_start: 0.7345 (mtt-85) cc_final: 0.6382 (ttt90) REVERT: P 3 GLN cc_start: 0.7364 (mp10) cc_final: 0.7044 (mp10) REVERT: P 4 MET cc_start: 0.8298 (OUTLIER) cc_final: 0.7831 (mtp) REVERT: P 24 ARG cc_start: 0.7841 (mtt-85) cc_final: 0.6949 (tpt170) REVERT: P 72 THR cc_start: 0.8105 (m) cc_final: 0.7574 (p) outliers start: 15 outliers final: 7 residues processed: 147 average time/residue: 0.0971 time to fit residues: 17.6745 Evaluate side-chains 130 residues out of total 598 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 121 time to evaluate : 0.145 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 31 THR Chi-restraints excluded: chain H residue 93 HIS Chi-restraints excluded: chain L residue 5 THR Chi-restraints excluded: chain L residue 58 VAL Chi-restraints excluded: chain L residue 63 SER Chi-restraints excluded: chain L residue 74 THR Chi-restraints excluded: chain N residue 74 THR Chi-restraints excluded: chain O residue 31 THR Chi-restraints excluded: chain P residue 4 MET Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 65 random chunks: chunk 46 optimal weight: 0.8980 chunk 31 optimal weight: 9.9990 chunk 10 optimal weight: 5.9990 chunk 28 optimal weight: 8.9990 chunk 55 optimal weight: 4.9990 chunk 40 optimal weight: 20.0000 chunk 36 optimal weight: 5.9990 chunk 2 optimal weight: 6.9990 chunk 8 optimal weight: 3.9990 chunk 58 optimal weight: 7.9990 chunk 35 optimal weight: 4.9990 overall best weight: 4.1788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: G 109 ASN G 113 ASN ** H 93 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** L 70 HIS ** O 76 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4022 r_free = 0.4022 target = 0.156198 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3682 r_free = 0.3682 target = 0.127826 restraints weight = 7602.529| |-----------------------------------------------------------------------------| r_work (start): 0.3678 rms_B_bonded: 2.47 r_work: 0.3564 rms_B_bonded: 2.96 restraints_weight: 0.5000 r_work: 0.3411 rms_B_bonded: 4.88 restraints_weight: 0.2500 r_work (final): 0.3411 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7614 moved from start: 0.4289 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.116 5649 Z= 0.344 Angle : 0.817 8.082 7665 Z= 0.441 Chirality : 0.051 0.199 812 Planarity : 0.005 0.035 983 Dihedral : 6.111 51.316 774 Min Nonbonded Distance : 2.294 Molprobity Statistics. All-atom Clashscore : 14.56 Ramachandran Plot: Outliers : 0.14 % Allowed : 5.51 % Favored : 94.35 % Rotamer: Outliers : 4.01 % Allowed : 12.54 % Favored : 83.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.55 (0.33), residues: 690 helix: None (None), residues: 0 sheet: -0.14 (0.30), residues: 291 loop : -0.47 (0.34), residues: 399 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG H 94 TYR 0.045 0.003 TYR N 49 PHE 0.024 0.003 PHE O 96 TRP 0.025 0.002 TRP O 52 HIS 0.010 0.004 HIS H 93 Details of bonding type rmsd covalent geometry : bond 0.00815 ( 5643) covalent geometry : angle 0.81610 ( 7653) SS BOND : bond 0.00509 ( 6) SS BOND : angle 1.45644 ( 12) hydrogen bonds : bond 0.04366 ( 218) hydrogen bonds : angle 6.42838 ( 516) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1380 Ramachandran restraints generated. 690 Oldfield, 0 Emsley, 690 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1380 Ramachandran restraints generated. 690 Oldfield, 0 Emsley, 690 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 144 residues out of total 598 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 120 time to evaluate : 0.215 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: H 18 LEU cc_start: 0.7944 (OUTLIER) cc_final: 0.7304 (tt) REVERT: H 34 MET cc_start: 0.8467 (mtt) cc_final: 0.8246 (mtt) REVERT: H 43 LYS cc_start: 0.7932 (mttp) cc_final: 0.7643 (mtmm) REVERT: H 93 HIS cc_start: 0.7080 (OUTLIER) cc_final: 0.6202 (t70) REVERT: L 79 GLN cc_start: 0.8246 (mm-40) cc_final: 0.7854 (mm-40) REVERT: L 82 ASP cc_start: 0.8491 (OUTLIER) cc_final: 0.7828 (m-30) REVERT: M 85 GLU cc_start: 0.8025 (tm-30) cc_final: 0.7620 (tm-30) REVERT: N 4 MET cc_start: 0.7098 (tpt) cc_final: 0.6783 (tpt) REVERT: N 55 GLU cc_start: 0.7464 (tt0) cc_final: 0.6981 (tt0) REVERT: N 89 GLN cc_start: 0.7552 (OUTLIER) cc_final: 0.6872 (tp40) REVERT: O 85 GLU cc_start: 0.6544 (OUTLIER) cc_final: 0.6229 (pm20) REVERT: P 3 GLN cc_start: 0.7577 (mp10) cc_final: 0.7264 (mp10) REVERT: P 4 MET cc_start: 0.8605 (OUTLIER) cc_final: 0.8172 (mtp) REVERT: P 18 ARG cc_start: 0.8799 (ttp80) cc_final: 0.8579 (mtp-110) REVERT: P 72 THR cc_start: 0.8413 (m) cc_final: 0.7846 (p) outliers start: 24 outliers final: 13 residues processed: 130 average time/residue: 0.1107 time to fit residues: 17.5855 Evaluate side-chains 131 residues out of total 598 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 112 time to evaluate : 0.209 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 109 ASN Chi-restraints excluded: chain G residue 113 ASN Chi-restraints excluded: chain H residue 18 LEU Chi-restraints excluded: chain H residue 31 THR Chi-restraints excluded: chain H residue 63 VAL Chi-restraints excluded: chain H residue 93 HIS Chi-restraints excluded: chain L residue 5 THR Chi-restraints excluded: chain L residue 26 SER Chi-restraints excluded: chain L residue 49 TYR Chi-restraints excluded: chain L residue 74 THR Chi-restraints excluded: chain L residue 82 ASP Chi-restraints excluded: chain M residue 69 ILE Chi-restraints excluded: chain N residue 74 THR Chi-restraints excluded: chain N residue 89 GLN Chi-restraints excluded: chain O residue 31 THR Chi-restraints excluded: chain O residue 66 ARG Chi-restraints excluded: chain O residue 82 MET Chi-restraints excluded: chain O residue 85 GLU Chi-restraints excluded: chain P residue 4 MET Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 65 random chunks: chunk 10 optimal weight: 1.9990 chunk 33 optimal weight: 1.9990 chunk 47 optimal weight: 0.9980 chunk 26 optimal weight: 2.9990 chunk 55 optimal weight: 3.9990 chunk 44 optimal weight: 0.9980 chunk 11 optimal weight: 3.9990 chunk 0 optimal weight: 7.9990 chunk 61 optimal weight: 6.9990 chunk 3 optimal weight: 1.9990 chunk 31 optimal weight: 5.9990 overall best weight: 1.5986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: G 109 ASN G 113 ASN ** H 93 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 1 GLN ** O 76 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4064 r_free = 0.4064 target = 0.160128 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3730 r_free = 0.3730 target = 0.131531 restraints weight = 7515.973| |-----------------------------------------------------------------------------| r_work (start): 0.3734 rms_B_bonded: 2.55 r_work: 0.3617 rms_B_bonded: 3.07 restraints_weight: 0.5000 r_work (final): 0.3617 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7445 moved from start: 0.4655 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.071 5649 Z= 0.175 Angle : 0.656 7.679 7665 Z= 0.352 Chirality : 0.047 0.180 812 Planarity : 0.005 0.033 983 Dihedral : 5.749 52.946 774 Min Nonbonded Distance : 2.251 Molprobity Statistics. All-atom Clashscore : 12.61 Ramachandran Plot: Outliers : 0.14 % Allowed : 5.94 % Favored : 93.91 % Rotamer: Outliers : 3.85 % Allowed : 14.21 % Favored : 81.94 % 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: -0.51 (0.34), residues: 690 helix: None (None), residues: 0 sheet: -0.11 (0.30), residues: 291 loop : -0.45 (0.35), residues: 399 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG O 94 TYR 0.028 0.002 TYR M 32 PHE 0.034 0.002 PHE O 96 TRP 0.012 0.001 TRP O 52 HIS 0.009 0.002 HIS H 93 Details of bonding type rmsd covalent geometry : bond 0.00411 ( 5643) covalent geometry : angle 0.65608 ( 7653) SS BOND : bond 0.00302 ( 6) SS BOND : angle 0.84022 ( 12) hydrogen bonds : bond 0.03457 ( 218) hydrogen bonds : angle 5.93989 ( 516) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1380 Ramachandran restraints generated. 690 Oldfield, 0 Emsley, 690 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1380 Ramachandran restraints generated. 690 Oldfield, 0 Emsley, 690 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 141 residues out of total 598 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 118 time to evaluate : 0.221 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: H 34 MET cc_start: 0.8397 (mtt) cc_final: 0.8158 (mtt) REVERT: H 43 LYS cc_start: 0.8104 (mttp) cc_final: 0.7821 (mtmm) REVERT: H 93 HIS cc_start: 0.7022 (OUTLIER) cc_final: 0.5910 (t70) REVERT: H 101 ASP cc_start: 0.7826 (p0) cc_final: 0.7168 (p0) REVERT: M 1 GLN cc_start: 0.4670 (OUTLIER) cc_final: 0.4405 (mt0) REVERT: M 85 GLU cc_start: 0.7940 (tm-30) cc_final: 0.7463 (tm-30) REVERT: N 4 MET cc_start: 0.7150 (tpt) cc_final: 0.6672 (mmm) REVERT: N 24 ARG cc_start: 0.7592 (mtp85) cc_final: 0.6400 (ttt90) REVERT: N 55 GLU cc_start: 0.7274 (tt0) cc_final: 0.6833 (tt0) REVERT: N 89 GLN cc_start: 0.7537 (OUTLIER) cc_final: 0.6830 (tp40) REVERT: N 102 THR cc_start: 0.7799 (OUTLIER) cc_final: 0.7542 (p) REVERT: O 7 SER cc_start: 0.8038 (t) cc_final: 0.7834 (p) REVERT: O 83 ARG cc_start: 0.8251 (mmm160) cc_final: 0.7548 (mmm160) REVERT: P 4 MET cc_start: 0.8305 (OUTLIER) cc_final: 0.7847 (mtp) REVERT: P 18 ARG cc_start: 0.8786 (ttp80) cc_final: 0.8561 (mtp-110) REVERT: P 24 ARG cc_start: 0.8004 (mtt-85) cc_final: 0.7547 (mtt-85) REVERT: P 72 THR cc_start: 0.8314 (m) cc_final: 0.7788 (p) outliers start: 23 outliers final: 14 residues processed: 129 average time/residue: 0.0985 time to fit residues: 15.5478 Evaluate side-chains 131 residues out of total 598 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 112 time to evaluate : 0.206 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 113 ASN Chi-restraints excluded: chain H residue 7 SER Chi-restraints excluded: chain H residue 31 THR Chi-restraints excluded: chain H residue 93 HIS Chi-restraints excluded: chain L residue 26 SER Chi-restraints excluded: chain L residue 49 TYR Chi-restraints excluded: chain L residue 74 THR Chi-restraints excluded: chain L residue 82 ASP Chi-restraints excluded: chain M residue 1 GLN Chi-restraints excluded: chain M residue 69 ILE Chi-restraints excluded: chain N residue 74 THR Chi-restraints excluded: chain N residue 89 GLN Chi-restraints excluded: chain N residue 102 THR Chi-restraints excluded: chain O residue 12 VAL Chi-restraints excluded: chain O residue 31 THR Chi-restraints excluded: chain O residue 48 VAL Chi-restraints excluded: chain O residue 82 MET Chi-restraints excluded: chain P residue 4 MET Chi-restraints excluded: chain P residue 7 SER Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 65 random chunks: chunk 30 optimal weight: 7.9990 chunk 11 optimal weight: 4.9990 chunk 44 optimal weight: 2.9990 chunk 40 optimal weight: 9.9990 chunk 31 optimal weight: 1.9990 chunk 24 optimal weight: 1.9990 chunk 58 optimal weight: 6.9990 chunk 10 optimal weight: 8.9990 chunk 13 optimal weight: 0.8980 chunk 7 optimal weight: 3.9990 chunk 21 optimal weight: 0.9990 overall best weight: 1.7788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: G 109 ASN G 113 ASN ** H 93 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 1 GLN ** O 76 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4057 r_free = 0.4057 target = 0.159328 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3738 r_free = 0.3738 target = 0.132342 restraints weight = 7696.464| |-----------------------------------------------------------------------------| r_work (start): 0.3741 rms_B_bonded: 2.32 r_work: 0.3629 rms_B_bonded: 2.82 restraints_weight: 0.5000 r_work: 0.3484 rms_B_bonded: 4.65 restraints_weight: 0.2500 r_work (final): 0.3484 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7594 moved from start: 0.4863 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.072 5649 Z= 0.178 Angle : 0.651 7.576 7665 Z= 0.347 Chirality : 0.047 0.157 812 Planarity : 0.004 0.036 983 Dihedral : 5.679 55.115 774 Min Nonbonded Distance : 2.369 Molprobity Statistics. All-atom Clashscore : 13.17 Ramachandran Plot: Outliers : 0.14 % Allowed : 6.38 % Favored : 93.48 % Rotamer: Outliers : 4.68 % Allowed : 13.55 % Favored : 81.77 % 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: -0.51 (0.34), residues: 690 helix: None (None), residues: 0 sheet: -0.12 (0.30), residues: 294 loop : -0.44 (0.35), residues: 396 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG L 61 TYR 0.023 0.002 TYR M 32 PHE 0.020 0.002 PHE O 52A TRP 0.014 0.001 TRP O 36 HIS 0.009 0.002 HIS H 93 Details of bonding type rmsd covalent geometry : bond 0.00421 ( 5643) covalent geometry : angle 0.65049 ( 7653) SS BOND : bond 0.00290 ( 6) SS BOND : angle 0.84127 ( 12) hydrogen bonds : bond 0.03305 ( 218) hydrogen bonds : angle 5.82709 ( 516) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1380 Ramachandran restraints generated. 690 Oldfield, 0 Emsley, 690 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1380 Ramachandran restraints generated. 690 Oldfield, 0 Emsley, 690 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 140 residues out of total 598 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 112 time to evaluate : 0.215 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: H 18 LEU cc_start: 0.8079 (OUTLIER) cc_final: 0.7527 (tt) REVERT: H 34 MET cc_start: 0.8425 (mtt) cc_final: 0.8212 (mtt) REVERT: H 43 LYS cc_start: 0.8148 (mttp) cc_final: 0.7872 (mtmm) REVERT: M 85 GLU cc_start: 0.7991 (tm-30) cc_final: 0.7434 (tm-30) REVERT: N 24 ARG cc_start: 0.7745 (mtp85) cc_final: 0.6524 (ttt90) REVERT: N 55 GLU cc_start: 0.7280 (tt0) cc_final: 0.6939 (tt0) REVERT: N 89 GLN cc_start: 0.7602 (OUTLIER) cc_final: 0.6905 (tp40) REVERT: N 102 THR cc_start: 0.7882 (OUTLIER) cc_final: 0.7625 (p) REVERT: O 83 ARG cc_start: 0.8403 (mmm160) cc_final: 0.7697 (mmm160) REVERT: O 85 GLU cc_start: 0.6767 (OUTLIER) cc_final: 0.6283 (pm20) REVERT: P 3 GLN cc_start: 0.7396 (mp10) cc_final: 0.7170 (mp10) REVERT: P 4 MET cc_start: 0.8405 (OUTLIER) cc_final: 0.7673 (mtm) REVERT: P 18 ARG cc_start: 0.8938 (ttp80) cc_final: 0.8689 (mtp-110) REVERT: P 24 ARG cc_start: 0.8185 (mtt-85) cc_final: 0.7746 (mtt-85) REVERT: P 72 THR cc_start: 0.8378 (m) cc_final: 0.7853 (p) outliers start: 28 outliers final: 21 residues processed: 127 average time/residue: 0.1075 time to fit residues: 16.6320 Evaluate side-chains 133 residues out of total 598 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 107 time to evaluate : 0.231 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 109 ASN Chi-restraints excluded: chain H residue 7 SER Chi-restraints excluded: chain H residue 18 LEU Chi-restraints excluded: chain H residue 31 THR Chi-restraints excluded: chain H residue 63 VAL Chi-restraints excluded: chain H residue 82 MET Chi-restraints excluded: chain H residue 93 HIS Chi-restraints excluded: chain L residue 26 SER Chi-restraints excluded: chain L residue 49 TYR Chi-restraints excluded: chain L residue 74 THR Chi-restraints excluded: chain M residue 1 GLN Chi-restraints excluded: chain M residue 69 ILE Chi-restraints excluded: chain N residue 74 THR Chi-restraints excluded: chain N residue 89 GLN Chi-restraints excluded: chain N residue 102 THR Chi-restraints excluded: chain O residue 12 VAL Chi-restraints excluded: chain O residue 31 THR Chi-restraints excluded: chain O residue 48 VAL Chi-restraints excluded: chain O residue 66 ARG Chi-restraints excluded: chain O residue 78 VAL Chi-restraints excluded: chain O residue 85 GLU Chi-restraints excluded: chain P residue 4 MET Chi-restraints excluded: chain P residue 7 SER Chi-restraints excluded: chain P residue 19 VAL Chi-restraints excluded: chain P residue 69 THR Chi-restraints excluded: chain P residue 90 GLU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 65 random chunks: chunk 24 optimal weight: 0.0870 chunk 59 optimal weight: 1.9990 chunk 42 optimal weight: 3.9990 chunk 48 optimal weight: 2.9990 chunk 27 optimal weight: 3.9990 chunk 6 optimal weight: 1.9990 chunk 49 optimal weight: 4.9990 chunk 54 optimal weight: 0.0970 chunk 41 optimal weight: 6.9990 chunk 13 optimal weight: 2.9990 chunk 64 optimal weight: 0.9980 overall best weight: 1.0360 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: G 109 ASN G 113 ASN ** H 93 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** L 6 GLN O 76 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4088 r_free = 0.4088 target = 0.161800 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3755 r_free = 0.3755 target = 0.133151 restraints weight = 7606.286| |-----------------------------------------------------------------------------| r_work (start): 0.3762 rms_B_bonded: 2.59 r_work: 0.3648 rms_B_bonded: 3.08 restraints_weight: 0.5000 r_work (final): 0.3648 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7406 moved from start: 0.5122 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.054 5649 Z= 0.131 Angle : 0.608 7.964 7665 Z= 0.321 Chirality : 0.046 0.143 812 Planarity : 0.004 0.038 983 Dihedral : 5.572 59.978 774 Min Nonbonded Distance : 2.405 Molprobity Statistics. All-atom Clashscore : 12.15 Ramachandran Plot: Outliers : 0.14 % Allowed : 5.51 % Favored : 94.35 % Rotamer: Outliers : 4.52 % Allowed : 15.22 % Favored : 80.27 % 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: -0.35 (0.34), residues: 690 helix: None (None), residues: 0 sheet: 0.34 (0.29), residues: 318 loop : -0.73 (0.36), residues: 372 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG H 71 TYR 0.015 0.002 TYR P 91 PHE 0.010 0.001 PHE O 52A TRP 0.015 0.001 TRP O 52 HIS 0.008 0.002 HIS H 93 Details of bonding type rmsd covalent geometry : bond 0.00307 ( 5643) covalent geometry : angle 0.60823 ( 7653) SS BOND : bond 0.00234 ( 6) SS BOND : angle 0.67214 ( 12) hydrogen bonds : bond 0.02967 ( 218) hydrogen bonds : angle 5.45405 ( 516) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1380 Ramachandran restraints generated. 690 Oldfield, 0 Emsley, 690 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1380 Ramachandran restraints generated. 690 Oldfield, 0 Emsley, 690 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 141 residues out of total 598 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 114 time to evaluate : 0.244 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: H 18 LEU cc_start: 0.8039 (OUTLIER) cc_final: 0.7485 (tt) REVERT: H 43 LYS cc_start: 0.8143 (mttp) cc_final: 0.7872 (mtmm) REVERT: M 85 GLU cc_start: 0.7918 (tm-30) cc_final: 0.7318 (tm-30) REVERT: N 4 MET cc_start: 0.6869 (mmm) cc_final: 0.6203 (mmm) REVERT: N 24 ARG cc_start: 0.7665 (mtp85) cc_final: 0.6556 (ttt90) REVERT: N 89 GLN cc_start: 0.7456 (OUTLIER) cc_final: 0.6721 (tp40) REVERT: O 83 ARG cc_start: 0.8241 (mmm160) cc_final: 0.7577 (mmm160) REVERT: O 95 ASN cc_start: 0.7264 (t0) cc_final: 0.6906 (t0) REVERT: P 4 MET cc_start: 0.8323 (OUTLIER) cc_final: 0.7561 (mtm) REVERT: P 72 THR cc_start: 0.8200 (m) cc_final: 0.7682 (p) outliers start: 27 outliers final: 17 residues processed: 132 average time/residue: 0.1004 time to fit residues: 16.3409 Evaluate side-chains 127 residues out of total 598 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 107 time to evaluate : 0.211 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 7 SER Chi-restraints excluded: chain H residue 18 LEU Chi-restraints excluded: chain H residue 31 THR Chi-restraints excluded: chain H residue 82 MET Chi-restraints excluded: chain H residue 93 HIS Chi-restraints excluded: chain L residue 26 SER Chi-restraints excluded: chain L residue 74 THR Chi-restraints excluded: chain M residue 69 ILE Chi-restraints excluded: chain N residue 2 ILE Chi-restraints excluded: chain N residue 58 VAL Chi-restraints excluded: chain N residue 74 THR Chi-restraints excluded: chain N residue 89 GLN Chi-restraints excluded: chain O residue 12 VAL Chi-restraints excluded: chain O residue 31 THR Chi-restraints excluded: chain O residue 48 VAL Chi-restraints excluded: chain O residue 78 VAL Chi-restraints excluded: chain P residue 4 MET Chi-restraints excluded: chain P residue 7 SER Chi-restraints excluded: chain P residue 19 VAL Chi-restraints excluded: chain P residue 90 GLU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 65 random chunks: chunk 47 optimal weight: 8.9990 chunk 57 optimal weight: 8.9990 chunk 18 optimal weight: 6.9990 chunk 30 optimal weight: 8.9990 chunk 10 optimal weight: 5.9990 chunk 23 optimal weight: 3.9990 chunk 44 optimal weight: 0.9980 chunk 24 optimal weight: 5.9990 chunk 4 optimal weight: 1.9990 chunk 19 optimal weight: 0.7980 chunk 59 optimal weight: 1.9990 overall best weight: 1.9586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** G 109 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 93 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** M 1 GLN ** M 95 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** M 105 GLN ** N 89 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4053 r_free = 0.4053 target = 0.158295 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3716 r_free = 0.3716 target = 0.129817 restraints weight = 7752.110| |-----------------------------------------------------------------------------| r_work (start): 0.3724 rms_B_bonded: 2.55 r_work: 0.3616 rms_B_bonded: 3.00 restraints_weight: 0.5000 r_work: 0.3461 rms_B_bonded: 4.98 restraints_weight: 0.2500 r_work (final): 0.3461 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7560 moved from start: 0.5228 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.077 5649 Z= 0.188 Angle : 0.646 8.515 7665 Z= 0.345 Chirality : 0.047 0.148 812 Planarity : 0.005 0.037 983 Dihedral : 5.631 57.074 774 Min Nonbonded Distance : 2.485 Molprobity Statistics. All-atom Clashscore : 13.54 Ramachandran Plot: Outliers : 0.14 % Allowed : 6.38 % Favored : 93.48 % Rotamer: Outliers : 4.68 % Allowed : 15.38 % Favored : 79.93 % 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: -0.45 (0.34), residues: 690 helix: None (None), residues: 0 sheet: 0.21 (0.29), residues: 324 loop : -0.73 (0.36), residues: 366 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG O 66 TYR 0.020 0.002 TYR M 32 PHE 0.023 0.002 PHE M 100C TRP 0.014 0.002 TRP O 52 HIS 0.008 0.002 HIS H 93 Details of bonding type rmsd covalent geometry : bond 0.00446 ( 5643) covalent geometry : angle 0.64585 ( 7653) SS BOND : bond 0.00255 ( 6) SS BOND : angle 0.80324 ( 12) hydrogen bonds : bond 0.03134 ( 218) hydrogen bonds : angle 5.53477 ( 516) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1380 Ramachandran restraints generated. 690 Oldfield, 0 Emsley, 690 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1380 Ramachandran restraints generated. 690 Oldfield, 0 Emsley, 690 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 133 residues out of total 598 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 105 time to evaluate : 0.221 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: H 18 LEU cc_start: 0.8021 (OUTLIER) cc_final: 0.7403 (tt) REVERT: H 43 LYS cc_start: 0.8132 (mttp) cc_final: 0.7853 (mtmm) REVERT: L 90 GLU cc_start: 0.8700 (OUTLIER) cc_final: 0.8490 (tm-30) REVERT: M 85 GLU cc_start: 0.7825 (tm-30) cc_final: 0.7111 (tm-30) REVERT: N 24 ARG cc_start: 0.7825 (mtp85) cc_final: 0.6574 (ttt90) REVERT: N 89 GLN cc_start: 0.7606 (OUTLIER) cc_final: 0.6905 (tp40) REVERT: O 83 ARG cc_start: 0.8368 (mmm160) cc_final: 0.7623 (mmm160) REVERT: P 18 ARG cc_start: 0.8896 (mtp-110) cc_final: 0.8527 (ttp80) REVERT: P 72 THR cc_start: 0.8347 (m) cc_final: 0.7793 (p) outliers start: 28 outliers final: 21 residues processed: 122 average time/residue: 0.0920 time to fit residues: 13.8858 Evaluate side-chains 125 residues out of total 598 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 101 time to evaluate : 0.208 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 7 SER Chi-restraints excluded: chain H residue 18 LEU Chi-restraints excluded: chain H residue 31 THR Chi-restraints excluded: chain H residue 63 VAL Chi-restraints excluded: chain H residue 93 HIS Chi-restraints excluded: chain L residue 26 SER Chi-restraints excluded: chain L residue 49 TYR Chi-restraints excluded: chain L residue 74 THR Chi-restraints excluded: chain L residue 90 GLU Chi-restraints excluded: chain M residue 66 ARG Chi-restraints excluded: chain M residue 69 ILE Chi-restraints excluded: chain N residue 74 THR Chi-restraints excluded: chain N residue 89 GLN Chi-restraints excluded: chain O residue 7 SER Chi-restraints excluded: chain O residue 12 VAL Chi-restraints excluded: chain O residue 31 THR Chi-restraints excluded: chain O residue 48 VAL Chi-restraints excluded: chain O residue 78 VAL Chi-restraints excluded: chain O residue 82 MET Chi-restraints excluded: chain P residue 4 MET Chi-restraints excluded: chain P residue 7 SER Chi-restraints excluded: chain P residue 19 VAL Chi-restraints excluded: chain P residue 69 THR Chi-restraints excluded: chain P residue 90 GLU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 65 random chunks: chunk 40 optimal weight: 0.8980 chunk 64 optimal weight: 0.9980 chunk 8 optimal weight: 5.9990 chunk 63 optimal weight: 0.9990 chunk 46 optimal weight: 5.9990 chunk 57 optimal weight: 0.9990 chunk 5 optimal weight: 2.9990 chunk 58 optimal weight: 0.9990 chunk 30 optimal weight: 9.9990 chunk 3 optimal weight: 0.9980 chunk 28 optimal weight: 5.9990 overall best weight: 0.9784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** G 109 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 129 ASN H 93 HIS L 79 GLN M 95 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4092 r_free = 0.4092 target = 0.161956 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3771 r_free = 0.3771 target = 0.134109 restraints weight = 7595.683| |-----------------------------------------------------------------------------| r_work (start): 0.3779 rms_B_bonded: 2.52 r_work: 0.3673 rms_B_bonded: 2.97 restraints_weight: 0.5000 r_work: 0.3520 rms_B_bonded: 4.96 restraints_weight: 0.2500 r_work (final): 0.3520 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7490 moved from start: 0.5445 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.051 5649 Z= 0.130 Angle : 0.608 8.042 7665 Z= 0.322 Chirality : 0.046 0.151 812 Planarity : 0.004 0.038 983 Dihedral : 5.056 43.015 774 Min Nonbonded Distance : 2.525 Molprobity Statistics. All-atom Clashscore : 11.78 Ramachandran Plot: Outliers : 0.14 % Allowed : 5.36 % Favored : 94.49 % Rotamer: Outliers : 3.68 % Allowed : 16.89 % Favored : 79.43 % 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: -0.31 (0.34), residues: 690 helix: None (None), residues: 0 sheet: 0.44 (0.29), residues: 318 loop : -0.76 (0.36), residues: 372 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG O 66 TYR 0.015 0.001 TYR P 49 PHE 0.016 0.002 PHE M 100C TRP 0.013 0.001 TRP O 52 HIS 0.005 0.001 HIS H 93 Details of bonding type rmsd covalent geometry : bond 0.00306 ( 5643) covalent geometry : angle 0.60766 ( 7653) SS BOND : bond 0.00235 ( 6) SS BOND : angle 0.53028 ( 12) hydrogen bonds : bond 0.02839 ( 218) hydrogen bonds : angle 5.33318 ( 516) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1380 Ramachandran restraints generated. 690 Oldfield, 0 Emsley, 690 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1380 Ramachandran restraints generated. 690 Oldfield, 0 Emsley, 690 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 128 residues out of total 598 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 106 time to evaluate : 0.272 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: H 18 LEU cc_start: 0.8044 (OUTLIER) cc_final: 0.7431 (tt) REVERT: H 43 LYS cc_start: 0.8088 (mttp) cc_final: 0.7833 (mtmm) REVERT: H 75 LYS cc_start: 0.6304 (tptp) cc_final: 0.6006 (tptt) REVERT: L 90 GLU cc_start: 0.8621 (OUTLIER) cc_final: 0.8405 (tm-30) REVERT: M 32 TYR cc_start: 0.7209 (m-10) cc_final: 0.6968 (m-10) REVERT: M 85 GLU cc_start: 0.7808 (tm-30) cc_final: 0.7112 (tm-30) REVERT: N 89 GLN cc_start: 0.7620 (OUTLIER) cc_final: 0.6891 (tp40) REVERT: O 83 ARG cc_start: 0.8300 (mmm160) cc_final: 0.7539 (mmm160) REVERT: P 72 THR cc_start: 0.8299 (m) cc_final: 0.7749 (p) outliers start: 22 outliers final: 18 residues processed: 121 average time/residue: 0.0845 time to fit residues: 12.6619 Evaluate side-chains 119 residues out of total 598 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 98 time to evaluate : 0.206 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 7 SER Chi-restraints excluded: chain H residue 18 LEU Chi-restraints excluded: chain H residue 31 THR Chi-restraints excluded: chain H residue 82 MET Chi-restraints excluded: chain H residue 93 HIS Chi-restraints excluded: chain L residue 26 SER Chi-restraints excluded: chain L residue 74 THR Chi-restraints excluded: chain L residue 90 GLU Chi-restraints excluded: chain M residue 69 ILE Chi-restraints excluded: chain N residue 74 THR Chi-restraints excluded: chain N residue 89 GLN Chi-restraints excluded: chain O residue 7 SER Chi-restraints excluded: chain O residue 12 VAL Chi-restraints excluded: chain O residue 31 THR Chi-restraints excluded: chain O residue 48 VAL Chi-restraints excluded: chain O residue 78 VAL Chi-restraints excluded: chain O residue 82 MET Chi-restraints excluded: chain P residue 4 MET Chi-restraints excluded: chain P residue 7 SER Chi-restraints excluded: chain P residue 19 VAL Chi-restraints excluded: chain P residue 90 GLU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 65 random chunks: chunk 52 optimal weight: 10.0000 chunk 24 optimal weight: 0.0470 chunk 53 optimal weight: 0.9980 chunk 37 optimal weight: 4.9990 chunk 51 optimal weight: 1.9990 chunk 60 optimal weight: 3.9990 chunk 47 optimal weight: 2.9990 chunk 28 optimal weight: 7.9990 chunk 11 optimal weight: 5.9990 chunk 36 optimal weight: 10.0000 chunk 54 optimal weight: 1.9990 overall best weight: 1.6084 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** G 109 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** M 105 GLN ** O 76 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4084 r_free = 0.4084 target = 0.161160 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3760 r_free = 0.3760 target = 0.133278 restraints weight = 7563.481| |-----------------------------------------------------------------------------| r_work (start): 0.3755 rms_B_bonded: 2.48 r_work: 0.3647 rms_B_bonded: 2.94 restraints_weight: 0.5000 r_work: 0.3493 rms_B_bonded: 4.88 restraints_weight: 0.2500 r_work (final): 0.3493 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7538 moved from start: 0.5493 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.068 5649 Z= 0.165 Angle : 0.624 8.021 7665 Z= 0.333 Chirality : 0.046 0.158 812 Planarity : 0.004 0.037 983 Dihedral : 5.153 49.862 774 Min Nonbonded Distance : 2.389 Molprobity Statistics. All-atom Clashscore : 11.97 Ramachandran Plot: Outliers : 0.14 % Allowed : 7.25 % Favored : 92.61 % Rotamer: Outliers : 4.18 % Allowed : 17.39 % Favored : 78.43 % 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: -0.41 (0.34), residues: 690 helix: None (None), residues: 0 sheet: 0.31 (0.29), residues: 324 loop : -0.78 (0.37), residues: 366 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG O 66 TYR 0.017 0.002 TYR P 49 PHE 0.023 0.002 PHE H 52A TRP 0.016 0.002 TRP O 36 HIS 0.008 0.002 HIS H 93 Details of bonding type rmsd covalent geometry : bond 0.00393 ( 5643) covalent geometry : angle 0.62348 ( 7653) SS BOND : bond 0.00238 ( 6) SS BOND : angle 0.73908 ( 12) hydrogen bonds : bond 0.02980 ( 218) hydrogen bonds : angle 5.42701 ( 516) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1380 Ramachandran restraints generated. 690 Oldfield, 0 Emsley, 690 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1380 Ramachandran restraints generated. 690 Oldfield, 0 Emsley, 690 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 124 residues out of total 598 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 99 time to evaluate : 0.201 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: H 18 LEU cc_start: 0.8087 (OUTLIER) cc_final: 0.7793 (tt) REVERT: H 43 LYS cc_start: 0.8080 (mttp) cc_final: 0.7828 (mtmm) REVERT: L 90 GLU cc_start: 0.8656 (OUTLIER) cc_final: 0.8455 (tm-30) REVERT: M 32 TYR cc_start: 0.7340 (m-10) cc_final: 0.7099 (m-10) REVERT: M 85 GLU cc_start: 0.7752 (tm-30) cc_final: 0.6963 (tm-30) REVERT: N 89 GLN cc_start: 0.7586 (OUTLIER) cc_final: 0.6848 (tp40) REVERT: O 83 ARG cc_start: 0.8263 (mmm160) cc_final: 0.7497 (mmm160) REVERT: P 3 GLN cc_start: 0.7300 (mp10) cc_final: 0.6881 (mp10) REVERT: P 72 THR cc_start: 0.8349 (m) cc_final: 0.7797 (p) outliers start: 25 outliers final: 20 residues processed: 116 average time/residue: 0.1052 time to fit residues: 14.9569 Evaluate side-chains 118 residues out of total 598 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 95 time to evaluate : 0.208 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 18 LEU Chi-restraints excluded: chain H residue 31 THR Chi-restraints excluded: chain H residue 93 HIS Chi-restraints excluded: chain L residue 26 SER Chi-restraints excluded: chain L residue 49 TYR Chi-restraints excluded: chain L residue 74 THR Chi-restraints excluded: chain L residue 90 GLU Chi-restraints excluded: chain M residue 69 ILE Chi-restraints excluded: chain N residue 74 THR Chi-restraints excluded: chain N residue 89 GLN Chi-restraints excluded: chain N residue 102 THR Chi-restraints excluded: chain O residue 7 SER Chi-restraints excluded: chain O residue 12 VAL Chi-restraints excluded: chain O residue 31 THR Chi-restraints excluded: chain O residue 48 VAL Chi-restraints excluded: chain O residue 52 TRP Chi-restraints excluded: chain O residue 78 VAL Chi-restraints excluded: chain O residue 82 MET Chi-restraints excluded: chain P residue 4 MET Chi-restraints excluded: chain P residue 7 SER Chi-restraints excluded: chain P residue 19 VAL Chi-restraints excluded: chain P residue 69 THR Chi-restraints excluded: chain P residue 90 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 65 random chunks: chunk 60 optimal weight: 5.9990 chunk 1 optimal weight: 0.6980 chunk 35 optimal weight: 0.2980 chunk 25 optimal weight: 0.9990 chunk 8 optimal weight: 6.9990 chunk 23 optimal weight: 0.9980 chunk 2 optimal weight: 6.9990 chunk 20 optimal weight: 7.9990 chunk 47 optimal weight: 5.9990 chunk 53 optimal weight: 2.9990 chunk 9 optimal weight: 1.9990 overall best weight: 0.9984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** G 109 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 76 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4107 r_free = 0.4107 target = 0.163340 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3791 r_free = 0.3791 target = 0.135678 restraints weight = 7539.909| |-----------------------------------------------------------------------------| r_work (start): 0.3787 rms_B_bonded: 2.48 r_work: 0.3676 rms_B_bonded: 2.95 restraints_weight: 0.5000 r_work: 0.3524 rms_B_bonded: 4.91 restraints_weight: 0.2500 r_work (final): 0.3524 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7503 moved from start: 0.5600 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.052 5649 Z= 0.130 Angle : 0.600 7.816 7665 Z= 0.320 Chirality : 0.046 0.154 812 Planarity : 0.004 0.038 983 Dihedral : 5.035 47.697 774 Min Nonbonded Distance : 2.373 Molprobity Statistics. All-atom Clashscore : 11.78 Ramachandran Plot: Outliers : 0.14 % Allowed : 6.52 % Favored : 93.33 % Rotamer: Outliers : 3.18 % Allowed : 18.39 % Favored : 78.43 % 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: -0.26 (0.34), residues: 690 helix: None (None), residues: 0 sheet: 0.52 (0.29), residues: 318 loop : -0.78 (0.37), residues: 372 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG O 66 TYR 0.015 0.001 TYR H 91 PHE 0.025 0.002 PHE H 52A TRP 0.016 0.001 TRP O 36 HIS 0.006 0.001 HIS H 93 Details of bonding type rmsd covalent geometry : bond 0.00305 ( 5643) covalent geometry : angle 0.60002 ( 7653) SS BOND : bond 0.00240 ( 6) SS BOND : angle 0.64076 ( 12) hydrogen bonds : bond 0.02835 ( 218) hydrogen bonds : angle 5.30299 ( 516) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1380 Ramachandran restraints generated. 690 Oldfield, 0 Emsley, 690 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1380 Ramachandran restraints generated. 690 Oldfield, 0 Emsley, 690 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 118 residues out of total 598 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 99 time to evaluate : 0.217 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: H 43 LYS cc_start: 0.8030 (mttp) cc_final: 0.7788 (mtmm) REVERT: L 90 GLU cc_start: 0.8603 (OUTLIER) cc_final: 0.8376 (tm-30) REVERT: M 32 TYR cc_start: 0.7237 (m-10) cc_final: 0.6965 (m-10) REVERT: N 89 GLN cc_start: 0.7592 (OUTLIER) cc_final: 0.6887 (tp40) REVERT: O 83 ARG cc_start: 0.8274 (mmm160) cc_final: 0.7513 (mmm160) REVERT: P 18 ARG cc_start: 0.8781 (mtp-110) cc_final: 0.8541 (ttp80) REVERT: P 72 THR cc_start: 0.8330 (m) cc_final: 0.7780 (p) outliers start: 19 outliers final: 16 residues processed: 113 average time/residue: 0.1070 time to fit residues: 14.8805 Evaluate side-chains 109 residues out of total 598 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 91 time to evaluate : 0.214 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 31 THR Chi-restraints excluded: chain H residue 93 HIS Chi-restraints excluded: chain L residue 26 SER Chi-restraints excluded: chain L residue 74 THR Chi-restraints excluded: chain L residue 90 GLU Chi-restraints excluded: chain M residue 69 ILE Chi-restraints excluded: chain N residue 74 THR Chi-restraints excluded: chain N residue 89 GLN Chi-restraints excluded: chain O residue 7 SER Chi-restraints excluded: chain O residue 12 VAL Chi-restraints excluded: chain O residue 31 THR Chi-restraints excluded: chain O residue 48 VAL Chi-restraints excluded: chain O residue 52 TRP Chi-restraints excluded: chain O residue 78 VAL Chi-restraints excluded: chain P residue 4 MET Chi-restraints excluded: chain P residue 7 SER Chi-restraints excluded: chain P residue 19 VAL Chi-restraints excluded: chain P residue 90 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 65 random chunks: chunk 36 optimal weight: 0.6980 chunk 2 optimal weight: 0.0370 chunk 53 optimal weight: 6.9990 chunk 50 optimal weight: 1.9990 chunk 9 optimal weight: 0.8980 chunk 41 optimal weight: 0.9990 chunk 8 optimal weight: 0.8980 chunk 24 optimal weight: 0.9990 chunk 54 optimal weight: 0.9990 chunk 23 optimal weight: 2.9990 chunk 10 optimal weight: 0.9980 overall best weight: 0.7058 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** G 109 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** M 105 GLN ** O 76 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4122 r_free = 0.4122 target = 0.162343 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3798 r_free = 0.3798 target = 0.133864 restraints weight = 7884.944| |-----------------------------------------------------------------------------| r_work (start): 0.3805 rms_B_bonded: 2.52 r_work: 0.3670 rms_B_bonded: 3.26 restraints_weight: 0.5000 r_work (final): 0.3670 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7434 moved from start: 0.5747 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 5649 Z= 0.116 Angle : 0.591 7.650 7665 Z= 0.314 Chirality : 0.045 0.147 812 Planarity : 0.004 0.039 983 Dihedral : 4.823 44.200 774 Min Nonbonded Distance : 2.394 Molprobity Statistics. All-atom Clashscore : 11.41 Ramachandran Plot: Outliers : 0.14 % Allowed : 6.96 % Favored : 92.90 % Rotamer: Outliers : 2.84 % Allowed : 18.23 % Favored : 78.93 % 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: -0.12 (0.34), residues: 690 helix: None (None), residues: 0 sheet: 0.60 (0.29), residues: 318 loop : -0.67 (0.37), residues: 372 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG O 66 TYR 0.014 0.001 TYR H 91 PHE 0.028 0.002 PHE O 100C TRP 0.015 0.001 TRP O 52 HIS 0.005 0.001 HIS H 93 Details of bonding type rmsd covalent geometry : bond 0.00267 ( 5643) covalent geometry : angle 0.59151 ( 7653) SS BOND : bond 0.00254 ( 6) SS BOND : angle 0.57407 ( 12) hydrogen bonds : bond 0.02755 ( 218) hydrogen bonds : angle 5.15769 ( 516) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1486.53 seconds wall clock time: 26 minutes 13.45 seconds (1573.45 seconds total)