Starting phenix.real_space_refine on Fri Dec 27 14:29:12 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8eh5_28135/12_2024/8eh5_28135.cif Found real_map, /net/cci-nas-00/data/ceres_data/8eh5_28135/12_2024/8eh5_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_28135/12_2024/8eh5_28135.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8eh5_28135/12_2024/8eh5_28135.map" model { file = "/net/cci-nas-00/data/ceres_data/8eh5_28135/12_2024/8eh5_28135.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8eh5_28135/12_2024/8eh5_28135.cif" } resolution = 3.36 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } 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): 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5532/modules/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: 3.82, per 1000 atoms: 0.69 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: 1.35 Conformation dependent library (CDL) restraints added in 682.1 milliseconds 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: 0.92 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: 1.48 Time building geometry restraints manager: 1.56 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: 0.240 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.010 Extract box with map and model: 0.210 Check model and map are aligned: 0.040 Set scattering table: 0.060 Process input model: 16.880 Find NCS groups from input model: 0.190 Set up NCS constraints: 0.030 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:3.100 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 20.770 ------------------------------------------------------------------------------- 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 5643 Z= 1.446 Angle : 1.807 13.013 7653 Z= 1.206 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. 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 TRP 0.049 0.009 TRP N 35 HIS 0.011 0.003 HIS H 93 PHE 0.033 0.006 PHE N 98 TYR 0.043 0.006 TYR N 49 ARG 0.007 0.001 ARG O 38 *********************** 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 : 0.632 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: 0.2182 time to fit residues: 50.7042 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 : 0.653 ------------------------------------------------------------------------------- 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 54 optimal weight: 0.9990 chunk 49 optimal weight: 3.9990 chunk 27 optimal weight: 0.9980 chunk 16 optimal weight: 0.6980 chunk 33 optimal weight: 0.7980 chunk 26 optimal weight: 0.9990 chunk 50 optimal weight: 2.9990 chunk 19 optimal weight: 9.9990 chunk 30 optimal weight: 5.9990 chunk 37 optimal weight: 0.9990 chunk 59 optimal weight: 0.6980 overall best weight: 0.8382 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7448 moved from start: 0.3414 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.068 5643 Z= 0.217 Angle : 0.687 8.950 7653 Z= 0.371 Chirality : 0.048 0.205 812 Planarity : 0.005 0.026 983 Dihedral : 5.655 45.457 776 Min Nonbonded Distance : 2.459 Molprobity Statistics. All-atom Clashscore : 10.76 Ramachandran Plot: Outliers : 0.14 % Allowed : 3.33 % Favored : 96.52 % Rotamer: Outliers : 1.84 % Allowed : 9.20 % Favored : 88.96 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.32 (0.34), residues: 690 helix: None (None), residues: 0 sheet: 0.09 (0.29), residues: 291 loop : 0.47 (0.35), residues: 399 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.001 TRP M 52 HIS 0.007 0.002 HIS H 93 PHE 0.020 0.002 PHE O 100C TYR 0.026 0.002 TYR M 32 ARG 0.006 0.001 ARG M 19 *********************** 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 150 residues out of total 598 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 139 time to evaluate : 0.674 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: H 43 LYS cc_start: 0.8089 (mttp) cc_final: 0.7847 (mtmm) REVERT: H 83 ARG cc_start: 0.7691 (tpt170) cc_final: 0.7454 (mmt-90) REVERT: H 93 HIS cc_start: 0.6960 (OUTLIER) cc_final: 0.6402 (t70) REVERT: H 101 ASP cc_start: 0.7626 (p0) cc_final: 0.7281 (p0) REVERT: M 34 MET cc_start: 0.7952 (tpp) cc_final: 0.7740 (mtt) REVERT: N 24 ARG cc_start: 0.7725 (mtt-85) cc_final: 0.7221 (ttt90) REVERT: P 4 MET cc_start: 0.7988 (OUTLIER) cc_final: 0.7663 (mtp) REVERT: P 24 ARG cc_start: 0.8199 (mtt-85) cc_final: 0.7652 (tpt170) REVERT: P 72 THR cc_start: 0.8065 (m) cc_final: 0.7648 (p) outliers start: 11 outliers final: 5 residues processed: 145 average time/residue: 0.2193 time to fit residues: 39.3612 Evaluate side-chains 127 residues out of total 598 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 120 time to evaluate : 0.670 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 93 HIS Chi-restraints excluded: chain L residue 5 THR 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 32 optimal weight: 7.9990 chunk 18 optimal weight: 2.9990 chunk 49 optimal weight: 5.9990 chunk 40 optimal weight: 20.0000 chunk 16 optimal weight: 2.9990 chunk 59 optimal weight: 0.9980 chunk 63 optimal weight: 5.9990 chunk 52 optimal weight: 0.9990 chunk 58 optimal weight: 2.9990 chunk 20 optimal weight: 0.8980 chunk 47 optimal weight: 0.9980 overall best weight: 1.3784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: G 109 ASN ** H 93 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 76 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7545 moved from start: 0.4101 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.066 5643 Z= 0.243 Angle : 0.650 8.302 7653 Z= 0.353 Chirality : 0.047 0.172 812 Planarity : 0.004 0.031 983 Dihedral : 5.401 46.882 774 Min Nonbonded Distance : 2.419 Molprobity Statistics. All-atom Clashscore : 10.57 Ramachandran Plot: Outliers : 0.14 % Allowed : 4.93 % Favored : 94.93 % Rotamer: Outliers : 3.68 % Allowed : 11.54 % Favored : 84.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.10 (0.34), residues: 690 helix: None (None), residues: 0 sheet: 0.11 (0.30), residues: 291 loop : 0.16 (0.35), residues: 399 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.001 TRP O 52 HIS 0.007 0.002 HIS H 93 PHE 0.019 0.002 PHE O 52A TYR 0.020 0.002 TYR M 32 ARG 0.004 0.001 ARG M 66 *********************** 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 143 residues out of total 598 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 121 time to evaluate : 0.633 Fit side-chains revert: symmetry clash REVERT: H 83 ARG cc_start: 0.7924 (tpt170) cc_final: 0.7679 (mmt180) REVERT: H 93 HIS cc_start: 0.7179 (OUTLIER) cc_final: 0.6725 (t70) REVERT: H 101 ASP cc_start: 0.7613 (p0) cc_final: 0.7299 (p0) REVERT: L 82 ASP cc_start: 0.7935 (OUTLIER) cc_final: 0.7086 (m-30) REVERT: M 85 GLU cc_start: 0.7894 (tm-30) cc_final: 0.7489 (tm-30) REVERT: N 24 ARG cc_start: 0.7761 (mtt-85) cc_final: 0.7231 (ttt90) REVERT: O 83 ARG cc_start: 0.8481 (mmm160) cc_final: 0.8202 (mmm160) REVERT: P 4 MET cc_start: 0.8041 (OUTLIER) cc_final: 0.7667 (mtp) REVERT: P 72 THR cc_start: 0.8066 (m) cc_final: 0.7679 (p) outliers start: 22 outliers final: 11 residues processed: 130 average time/residue: 0.2308 time to fit residues: 36.7754 Evaluate side-chains 122 residues out of total 598 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 108 time to evaluate : 0.634 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 109 ASN 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 74 THR Chi-restraints excluded: chain L residue 82 ASP Chi-restraints excluded: chain M residue 69 ILE Chi-restraints excluded: chain N residue 22 THR Chi-restraints excluded: chain N residue 74 THR 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 Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 65 random chunks: chunk 58 optimal weight: 4.9990 chunk 44 optimal weight: 2.9990 chunk 30 optimal weight: 7.9990 chunk 6 optimal weight: 3.9990 chunk 28 optimal weight: 10.0000 chunk 39 optimal weight: 7.9990 chunk 59 optimal weight: 0.8980 chunk 62 optimal weight: 0.9990 chunk 31 optimal weight: 6.9990 chunk 56 optimal weight: 6.9990 chunk 16 optimal weight: 1.9990 overall best weight: 2.1788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: G 109 ASN G 129 ASN ** H 93 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 76 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7623 moved from start: 0.4536 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.083 5643 Z= 0.314 Angle : 0.670 8.023 7653 Z= 0.360 Chirality : 0.047 0.170 812 Planarity : 0.005 0.037 983 Dihedral : 5.560 50.020 774 Min Nonbonded Distance : 2.489 Molprobity Statistics. All-atom Clashscore : 12.06 Ramachandran Plot: Outliers : 0.14 % Allowed : 5.80 % Favored : 94.06 % Rotamer: Outliers : 4.35 % Allowed : 11.37 % Favored : 84.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.20 (0.34), residues: 690 helix: None (None), residues: 0 sheet: 0.04 (0.30), residues: 294 loop : -0.17 (0.35), residues: 396 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP O 52 HIS 0.009 0.003 HIS H 93 PHE 0.022 0.002 PHE O 52A TYR 0.026 0.002 TYR N 49 ARG 0.003 0.000 ARG H 71 *********************** 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 137 residues out of total 598 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 111 time to evaluate : 0.639 Fit side-chains revert: symmetry clash REVERT: H 18 LEU cc_start: 0.8173 (OUTLIER) cc_final: 0.7803 (tt) REVERT: H 93 HIS cc_start: 0.7095 (OUTLIER) cc_final: 0.6447 (t70) REVERT: H 101 ASP cc_start: 0.7551 (p0) cc_final: 0.7157 (p0) REVERT: M 77 THR cc_start: 0.7144 (p) cc_final: 0.6850 (p) REVERT: M 85 GLU cc_start: 0.7951 (tm-30) cc_final: 0.7458 (tm-30) REVERT: N 4 MET cc_start: 0.6450 (mmm) cc_final: 0.5979 (mmm) REVERT: N 49 TYR cc_start: 0.6903 (OUTLIER) cc_final: 0.5842 (t80) REVERT: N 102 THR cc_start: 0.7807 (OUTLIER) cc_final: 0.7582 (p) REVERT: O 85 GLU cc_start: 0.7034 (OUTLIER) cc_final: 0.6476 (pm20) REVERT: P 4 MET cc_start: 0.8080 (OUTLIER) cc_final: 0.7718 (mtp) REVERT: P 72 THR cc_start: 0.8175 (m) cc_final: 0.7776 (p) outliers start: 26 outliers final: 15 residues processed: 124 average time/residue: 0.2307 time to fit residues: 35.2600 Evaluate side-chains 124 residues out of total 598 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 103 time to evaluate : 0.579 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 109 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 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 58 VAL 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 22 THR Chi-restraints excluded: chain N residue 49 TYR Chi-restraints excluded: chain N residue 74 THR 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 85 GLU 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 52 optimal weight: 10.0000 chunk 35 optimal weight: 3.9990 chunk 0 optimal weight: 10.0000 chunk 46 optimal weight: 3.9990 chunk 25 optimal weight: 7.9990 chunk 53 optimal weight: 0.8980 chunk 43 optimal weight: 5.9990 chunk 32 optimal weight: 1.9990 chunk 56 optimal weight: 0.0570 chunk 15 optimal weight: 1.9990 chunk 21 optimal weight: 0.7980 overall best weight: 1.1502 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: G 109 ASN ** H 93 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** L 70 HIS M 105 GLN O 76 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7574 moved from start: 0.4776 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.054 5643 Z= 0.208 Angle : 0.607 7.670 7653 Z= 0.324 Chirality : 0.046 0.144 812 Planarity : 0.004 0.036 983 Dihedral : 5.415 53.374 774 Min Nonbonded Distance : 2.468 Molprobity Statistics. All-atom Clashscore : 11.69 Ramachandran Plot: Outliers : 0.14 % Allowed : 5.94 % Favored : 93.91 % Rotamer: Outliers : 3.34 % Allowed : 13.21 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.25 (0.34), residues: 690 helix: None (None), residues: 0 sheet: 0.19 (0.29), residues: 324 loop : -0.42 (0.37), residues: 366 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP O 52 HIS 0.008 0.002 HIS H 93 PHE 0.018 0.002 PHE O 52A TYR 0.015 0.002 TYR N 49 ARG 0.004 0.000 ARG N 96 *********************** 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 130 residues out of total 598 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 110 time to evaluate : 0.667 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: H 18 LEU cc_start: 0.8190 (OUTLIER) cc_final: 0.7788 (tt) REVERT: H 83 ARG cc_start: 0.8135 (tpt170) cc_final: 0.7865 (mmt180) REVERT: H 93 HIS cc_start: 0.7041 (OUTLIER) cc_final: 0.6059 (t70) REVERT: H 101 ASP cc_start: 0.7622 (p0) cc_final: 0.7086 (p0) REVERT: L 4 MET cc_start: 0.8262 (mmm) cc_final: 0.7928 (mmm) REVERT: M 85 GLU cc_start: 0.7943 (tm-30) cc_final: 0.7438 (tm-30) REVERT: O 83 ARG cc_start: 0.8558 (mmm160) cc_final: 0.8225 (mmm160) REVERT: P 3 GLN cc_start: 0.7703 (mp10) cc_final: 0.7462 (mp10) REVERT: P 4 MET cc_start: 0.8040 (OUTLIER) cc_final: 0.7331 (mtm) REVERT: P 72 THR cc_start: 0.8061 (m) cc_final: 0.7686 (p) outliers start: 20 outliers final: 12 residues processed: 123 average time/residue: 0.2248 time to fit residues: 34.6644 Evaluate side-chains 113 residues out of total 598 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 98 time to evaluate : 0.592 ------------------------------------------------------------------------------- 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 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 58 VAL Chi-restraints excluded: chain L residue 74 THR Chi-restraints excluded: chain N residue 2 ILE Chi-restraints excluded: chain N residue 74 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 P residue 4 MET Chi-restraints excluded: chain P residue 7 SER Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 65 random chunks: chunk 56 optimal weight: 6.9990 chunk 12 optimal weight: 3.9990 chunk 36 optimal weight: 9.9990 chunk 15 optimal weight: 4.9990 chunk 62 optimal weight: 0.9990 chunk 52 optimal weight: 1.9990 chunk 29 optimal weight: 4.9990 chunk 5 optimal weight: 5.9990 chunk 20 optimal weight: 4.9990 chunk 33 optimal weight: 3.9990 chunk 60 optimal weight: 0.9980 overall best weight: 2.3988 ------------------------------------------------------------------------------- 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** M 1 GLN ** N 89 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7666 moved from start: 0.4991 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.086 5643 Z= 0.329 Angle : 0.672 7.474 7653 Z= 0.360 Chirality : 0.047 0.156 812 Planarity : 0.005 0.042 983 Dihedral : 5.709 58.447 774 Min Nonbonded Distance : 2.300 Molprobity Statistics. All-atom Clashscore : 12.24 Ramachandran Plot: Outliers : 0.14 % Allowed : 6.67 % Favored : 93.19 % Rotamer: Outliers : 4.52 % Allowed : 12.37 % Favored : 83.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.44 (0.34), residues: 690 helix: None (None), residues: 0 sheet: 0.01 (0.30), residues: 294 loop : -0.45 (0.35), residues: 396 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP O 52 HIS 0.009 0.003 HIS H 93 PHE 0.016 0.002 PHE M 100C TYR 0.028 0.002 TYR N 49 ARG 0.006 0.001 ARG L 61 *********************** 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 133 residues out of total 598 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 106 time to evaluate : 0.641 Fit side-chains revert: symmetry clash REVERT: H 18 LEU cc_start: 0.8240 (OUTLIER) cc_final: 0.7746 (tt) REVERT: H 75 LYS cc_start: 0.6117 (tptp) cc_final: 0.5910 (tptt) REVERT: L 4 MET cc_start: 0.8391 (mmm) cc_final: 0.8094 (mmm) REVERT: M 77 THR cc_start: 0.7135 (p) cc_final: 0.6915 (p) REVERT: M 85 GLU cc_start: 0.8004 (tm-30) cc_final: 0.7443 (tm-30) REVERT: O 83 ARG cc_start: 0.8627 (mmm160) cc_final: 0.8285 (mmm160) REVERT: O 85 GLU cc_start: 0.7147 (OUTLIER) cc_final: 0.6570 (pm20) REVERT: P 3 GLN cc_start: 0.7692 (mp10) cc_final: 0.7409 (mp10) REVERT: P 4 MET cc_start: 0.8071 (OUTLIER) cc_final: 0.7364 (mtm) REVERT: P 24 ARG cc_start: 0.8185 (mtt-85) cc_final: 0.7852 (mtt-85) REVERT: P 72 THR cc_start: 0.8158 (m) cc_final: 0.7758 (p) outliers start: 27 outliers final: 19 residues processed: 121 average time/residue: 0.2039 time to fit residues: 31.0392 Evaluate side-chains 119 residues out of total 598 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 97 time to evaluate : 0.618 ------------------------------------------------------------------------------- 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 26 SER Chi-restraints excluded: chain L residue 49 TYR Chi-restraints excluded: chain L residue 58 VAL Chi-restraints excluded: chain L residue 74 THR 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 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 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=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 65 random chunks: chunk 7 optimal weight: 2.9990 chunk 35 optimal weight: 8.9990 chunk 45 optimal weight: 8.9990 chunk 52 optimal weight: 3.9990 chunk 62 optimal weight: 2.9990 chunk 39 optimal weight: 0.3980 chunk 38 optimal weight: 2.9990 chunk 28 optimal weight: 3.9990 chunk 25 optimal weight: 5.9990 chunk 37 optimal weight: 0.7980 chunk 18 optimal weight: 5.9990 overall best weight: 2.0386 ------------------------------------------------------------------------------- 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** M 105 GLN ** N 89 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 76 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7658 moved from start: 0.5174 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.076 5643 Z= 0.291 Angle : 0.640 7.444 7653 Z= 0.345 Chirality : 0.047 0.155 812 Planarity : 0.005 0.038 983 Dihedral : 5.705 55.942 774 Min Nonbonded Distance : 2.336 Molprobity Statistics. All-atom Clashscore : 13.17 Ramachandran Plot: Outliers : 0.14 % Allowed : 7.25 % Favored : 92.61 % Rotamer: Outliers : 5.52 % Allowed : 12.21 % Favored : 82.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.58 (0.34), residues: 690 helix: None (None), residues: 0 sheet: 0.13 (0.29), residues: 324 loop : -0.82 (0.36), residues: 366 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP O 52 HIS 0.009 0.002 HIS H 93 PHE 0.018 0.002 PHE O 100C TYR 0.023 0.002 TYR N 49 ARG 0.004 0.000 ARG L 61 *********************** 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 132 residues out of total 598 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 99 time to evaluate : 0.657 Fit side-chains revert: symmetry clash REVERT: H 18 LEU cc_start: 0.8275 (OUTLIER) cc_final: 0.7829 (tt) REVERT: L 4 MET cc_start: 0.8411 (mmm) cc_final: 0.8082 (mmm) REVERT: M 85 GLU cc_start: 0.7920 (tm-30) cc_final: 0.7280 (tm-30) REVERT: N 4 MET cc_start: 0.6990 (mmm) cc_final: 0.6538 (mmm) REVERT: N 49 TYR cc_start: 0.6823 (OUTLIER) cc_final: 0.5709 (t80) REVERT: N 89 GLN cc_start: 0.7080 (OUTLIER) cc_final: 0.6272 (tt0) REVERT: O 83 ARG cc_start: 0.8722 (mmm160) cc_final: 0.8337 (mmm160) REVERT: O 85 GLU cc_start: 0.7089 (OUTLIER) cc_final: 0.6508 (pm20) REVERT: O 107 THR cc_start: 0.8162 (OUTLIER) cc_final: 0.7961 (t) REVERT: P 4 MET cc_start: 0.8048 (OUTLIER) cc_final: 0.7340 (mtm) REVERT: P 24 ARG cc_start: 0.8166 (mtt-85) cc_final: 0.7841 (mtt-85) REVERT: P 72 THR cc_start: 0.8202 (m) cc_final: 0.7805 (p) outliers start: 33 outliers final: 23 residues processed: 122 average time/residue: 0.2177 time to fit residues: 33.2228 Evaluate side-chains 126 residues out of total 598 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 97 time to evaluate : 0.633 ------------------------------------------------------------------------------- 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 58 VAL Chi-restraints excluded: chain L residue 74 THR Chi-restraints excluded: chain M residue 66 ARG Chi-restraints excluded: chain M residue 69 ILE Chi-restraints excluded: chain N residue 49 TYR 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 78 VAL Chi-restraints excluded: chain O residue 85 GLU Chi-restraints excluded: chain O residue 107 THR 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 12 optimal weight: 0.7980 chunk 39 optimal weight: 8.9990 chunk 42 optimal weight: 3.9990 chunk 30 optimal weight: 9.9990 chunk 5 optimal weight: 3.9990 chunk 49 optimal weight: 0.9990 chunk 56 optimal weight: 3.9990 chunk 60 optimal weight: 6.9990 chunk 54 optimal weight: 0.6980 chunk 58 optimal weight: 0.9980 chunk 35 optimal weight: 5.9990 overall best weight: 1.4984 ------------------------------------------------------------------------------- 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 113 ASN ** H 93 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 89 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 76 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7630 moved from start: 0.5316 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.063 5643 Z= 0.249 Angle : 0.644 10.133 7653 Z= 0.345 Chirality : 0.046 0.156 812 Planarity : 0.005 0.038 983 Dihedral : 5.579 57.234 774 Min Nonbonded Distance : 2.335 Molprobity Statistics. All-atom Clashscore : 13.17 Ramachandran Plot: Outliers : 0.14 % Allowed : 7.25 % Favored : 92.61 % Rotamer: Outliers : 5.02 % Allowed : 14.05 % Favored : 80.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.50 (0.34), residues: 690 helix: None (None), residues: 0 sheet: 0.19 (0.29), residues: 324 loop : -0.79 (0.36), residues: 366 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP O 36 HIS 0.008 0.002 HIS H 93 PHE 0.021 0.002 PHE H 52A TYR 0.018 0.002 TYR N 49 ARG 0.005 0.001 ARG O 94 *********************** 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 129 residues out of total 598 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 99 time to evaluate : 0.618 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: H 18 LEU cc_start: 0.8247 (OUTLIER) cc_final: 0.7835 (tt) REVERT: L 4 MET cc_start: 0.8357 (mmm) cc_final: 0.8028 (mmm) REVERT: M 85 GLU cc_start: 0.7833 (tm-30) cc_final: 0.7176 (tm-30) REVERT: N 4 MET cc_start: 0.7042 (mmm) cc_final: 0.6635 (mmm) REVERT: N 49 TYR cc_start: 0.6751 (OUTLIER) cc_final: 0.5615 (t80) REVERT: O 83 ARG cc_start: 0.8702 (mmm160) cc_final: 0.8337 (mmm160) REVERT: O 85 GLU cc_start: 0.7063 (OUTLIER) cc_final: 0.6445 (pm20) REVERT: O 107 THR cc_start: 0.8150 (OUTLIER) cc_final: 0.7937 (t) REVERT: P 3 GLN cc_start: 0.7656 (mp10) cc_final: 0.7416 (mp10) REVERT: P 24 ARG cc_start: 0.8184 (mtt-85) cc_final: 0.7898 (mtt-85) REVERT: P 72 THR cc_start: 0.8225 (m) cc_final: 0.7840 (p) outliers start: 30 outliers final: 21 residues processed: 118 average time/residue: 0.2141 time to fit residues: 31.4656 Evaluate side-chains 120 residues out of total 598 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 95 time to evaluate : 0.674 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 26 SER Chi-restraints excluded: chain L residue 49 TYR Chi-restraints excluded: chain L residue 58 VAL Chi-restraints excluded: chain L residue 74 THR Chi-restraints excluded: chain M residue 66 ARG Chi-restraints excluded: chain M residue 69 ILE Chi-restraints excluded: chain N residue 49 TYR Chi-restraints excluded: chain N residue 74 THR 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 78 VAL Chi-restraints excluded: chain O residue 85 GLU Chi-restraints excluded: chain O residue 107 THR 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 25 optimal weight: 2.9990 chunk 45 optimal weight: 5.9990 chunk 17 optimal weight: 0.8980 chunk 52 optimal weight: 0.9990 chunk 55 optimal weight: 3.9990 chunk 58 optimal weight: 2.9990 chunk 38 optimal weight: 0.9980 chunk 61 optimal weight: 10.0000 chunk 37 optimal weight: 1.9990 chunk 29 optimal weight: 0.2980 chunk 42 optimal weight: 6.9990 overall best weight: 1.0384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: G 113 ASN H 93 HIS M 105 GLN ** N 89 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 76 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7588 moved from start: 0.5451 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.052 5643 Z= 0.201 Angle : 0.610 8.988 7653 Z= 0.328 Chirality : 0.046 0.153 812 Planarity : 0.005 0.039 983 Dihedral : 5.055 43.491 774 Min Nonbonded Distance : 2.349 Molprobity Statistics. All-atom Clashscore : 12.71 Ramachandran Plot: Outliers : 0.14 % Allowed : 7.10 % Favored : 92.75 % Rotamer: Outliers : 4.18 % Allowed : 14.72 % Favored : 81.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.33 (0.34), residues: 690 helix: None (None), residues: 0 sheet: 0.45 (0.29), residues: 318 loop : -0.81 (0.36), residues: 372 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP O 36 HIS 0.006 0.001 HIS H 93 PHE 0.014 0.002 PHE O 100C TYR 0.019 0.002 TYR M 32 ARG 0.006 0.000 ARG L 61 *********************** 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 120 residues out of total 598 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 95 time to evaluate : 0.593 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: H 18 LEU cc_start: 0.8215 (OUTLIER) cc_final: 0.7800 (tt) REVERT: L 4 MET cc_start: 0.8337 (mmm) cc_final: 0.7961 (mmm) REVERT: M 85 GLU cc_start: 0.7894 (tm-30) cc_final: 0.7225 (tm-30) REVERT: N 4 MET cc_start: 0.7075 (mmm) cc_final: 0.6644 (mmm) REVERT: N 89 GLN cc_start: 0.6990 (OUTLIER) cc_final: 0.6247 (tt0) REVERT: O 83 ARG cc_start: 0.8633 (mmm160) cc_final: 0.8283 (mmm160) REVERT: O 107 THR cc_start: 0.8092 (OUTLIER) cc_final: 0.7869 (t) REVERT: P 3 GLN cc_start: 0.7600 (mp10) cc_final: 0.7375 (mp10) REVERT: P 72 THR cc_start: 0.8198 (m) cc_final: 0.7828 (p) outliers start: 25 outliers final: 18 residues processed: 114 average time/residue: 0.2146 time to fit residues: 30.7283 Evaluate side-chains 112 residues out of total 598 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 91 time to evaluate : 0.639 ------------------------------------------------------------------------------- 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 82 MET Chi-restraints excluded: chain H residue 93 HIS Chi-restraints excluded: chain L residue 26 SER Chi-restraints excluded: chain L residue 58 VAL Chi-restraints excluded: chain L residue 74 THR 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 78 VAL Chi-restraints excluded: chain O residue 107 THR 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 64 optimal weight: 3.9990 chunk 59 optimal weight: 0.8980 chunk 51 optimal weight: 9.9990 chunk 5 optimal weight: 2.9990 chunk 39 optimal weight: 6.9990 chunk 31 optimal weight: 8.9990 chunk 40 optimal weight: 10.0000 chunk 54 optimal weight: 0.9980 chunk 15 optimal weight: 0.7980 chunk 47 optimal weight: 2.9990 chunk 7 optimal weight: 4.9990 overall best weight: 1.7384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: G 109 ASN ** L 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 105 GLN ** N 89 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 76 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7631 moved from start: 0.5503 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.068 5643 Z= 0.263 Angle : 0.634 9.409 7653 Z= 0.341 Chirality : 0.047 0.155 812 Planarity : 0.005 0.052 983 Dihedral : 5.172 51.318 774 Min Nonbonded Distance : 2.443 Molprobity Statistics. All-atom Clashscore : 12.99 Ramachandran Plot: Outliers : 0.14 % Allowed : 7.68 % Favored : 92.17 % Rotamer: Outliers : 4.18 % Allowed : 15.22 % Favored : 80.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.42 (0.34), residues: 690 helix: None (None), residues: 0 sheet: 0.26 (0.29), residues: 324 loop : -0.75 (0.36), residues: 366 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.002 TRP O 36 HIS 0.008 0.002 HIS H 93 PHE 0.013 0.002 PHE M 100C TYR 0.021 0.002 TYR N 49 ARG 0.005 0.001 ARG L 61 ********************** 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: 25 poor density : 93 time to evaluate : 0.692 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: H 18 LEU cc_start: 0.8242 (OUTLIER) cc_final: 0.7811 (tt) REVERT: L 4 MET cc_start: 0.8416 (mmm) cc_final: 0.8051 (mmm) REVERT: M 85 GLU cc_start: 0.7815 (tm-30) cc_final: 0.7090 (tm-30) REVERT: N 4 MET cc_start: 0.6985 (mmm) cc_final: 0.6486 (mmm) REVERT: N 89 GLN cc_start: 0.7117 (OUTLIER) cc_final: 0.6320 (tt0) REVERT: O 107 THR cc_start: 0.8172 (OUTLIER) cc_final: 0.7956 (t) REVERT: P 3 GLN cc_start: 0.7619 (mp10) cc_final: 0.7397 (mp10) REVERT: P 18 ARG cc_start: 0.8599 (mtp-110) cc_final: 0.8344 (ttp80) REVERT: P 72 THR cc_start: 0.8232 (m) cc_final: 0.7846 (p) outliers start: 25 outliers final: 18 residues processed: 111 average time/residue: 0.2053 time to fit residues: 28.9074 Evaluate side-chains 111 residues out of total 598 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 90 time to evaluate : 0.639 ------------------------------------------------------------------------------- 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 58 VAL Chi-restraints excluded: chain L residue 74 THR 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 78 VAL Chi-restraints excluded: chain O residue 107 THR 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 14 optimal weight: 10.0000 chunk 51 optimal weight: 5.9990 chunk 21 optimal weight: 1.9990 chunk 53 optimal weight: 3.9990 chunk 6 optimal weight: 0.8980 chunk 9 optimal weight: 0.9980 chunk 45 optimal weight: 7.9990 chunk 2 optimal weight: 5.9990 chunk 37 optimal weight: 2.9990 chunk 59 optimal weight: 0.1980 chunk 34 optimal weight: 3.9990 overall best weight: 1.4184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: G 109 ASN ** L 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 105 GLN ** N 89 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 76 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4083 r_free = 0.4083 target = 0.161272 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3760 r_free = 0.3760 target = 0.133403 restraints weight = 7469.714| |-----------------------------------------------------------------------------| r_work (start): 0.3761 rms_B_bonded: 2.51 r_work: 0.3645 rms_B_bonded: 3.05 restraints_weight: 0.5000 r_work (final): 0.3645 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7410 moved from start: 0.5615 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.061 5643 Z= 0.233 Angle : 0.625 8.693 7653 Z= 0.335 Chirality : 0.046 0.153 812 Planarity : 0.004 0.037 983 Dihedral : 5.113 50.045 774 Min Nonbonded Distance : 2.456 Molprobity Statistics. All-atom Clashscore : 12.71 Ramachandran Plot: Outliers : 0.14 % Allowed : 7.39 % Favored : 92.46 % Rotamer: Outliers : 3.68 % Allowed : 16.22 % Favored : 80.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.37 (0.34), residues: 690 helix: None (None), residues: 0 sheet: 0.42 (0.29), residues: 318 loop : -0.83 (0.36), residues: 372 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.001 TRP O 36 HIS 0.007 0.002 HIS H 93 PHE 0.012 0.002 PHE M 100C TYR 0.017 0.002 TYR N 49 ARG 0.006 0.000 ARG L 61 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1556.56 seconds wall clock time: 29 minutes 20.36 seconds (1760.36 seconds total)