Starting phenix.real_space_refine on Thu Jul 24 05:46:17 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8eh5_28135/07_2025/8eh5_28135.cif Found real_map, /net/cci-nas-00/data/ceres_data/8eh5_28135/07_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_28135/07_2025/8eh5_28135.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8eh5_28135/07_2025/8eh5_28135.map" model { file = "/net/cci-nas-00/data/ceres_data/8eh5_28135/07_2025/8eh5_28135.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8eh5_28135/07_2025/8eh5_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-5711/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: 3.93, per 1000 atoms: 0.71 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 762.8 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: 0.91 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: 1.57 Time building geometry restraints manager: 1.61 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: 0.260 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: 0.220 Check model and map are aligned: 0.050 Set scattering table: 0.050 Process input model: 17.490 Find NCS groups from input model: 0.240 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:2.810 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 21.160 ------------------------------------------------------------------------------- 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 (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 Details of bonding type rmsd hydrogen bonds : bond 0.15722 ( 218) hydrogen bonds : angle 8.79862 ( 516) SS BOND : bond 0.00857 ( 6) SS BOND : angle 3.74495 ( 12) covalent geometry : bond 0.02253 ( 5643) covalent geometry : angle 1.80746 ( 7653) *********************** 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 : 0.586 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: 0.2346 time to fit residues: 53.9801 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 : 0.644 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4126 r_free = 0.4126 target = 0.165778 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3811 r_free = 0.3811 target = 0.137406 restraints weight = 7425.767| |-----------------------------------------------------------------------------| r_work (start): 0.3853 rms_B_bonded: 2.56 r_work: 0.3736 rms_B_bonded: 3.10 restraints_weight: 0.5000 r_work (final): 0.3736 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7222 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 5649 Z= 0.150 Angle : 0.688 8.950 7665 Z= 0.372 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 Details of bonding type rmsd hydrogen bonds : bond 0.04093 ( 218) hydrogen bonds : angle 6.22170 ( 516) SS BOND : bond 0.00263 ( 6) SS BOND : angle 1.04422 ( 12) covalent geometry : bond 0.00335 ( 5643) covalent geometry : angle 0.68726 ( 7653) *********************** 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 : 0.627 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: H 43 LYS cc_start: 0.7921 (mttp) cc_final: 0.7630 (mtmm) REVERT: H 83 ARG cc_start: 0.7601 (tpt170) cc_final: 0.7047 (mmt-90) REVERT: H 93 HIS cc_start: 0.7025 (OUTLIER) cc_final: 0.6301 (t70) REVERT: H 101 ASP cc_start: 0.7735 (p0) cc_final: 0.7307 (p0) REVERT: L 61 ARG cc_start: 0.8119 (mtm-85) cc_final: 0.7873 (mtm180) REVERT: M 34 MET cc_start: 0.7908 (tpp) cc_final: 0.7692 (mtt) REVERT: N 24 ARG cc_start: 0.7334 (mtt-85) cc_final: 0.6374 (ttt90) REVERT: O 102 TYR cc_start: 0.6881 (m-80) cc_final: 0.6665 (m-10) REVERT: P 3 GLN cc_start: 0.7371 (mp10) cc_final: 0.7040 (mp10) REVERT: P 4 MET cc_start: 0.8305 (OUTLIER) cc_final: 0.7829 (mtp) REVERT: P 24 ARG cc_start: 0.7874 (mtt-85) cc_final: 0.7008 (tpt170) REVERT: P 72 THR cc_start: 0.8111 (m) cc_final: 0.7583 (p) outliers start: 11 outliers final: 5 residues processed: 145 average time/residue: 0.2042 time to fit residues: 36.6865 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 : 0.621 ------------------------------------------------------------------------------- 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 33 optimal weight: 0.9990 chunk 49 optimal weight: 5.9990 chunk 25 optimal weight: 7.9990 chunk 64 optimal weight: 5.9990 chunk 22 optimal weight: 4.9990 chunk 19 optimal weight: 0.8980 chunk 44 optimal weight: 0.2980 chunk 45 optimal weight: 0.5980 chunk 24 optimal weight: 8.9990 chunk 26 optimal weight: 5.9990 chunk 13 optimal weight: 2.9990 overall best weight: 1.1584 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4107 r_free = 0.4107 target = 0.161493 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3778 r_free = 0.3778 target = 0.133274 restraints weight = 7758.820| |-----------------------------------------------------------------------------| r_work (start): 0.3795 rms_B_bonded: 2.51 r_work: 0.3664 rms_B_bonded: 3.25 restraints_weight: 0.5000 r_work (final): 0.3664 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7380 moved from start: 0.4135 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.061 5649 Z= 0.147 Angle : 0.635 8.330 7665 Z= 0.346 Chirality : 0.047 0.170 812 Planarity : 0.004 0.030 983 Dihedral : 5.347 46.717 774 Min Nonbonded Distance : 2.420 Molprobity Statistics. All-atom Clashscore : 10.02 Ramachandran Plot: Outliers : 0.14 % Allowed : 4.93 % Favored : 94.93 % Rotamer: Outliers : 3.68 % Allowed : 11.71 % Favored : 84.62 % 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: 0.17 (0.33), residues: 690 helix: None (None), residues: 0 sheet: 0.29 (0.29), residues: 285 loop : 0.09 (0.35), residues: 405 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.001 TRP O 52 HIS 0.007 0.002 HIS H 93 PHE 0.020 0.002 PHE O 52A TYR 0.018 0.002 TYR M 32 ARG 0.004 0.001 ARG M 66 Details of bonding type rmsd hydrogen bonds : bond 0.03479 ( 218) hydrogen bonds : angle 5.65799 ( 516) SS BOND : bond 0.00290 ( 6) SS BOND : angle 0.82540 ( 12) covalent geometry : bond 0.00338 ( 5643) covalent geometry : angle 0.63434 ( 7653) *********************** 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 145 residues out of total 598 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 123 time to evaluate : 0.642 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: H 18 LEU cc_start: 0.8019 (OUTLIER) cc_final: 0.7491 (tt) REVERT: H 43 LYS cc_start: 0.7979 (mttp) cc_final: 0.7747 (mtmm) REVERT: H 83 ARG cc_start: 0.7819 (tpt170) cc_final: 0.7321 (mmt180) REVERT: H 93 HIS cc_start: 0.7170 (OUTLIER) cc_final: 0.6637 (t70) REVERT: H 101 ASP cc_start: 0.7625 (p0) cc_final: 0.7271 (p0) REVERT: L 82 ASP cc_start: 0.8038 (OUTLIER) cc_final: 0.7744 (t0) REVERT: M 85 GLU cc_start: 0.7870 (tm-30) cc_final: 0.7450 (tm-30) REVERT: N 24 ARG cc_start: 0.7244 (mtt-85) cc_final: 0.6394 (ttt90) REVERT: N 89 GLN cc_start: 0.6697 (tt0) cc_final: 0.6354 (tp40) REVERT: O 83 ARG cc_start: 0.8125 (mmm160) cc_final: 0.7583 (mmm160) REVERT: P 4 MET cc_start: 0.8226 (OUTLIER) cc_final: 0.7709 (mtp) REVERT: P 18 ARG cc_start: 0.8767 (ttp80) cc_final: 0.8500 (mtp-110) REVERT: P 24 ARG cc_start: 0.7701 (mtt-85) cc_final: 0.7239 (mtt-85) REVERT: P 72 THR cc_start: 0.8015 (m) cc_final: 0.7535 (p) outliers start: 22 outliers final: 11 residues processed: 133 average time/residue: 0.2227 time to fit residues: 36.4786 Evaluate side-chains 129 residues out of total 598 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 114 time to evaluate : 0.679 ------------------------------------------------------------------------------- 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 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 66 ARG 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 33 optimal weight: 4.9990 chunk 27 optimal weight: 4.9990 chunk 48 optimal weight: 3.9990 chunk 46 optimal weight: 0.9980 chunk 9 optimal weight: 0.9980 chunk 19 optimal weight: 4.9990 chunk 47 optimal weight: 3.9990 chunk 40 optimal weight: 20.0000 chunk 18 optimal weight: 0.9980 chunk 28 optimal weight: 10.0000 chunk 62 optimal weight: 7.9990 overall best weight: 2.1984 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4066 r_free = 0.4066 target = 0.159930 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3736 r_free = 0.3736 target = 0.131651 restraints weight = 7597.079| |-----------------------------------------------------------------------------| r_work (start): 0.3747 rms_B_bonded: 2.53 r_work: 0.3629 rms_B_bonded: 3.07 restraints_weight: 0.5000 r_work (final): 0.3629 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7415 moved from start: 0.4532 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.082 5649 Z= 0.206 Angle : 0.671 8.006 7665 Z= 0.360 Chirality : 0.047 0.179 812 Planarity : 0.005 0.047 983 Dihedral : 5.562 49.443 774 Min Nonbonded Distance : 2.508 Molprobity Statistics. All-atom Clashscore : 11.87 Ramachandran Plot: Outliers : 0.14 % Allowed : 5.80 % Favored : 94.06 % Rotamer: Outliers : 4.52 % Allowed : 11.54 % Favored : 83.95 % 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: -0.17 (0.34), residues: 690 helix: None (None), residues: 0 sheet: 0.11 (0.30), residues: 291 loop : -0.20 (0.34), residues: 399 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 0.019 0.002 PHE O 52A TYR 0.026 0.002 TYR N 49 ARG 0.003 0.001 ARG H 71 Details of bonding type rmsd hydrogen bonds : bond 0.03527 ( 218) hydrogen bonds : angle 5.84738 ( 516) SS BOND : bond 0.00320 ( 6) SS BOND : angle 1.26170 ( 12) covalent geometry : bond 0.00488 ( 5643) covalent geometry : angle 0.66944 ( 7653) *********************** 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 140 residues out of total 598 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 113 time to evaluate : 0.587 Fit side-chains revert: symmetry clash REVERT: H 43 LYS cc_start: 0.7928 (mttp) cc_final: 0.7681 (mtmm) REVERT: H 93 HIS cc_start: 0.7139 (OUTLIER) cc_final: 0.6413 (t70) REVERT: H 101 ASP cc_start: 0.7684 (p0) cc_final: 0.7248 (p0) REVERT: M 85 GLU cc_start: 0.7905 (tm-30) cc_final: 0.7393 (tm-30) REVERT: N 89 GLN cc_start: 0.7524 (OUTLIER) cc_final: 0.6740 (tp40) REVERT: N 102 THR cc_start: 0.7698 (OUTLIER) cc_final: 0.7431 (p) REVERT: O 85 GLU cc_start: 0.6746 (OUTLIER) cc_final: 0.6303 (pm20) REVERT: P 3 GLN cc_start: 0.7242 (mp10) cc_final: 0.7041 (mp10) REVERT: P 4 MET cc_start: 0.8309 (OUTLIER) cc_final: 0.7837 (mtp) REVERT: P 24 ARG cc_start: 0.7819 (mtt-85) cc_final: 0.7341 (mtt-85) REVERT: P 72 THR cc_start: 0.8205 (m) cc_final: 0.7668 (p) outliers start: 27 outliers final: 16 residues processed: 125 average time/residue: 0.2258 time to fit residues: 34.9266 Evaluate side-chains 128 residues out of total 598 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 107 time to evaluate : 0.636 ------------------------------------------------------------------------------- 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 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 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 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 0 optimal weight: 10.0000 chunk 60 optimal weight: 3.9990 chunk 57 optimal weight: 1.9990 chunk 16 optimal weight: 0.9980 chunk 38 optimal weight: 3.9990 chunk 59 optimal weight: 0.3980 chunk 23 optimal weight: 5.9990 chunk 37 optimal weight: 0.8980 chunk 33 optimal weight: 0.2980 chunk 40 optimal weight: 10.0000 chunk 7 optimal weight: 0.0000 overall best weight: 0.5184 ------------------------------------------------------------------------------- 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** M 105 GLN O 76 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4131 r_free = 0.4131 target = 0.165779 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3819 r_free = 0.3819 target = 0.138255 restraints weight = 7442.501| |-----------------------------------------------------------------------------| r_work (start): 0.3822 rms_B_bonded: 2.48 r_work: 0.3713 rms_B_bonded: 2.96 restraints_weight: 0.5000 r_work: 0.3559 rms_B_bonded: 4.93 restraints_weight: 0.2500 r_work (final): 0.3559 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7419 moved from start: 0.4841 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.036 5649 Z= 0.111 Angle : 0.585 7.713 7665 Z= 0.312 Chirality : 0.045 0.146 812 Planarity : 0.004 0.039 983 Dihedral : 5.296 52.211 774 Min Nonbonded Distance : 2.468 Molprobity Statistics. All-atom Clashscore : 10.30 Ramachandran Plot: Outliers : 0.14 % Allowed : 4.78 % Favored : 95.07 % Rotamer: Outliers : 2.84 % Allowed : 13.38 % Favored : 83.78 % 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: -0.03 (0.34), residues: 690 helix: None (None), residues: 0 sheet: 0.48 (0.29), residues: 318 loop : -0.41 (0.36), residues: 372 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP O 52 HIS 0.007 0.001 HIS H 93 PHE 0.015 0.001 PHE O 52A TYR 0.018 0.001 TYR M 32 ARG 0.003 0.000 ARG N 31 Details of bonding type rmsd hydrogen bonds : bond 0.02970 ( 218) hydrogen bonds : angle 5.45244 ( 516) SS BOND : bond 0.00252 ( 6) SS BOND : angle 0.69819 ( 12) covalent geometry : bond 0.00249 ( 5643) covalent geometry : angle 0.58493 ( 7653) *********************** 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: 17 poor density : 113 time to evaluate : 0.650 Fit side-chains revert: symmetry clash REVERT: H 43 LYS cc_start: 0.8058 (mttp) cc_final: 0.7783 (mtmm) REVERT: H 83 ARG cc_start: 0.8134 (tpt170) cc_final: 0.7424 (mmt180) REVERT: H 93 HIS cc_start: 0.7198 (OUTLIER) cc_final: 0.6138 (t70) REVERT: H 101 ASP cc_start: 0.7742 (p0) cc_final: 0.7151 (p0) REVERT: M 77 THR cc_start: 0.6950 (p) cc_final: 0.6726 (p) REVERT: M 85 GLU cc_start: 0.7917 (tm-30) cc_final: 0.7375 (tm-30) REVERT: N 89 GLN cc_start: 0.7637 (OUTLIER) cc_final: 0.6974 (tp40) REVERT: N 102 THR cc_start: 0.7561 (OUTLIER) cc_final: 0.7326 (p) REVERT: O 83 ARG cc_start: 0.8243 (mmm160) cc_final: 0.7555 (mmm160) REVERT: O 100 PHE cc_start: 0.6899 (m-80) cc_final: 0.6606 (m-80) REVERT: P 3 GLN cc_start: 0.7176 (mp10) cc_final: 0.6461 (mp10) REVERT: P 4 MET cc_start: 0.8513 (OUTLIER) cc_final: 0.7942 (mtp) REVERT: P 72 THR cc_start: 0.8126 (m) cc_final: 0.7647 (p) outliers start: 17 outliers final: 11 residues processed: 123 average time/residue: 0.2306 time to fit residues: 34.9588 Evaluate side-chains 115 residues out of total 598 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 100 time to evaluate : 0.648 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 N residue 2 ILE Chi-restraints excluded: chain N residue 22 THR 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 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 35 optimal weight: 4.9990 chunk 32 optimal weight: 6.9990 chunk 24 optimal weight: 0.0070 chunk 47 optimal weight: 0.9980 chunk 63 optimal weight: 4.9990 chunk 38 optimal weight: 0.8980 chunk 52 optimal weight: 10.0000 chunk 31 optimal weight: 4.9990 chunk 1 optimal weight: 0.5980 chunk 30 optimal weight: 1.9990 chunk 40 optimal weight: 10.0000 overall best weight: 0.9000 ------------------------------------------------------------------------------- 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 ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 70 HIS M 95 ASN ** 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 = 0.4137 r_free = 0.4137 target = 0.163566 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3803 r_free = 0.3803 target = 0.134550 restraints weight = 7885.686| |-----------------------------------------------------------------------------| r_work (start): 0.3793 rms_B_bonded: 2.57 r_work: 0.3662 rms_B_bonded: 3.28 restraints_weight: 0.5000 r_work (final): 0.3662 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7402 moved from start: 0.5077 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 5649 Z= 0.125 Angle : 0.603 7.694 7665 Z= 0.322 Chirality : 0.046 0.147 812 Planarity : 0.004 0.036 983 Dihedral : 5.367 58.326 774 Min Nonbonded Distance : 2.296 Molprobity Statistics. All-atom Clashscore : 10.57 Ramachandran Plot: Outliers : 0.14 % Allowed : 6.09 % Favored : 93.77 % Rotamer: Outliers : 3.68 % Allowed : 12.88 % 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: 0.04 (0.34), residues: 690 helix: None (None), residues: 0 sheet: 0.65 (0.29), residues: 318 loop : -0.50 (0.37), residues: 372 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP O 52 HIS 0.007 0.002 HIS H 93 PHE 0.016 0.002 PHE M 100C TYR 0.014 0.001 TYR P 49 ARG 0.005 0.000 ARG L 31 Details of bonding type rmsd hydrogen bonds : bond 0.02903 ( 218) hydrogen bonds : angle 5.25264 ( 516) SS BOND : bond 0.00237 ( 6) SS BOND : angle 0.70108 ( 12) covalent geometry : bond 0.00288 ( 5643) covalent geometry : angle 0.60294 ( 7653) *********************** 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 127 residues out of total 598 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 105 time to evaluate : 0.589 Fit side-chains revert: symmetry clash REVERT: H 18 LEU cc_start: 0.8135 (OUTLIER) cc_final: 0.7538 (tt) REVERT: H 43 LYS cc_start: 0.8143 (mttp) cc_final: 0.7905 (mtmm) REVERT: H 83 ARG cc_start: 0.8061 (tpt170) cc_final: 0.7495 (mmt180) REVERT: M 32 TYR cc_start: 0.6894 (m-10) cc_final: 0.6679 (m-10) REVERT: M 77 THR cc_start: 0.6960 (p) cc_final: 0.6699 (p) REVERT: M 85 GLU cc_start: 0.7895 (tm-30) cc_final: 0.7260 (tm-30) REVERT: N 89 GLN cc_start: 0.7428 (OUTLIER) cc_final: 0.6777 (tp40) REVERT: N 102 THR cc_start: 0.7525 (OUTLIER) cc_final: 0.7322 (p) REVERT: O 83 ARG cc_start: 0.8304 (mmm160) cc_final: 0.7728 (mmm160) REVERT: P 4 MET cc_start: 0.8269 (OUTLIER) cc_final: 0.7770 (mtp) REVERT: P 94 TYR cc_start: 0.7041 (m-80) cc_final: 0.6813 (m-10) outliers start: 22 outliers final: 13 residues processed: 121 average time/residue: 0.2211 time to fit residues: 32.9014 Evaluate side-chains 116 residues out of total 598 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 99 time to evaluate : 0.605 ------------------------------------------------------------------------------- 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 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 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 P residue 4 MET Chi-restraints excluded: chain P residue 7 SER Chi-restraints excluded: chain P residue 19 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 65 random chunks: chunk 11 optimal weight: 0.9990 chunk 13 optimal weight: 3.9990 chunk 56 optimal weight: 1.9990 chunk 2 optimal weight: 0.9980 chunk 43 optimal weight: 0.9990 chunk 10 optimal weight: 4.9990 chunk 27 optimal weight: 0.0060 chunk 23 optimal weight: 5.9990 chunk 26 optimal weight: 0.9990 chunk 3 optimal weight: 10.0000 chunk 21 optimal weight: 0.7980 overall best weight: 0.7600 ------------------------------------------------------------------------------- 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 81 GLN ** H 93 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** L 6 GLN M 1 GLN M 105 GLN O 76 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4122 r_free = 0.4122 target = 0.162100 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3810 r_free = 0.3810 target = 0.134721 restraints weight = 7694.559| |-----------------------------------------------------------------------------| r_work (start): 0.3820 rms_B_bonded: 2.40 r_work: 0.3686 rms_B_bonded: 3.19 restraints_weight: 0.5000 r_work (final): 0.3686 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7378 moved from start: 0.5271 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 5649 Z= 0.117 Angle : 0.582 8.798 7665 Z= 0.309 Chirality : 0.045 0.138 812 Planarity : 0.004 0.039 983 Dihedral : 5.267 52.776 774 Min Nonbonded Distance : 2.294 Molprobity Statistics. All-atom Clashscore : 11.04 Ramachandran Plot: Outliers : 0.14 % Allowed : 5.94 % Favored : 93.91 % Rotamer: Outliers : 3.51 % Allowed : 14.05 % Favored : 82.44 % 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: 0.12 (0.34), residues: 690 helix: None (None), residues: 0 sheet: 0.76 (0.29), residues: 318 loop : -0.50 (0.37), residues: 372 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP O 36 HIS 0.006 0.001 HIS H 93 PHE 0.014 0.002 PHE M 29 TYR 0.013 0.001 TYR H 91 ARG 0.005 0.000 ARG O 19 Details of bonding type rmsd hydrogen bonds : bond 0.02825 ( 218) hydrogen bonds : angle 5.17365 ( 516) SS BOND : bond 0.00262 ( 6) SS BOND : angle 0.68636 ( 12) covalent geometry : bond 0.00268 ( 5643) covalent geometry : angle 0.58156 ( 7653) *********************** 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 119 residues out of total 598 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 98 time to evaluate : 0.686 Fit side-chains revert: symmetry clash REVERT: H 43 LYS cc_start: 0.8126 (mttp) cc_final: 0.7896 (mtmm) REVERT: M 32 TYR cc_start: 0.6660 (m-10) cc_final: 0.6440 (m-10) REVERT: M 85 GLU cc_start: 0.7826 (tm-30) cc_final: 0.7111 (tm-30) REVERT: N 89 GLN cc_start: 0.7445 (OUTLIER) cc_final: 0.6831 (tp40) REVERT: O 83 ARG cc_start: 0.8232 (mmm160) cc_final: 0.7692 (mmm160) outliers start: 21 outliers final: 14 residues processed: 112 average time/residue: 0.2257 time to fit residues: 31.1681 Evaluate side-chains 109 residues out of total 598 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 94 time to evaluate : 0.638 ------------------------------------------------------------------------------- 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 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 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=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 65 random chunks: chunk 50 optimal weight: 3.9990 chunk 35 optimal weight: 0.0000 chunk 14 optimal weight: 0.7980 chunk 37 optimal weight: 0.9980 chunk 13 optimal weight: 1.9990 chunk 32 optimal weight: 1.9990 chunk 1 optimal weight: 0.6980 chunk 40 optimal weight: 20.0000 chunk 48 optimal weight: 1.9990 chunk 7 optimal weight: 0.2980 chunk 51 optimal weight: 3.9990 overall best weight: 0.5584 ------------------------------------------------------------------------------- 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 M 1 GLN M 105 GLN ** O 76 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4141 r_free = 0.4141 target = 0.163624 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.3835 r_free = 0.3835 target = 0.136558 restraints weight = 7613.719| |-----------------------------------------------------------------------------| r_work (start): 0.3854 rms_B_bonded: 2.39 r_work: 0.3720 rms_B_bonded: 3.20 restraints_weight: 0.5000 r_work (final): 0.3720 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7331 moved from start: 0.5536 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.034 5649 Z= 0.110 Angle : 0.573 9.230 7665 Z= 0.305 Chirality : 0.045 0.137 812 Planarity : 0.004 0.036 983 Dihedral : 4.759 41.044 774 Min Nonbonded Distance : 2.384 Molprobity Statistics. All-atom Clashscore : 10.11 Ramachandran Plot: Outliers : 0.14 % Allowed : 6.23 % Favored : 93.62 % Rotamer: Outliers : 3.18 % Allowed : 14.05 % Favored : 82.78 % 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: 0.23 (0.34), residues: 690 helix: None (None), residues: 0 sheet: 0.89 (0.29), residues: 318 loop : -0.49 (0.37), residues: 372 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP O 36 HIS 0.004 0.001 HIS H 93 PHE 0.025 0.002 PHE M 52A TYR 0.013 0.001 TYR H 91 ARG 0.005 0.000 ARG O 19 Details of bonding type rmsd hydrogen bonds : bond 0.02659 ( 218) hydrogen bonds : angle 4.98767 ( 516) SS BOND : bond 0.00268 ( 6) SS BOND : angle 0.55651 ( 12) covalent geometry : bond 0.00245 ( 5643) covalent geometry : angle 0.57262 ( 7653) *********************** 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 116 residues out of total 598 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 97 time to evaluate : 0.688 Fit side-chains revert: symmetry clash REVERT: H 43 LYS cc_start: 0.8102 (mttp) cc_final: 0.7873 (mtmm) REVERT: M 32 TYR cc_start: 0.6043 (m-10) cc_final: 0.5592 (m-10) REVERT: N 89 GLN cc_start: 0.7494 (OUTLIER) cc_final: 0.6854 (tp40) REVERT: O 83 ARG cc_start: 0.8232 (mmm160) cc_final: 0.7728 (mmm160) REVERT: P 4 MET cc_start: 0.8239 (OUTLIER) cc_final: 0.7446 (mtm) outliers start: 19 outliers final: 12 residues processed: 110 average time/residue: 0.2384 time to fit residues: 32.4954 Evaluate side-chains 108 residues out of total 598 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 94 time to evaluate : 0.671 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 113 ASN 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 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 O residue 12 VAL Chi-restraints excluded: chain O residue 48 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 Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 65 random chunks: chunk 40 optimal weight: 10.0000 chunk 15 optimal weight: 5.9990 chunk 47 optimal weight: 5.9990 chunk 22 optimal weight: 4.9990 chunk 17 optimal weight: 0.9990 chunk 35 optimal weight: 0.8980 chunk 59 optimal weight: 0.9980 chunk 61 optimal weight: 10.0000 chunk 12 optimal weight: 2.9990 chunk 64 optimal weight: 4.9990 chunk 8 optimal weight: 5.9990 overall best weight: 2.1786 ------------------------------------------------------------------------------- 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 M 1 GLN M 35 HIS M 105 GLN ** O 76 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4083 r_free = 0.4083 target = 0.158882 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3742 r_free = 0.3742 target = 0.129848 restraints weight = 7970.232| |-----------------------------------------------------------------------------| r_work (start): 0.3743 rms_B_bonded: 2.55 r_work: 0.3611 rms_B_bonded: 3.29 restraints_weight: 0.5000 r_work (final): 0.3611 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7494 moved from start: 0.5473 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.082 5649 Z= 0.204 Angle : 0.645 9.058 7665 Z= 0.345 Chirality : 0.046 0.145 812 Planarity : 0.005 0.044 983 Dihedral : 5.131 49.922 774 Min Nonbonded Distance : 2.276 Molprobity Statistics. All-atom Clashscore : 11.97 Ramachandran Plot: Outliers : 0.14 % Allowed : 7.39 % Favored : 92.46 % Rotamer: Outliers : 3.51 % Allowed : 13.88 % Favored : 82.61 % 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: -0.07 (0.34), residues: 690 helix: None (None), residues: 0 sheet: 0.65 (0.28), residues: 318 loop : -0.66 (0.37), residues: 372 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP O 36 HIS 0.009 0.003 HIS H 93 PHE 0.035 0.003 PHE M 52A TYR 0.024 0.002 TYR N 49 ARG 0.005 0.001 ARG L 61 Details of bonding type rmsd hydrogen bonds : bond 0.03188 ( 218) hydrogen bonds : angle 5.46748 ( 516) SS BOND : bond 0.00256 ( 6) SS BOND : angle 1.01196 ( 12) covalent geometry : bond 0.00481 ( 5643) covalent geometry : angle 0.64448 ( 7653) *********************** 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 121 residues out of total 598 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 100 time to evaluate : 0.651 Fit side-chains revert: symmetry clash REVERT: H 18 LEU cc_start: 0.8196 (OUTLIER) cc_final: 0.7548 (tt) REVERT: H 43 LYS cc_start: 0.8178 (mttp) cc_final: 0.7918 (mtmm) REVERT: H 75 LYS cc_start: 0.6157 (tptp) cc_final: 0.5824 (tptt) REVERT: N 89 GLN cc_start: 0.7462 (OUTLIER) cc_final: 0.6815 (tp40) REVERT: P 72 THR cc_start: 0.8194 (m) cc_final: 0.7706 (p) REVERT: P 94 TYR cc_start: 0.7105 (m-80) cc_final: 0.6848 (m-10) outliers start: 21 outliers final: 18 residues processed: 113 average time/residue: 0.2149 time to fit residues: 30.3312 Evaluate side-chains 117 residues out of total 598 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 97 time to evaluate : 0.686 ------------------------------------------------------------------------------- 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 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 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 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 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 59 optimal weight: 1.9990 chunk 57 optimal weight: 6.9990 chunk 30 optimal weight: 5.9990 chunk 3 optimal weight: 0.6980 chunk 32 optimal weight: 1.9990 chunk 18 optimal weight: 1.9990 chunk 46 optimal weight: 5.9990 chunk 15 optimal weight: 0.9990 chunk 47 optimal weight: 1.9990 chunk 26 optimal weight: 0.5980 chunk 58 optimal weight: 2.9990 overall best weight: 1.2586 ------------------------------------------------------------------------------- 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 M 105 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 = 0.4118 r_free = 0.4118 target = 0.161694 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3782 r_free = 0.3782 target = 0.132658 restraints weight = 7878.263| |-----------------------------------------------------------------------------| r_work (start): 0.3785 rms_B_bonded: 2.56 r_work: 0.3651 rms_B_bonded: 3.31 restraints_weight: 0.5000 r_work (final): 0.3651 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7444 moved from start: 0.5625 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.058 5649 Z= 0.147 Angle : 0.601 7.021 7665 Z= 0.323 Chirality : 0.045 0.147 812 Planarity : 0.005 0.039 983 Dihedral : 5.098 49.862 774 Min Nonbonded Distance : 2.384 Molprobity Statistics. All-atom Clashscore : 12.24 Ramachandran Plot: Outliers : 0.14 % Allowed : 6.23 % Favored : 93.62 % Rotamer: Outliers : 2.84 % Allowed : 14.72 % Favored : 82.44 % 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: -0.05 (0.34), residues: 690 helix: None (None), residues: 0 sheet: 0.66 (0.29), residues: 318 loop : -0.64 (0.37), residues: 372 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP O 36 HIS 0.007 0.002 HIS H 93 PHE 0.026 0.003 PHE M 29 TYR 0.016 0.002 TYR H 91 ARG 0.004 0.000 ARG L 31 Details of bonding type rmsd hydrogen bonds : bond 0.02974 ( 218) hydrogen bonds : angle 5.31010 ( 516) SS BOND : bond 0.00284 ( 6) SS BOND : angle 0.83149 ( 12) covalent geometry : bond 0.00346 ( 5643) covalent geometry : angle 0.60088 ( 7653) ********************** 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 111 residues out of total 598 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 94 time to evaluate : 0.611 Fit side-chains revert: symmetry clash REVERT: H 43 LYS cc_start: 0.8151 (mttp) cc_final: 0.7913 (mtmm) REVERT: N 89 GLN cc_start: 0.7531 (OUTLIER) cc_final: 0.6890 (tp40) REVERT: P 72 THR cc_start: 0.8184 (m) cc_final: 0.7685 (p) outliers start: 17 outliers final: 15 residues processed: 106 average time/residue: 0.2165 time to fit residues: 28.5748 Evaluate side-chains 105 residues out of total 598 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 89 time to evaluate : 0.588 ------------------------------------------------------------------------------- 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 82 MET Chi-restraints excluded: chain H residue 93 HIS 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 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 P residue 4 MET Chi-restraints excluded: chain P residue 7 SER Chi-restraints excluded: chain P residue 19 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 65 random chunks: chunk 38 optimal weight: 4.9990 chunk 62 optimal weight: 10.0000 chunk 44 optimal weight: 2.9990 chunk 16 optimal weight: 1.9990 chunk 61 optimal weight: 6.9990 chunk 35 optimal weight: 0.0870 chunk 5 optimal weight: 5.9990 chunk 52 optimal weight: 1.9990 chunk 57 optimal weight: 0.9990 chunk 7 optimal weight: 0.9980 chunk 25 optimal weight: 5.9990 overall best weight: 1.2164 ------------------------------------------------------------------------------- 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 M 105 GLN O 76 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4117 r_free = 0.4117 target = 0.161650 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3783 r_free = 0.3783 target = 0.132631 restraints weight = 7941.048| |-----------------------------------------------------------------------------| r_work (start): 0.3788 rms_B_bonded: 2.56 r_work: 0.3653 rms_B_bonded: 3.32 restraints_weight: 0.5000 r_work (final): 0.3653 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7440 moved from start: 0.5631 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.091 5649 Z= 0.207 Angle : 1.082 59.194 7665 Z= 0.659 Chirality : 0.048 0.453 812 Planarity : 0.005 0.053 983 Dihedral : 5.240 49.862 774 Min Nonbonded Distance : 1.917 Molprobity Statistics. All-atom Clashscore : 13.82 Ramachandran Plot: Outliers : 0.29 % Allowed : 6.96 % Favored : 92.75 % Rotamer: Outliers : 3.34 % Allowed : 14.21 % Favored : 82.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.15 % 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: -0.12 (0.34), residues: 690 helix: None (None), residues: 0 sheet: 0.67 (0.29), residues: 318 loop : -0.75 (0.37), residues: 372 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP O 36 HIS 0.007 0.002 HIS H 93 PHE 0.025 0.003 PHE M 29 TYR 0.041 0.002 TYR L 86 ARG 0.004 0.000 ARG O 83 Details of bonding type rmsd hydrogen bonds : bond 0.02979 ( 218) hydrogen bonds : angle 5.31136 ( 516) SS BOND : bond 0.00289 ( 6) SS BOND : angle 0.80981 ( 12) covalent geometry : bond 0.00460 ( 5643) covalent geometry : angle 1.08195 ( 7653) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2934.67 seconds wall clock time: 51 minutes 11.11 seconds (3071.11 seconds total)