Starting phenix.real_space_refine on Thu Sep 26 01:51:15 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8guk_34275/09_2024/8guk_34275.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8guk_34275/09_2024/8guk_34275.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.51 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8guk_34275/09_2024/8guk_34275.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8guk_34275/09_2024/8guk_34275.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8guk_34275/09_2024/8guk_34275.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8guk_34275/09_2024/8guk_34275.cif" } resolution = 2.51 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= -0.005 sd= 0.055 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians P 294 5.49 5 S 14 5.16 5 C 6686 2.51 5 N 2277 2.21 5 O 2827 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 31 residue(s): 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5461/modules/chem_data/mon_lib" Total number of atoms: 12098 Number of models: 1 Model: "" Number of chains: 10 Chain: "A" Number of atoms: 810 Number of conformers: 1 Conformer: "" Number of residues, atoms: 98, 810 Classifications: {'peptide': 98} Link IDs: {'PTRANS': 4, 'TRANS': 93} Chain: "B" Number of atoms: 641 Number of conformers: 1 Conformer: "" Number of residues, atoms: 80, 641 Classifications: {'peptide': 80} Link IDs: {'PTRANS': 1, 'TRANS': 78} Chain: "C" Number of atoms: 846 Number of conformers: 1 Conformer: "" Number of residues, atoms: 110, 846 Classifications: {'peptide': 110} Link IDs: {'PTRANS': 5, 'TRANS': 104} Chain: "D" Number of atoms: 736 Number of conformers: 1 Conformer: "" Number of residues, atoms: 94, 736 Classifications: {'peptide': 94} Link IDs: {'PTRANS': 2, 'TRANS': 91} Chain: "E" Number of atoms: 810 Number of conformers: 1 Conformer: "" Number of residues, atoms: 98, 810 Classifications: {'peptide': 98} Link IDs: {'PTRANS': 4, 'TRANS': 93} Chain: "F" Number of atoms: 641 Number of conformers: 1 Conformer: "" Number of residues, atoms: 80, 641 Classifications: {'peptide': 80} Link IDs: {'PTRANS': 1, 'TRANS': 78} Chain: "G" Number of atoms: 851 Number of conformers: 1 Conformer: "" Number of residues, atoms: 111, 851 Classifications: {'peptide': 111} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 5, 'TRANS': 105} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 4 Chain: "H" Number of atoms: 736 Number of conformers: 1 Conformer: "" Number of residues, atoms: 94, 736 Classifications: {'peptide': 94} Link IDs: {'PTRANS': 2, 'TRANS': 91} Chain: "I" Number of atoms: 2996 Number of conformers: 1 Conformer: "" Number of residues, atoms: 147, 2996 Classifications: {'DNA': 147} Link IDs: {'rna3p': 146} Chain: "J" Number of atoms: 3031 Number of conformers: 1 Conformer: "" Number of residues, atoms: 147, 3031 Classifications: {'DNA': 147} Link IDs: {'rna3p': 146} Time building chain proxies: 7.71, per 1000 atoms: 0.64 Number of scatterers: 12098 At special positions: 0 Unit cell: (72.45, 113.4, 119.7, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 14 16.00 P 294 15.00 O 2827 8.00 N 2277 7.00 C 6686 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 2.90 Conformation dependent library (CDL) restraints added in 954.7 milliseconds 1498 Ramachandran restraints generated. 749 Oldfield, 0 Emsley, 749 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1430 Finding SS restraints... Secondary structure from input PDB file: 36 helices and 10 sheets defined 73.7% alpha, 2.9% beta 146 base pairs and 260 stacking pairs defined. Time for finding SS restraints: 5.99 Creating SS restraints... Processing helix chain 'A' and resid 44 through 57 Processing helix chain 'A' and resid 63 through 79 Processing helix chain 'A' and resid 85 through 114 Processing helix chain 'A' and resid 120 through 132 Processing helix chain 'B' and resid 24 through 29 Processing helix chain 'B' and resid 30 through 41 Processing helix chain 'B' and resid 49 through 76 removed outlier: 3.552A pdb=" N GLU B 53 " --> pdb=" O LEU B 49 " (cutoff:3.500A) Processing helix chain 'B' and resid 82 through 93 Processing helix chain 'C' and resid 16 through 21 Processing helix chain 'C' and resid 26 through 37 Processing helix chain 'C' and resid 45 through 73 removed outlier: 4.373A pdb=" N VAL C 49 " --> pdb=" O ALA C 45 " (cutoff:3.500A) Processing helix chain 'C' and resid 79 through 90 Processing helix chain 'C' and resid 90 through 97 Processing helix chain 'C' and resid 112 through 116 Processing helix chain 'D' and resid 37 through 49 Processing helix chain 'D' and resid 55 through 84 Processing helix chain 'D' and resid 90 through 102 Processing helix chain 'D' and resid 103 through 123 removed outlier: 3.593A pdb=" N ALA D 107 " --> pdb=" O PRO D 103 " (cutoff:3.500A) Processing helix chain 'E' and resid 44 through 57 Processing helix chain 'E' and resid 63 through 79 removed outlier: 4.096A pdb=" N ASP E 77 " --> pdb=" O GLU E 73 " (cutoff:3.500A) removed outlier: 4.304A pdb=" N PHE E 78 " --> pdb=" O ILE E 74 " (cutoff:3.500A) Processing helix chain 'E' and resid 85 through 114 Processing helix chain 'E' and resid 120 through 132 Processing helix chain 'F' and resid 24 through 29 Processing helix chain 'F' and resid 30 through 41 Processing helix chain 'F' and resid 49 through 76 removed outlier: 3.576A pdb=" N GLU F 53 " --> pdb=" O LEU F 49 " (cutoff:3.500A) Processing helix chain 'F' and resid 82 through 93 Processing helix chain 'G' and resid 16 through 22 Processing helix chain 'G' and resid 26 through 37 Processing helix chain 'G' and resid 45 through 73 removed outlier: 4.228A pdb=" N VAL G 49 " --> pdb=" O ALA G 45 " (cutoff:3.500A) Processing helix chain 'G' and resid 79 through 90 Processing helix chain 'G' and resid 90 through 97 Processing helix chain 'G' and resid 112 through 116 Processing helix chain 'H' and resid 37 through 49 Processing helix chain 'H' and resid 55 through 84 Processing helix chain 'H' and resid 90 through 102 Processing helix chain 'H' and resid 103 through 124 Processing sheet with id=AA1, first strand: chain 'A' and resid 83 through 84 removed outlier: 6.643A pdb=" N ARG A 83 " --> pdb=" O VAL B 81 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA1 Processing sheet with id=AA2, first strand: chain 'A' and resid 118 through 119 Processing sheet with id=AA3, first strand: chain 'B' and resid 97 through 98 Processing sheet with id=AA4, first strand: chain 'C' and resid 42 through 43 removed outlier: 7.120A pdb=" N ARG C 42 " --> pdb=" O ILE D 89 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA4 Processing sheet with id=AA5, first strand: chain 'C' and resid 77 through 78 Processing sheet with id=AA6, first strand: chain 'C' and resid 100 through 102 Processing sheet with id=AA7, first strand: chain 'E' and resid 83 through 84 removed outlier: 6.724A pdb=" N ARG E 83 " --> pdb=" O VAL F 81 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA7 Processing sheet with id=AA8, first strand: chain 'E' and resid 118 through 119 Processing sheet with id=AA9, first strand: chain 'G' and resid 42 through 43 removed outlier: 7.137A pdb=" N ARG G 42 " --> pdb=" O ILE H 89 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA9 Processing sheet with id=AB1, first strand: chain 'G' and resid 77 through 78 424 hydrogen bonds defined for protein. 1242 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 375 hydrogen bonds 750 hydrogen bond angles 0 basepair planarities 146 basepair parallelities 260 stacking parallelities Total time for adding SS restraints: 4.41 Time building geometry restraints manager: 3.44 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 2168 1.33 - 1.45: 4244 1.45 - 1.57: 5889 1.57 - 1.69: 586 1.69 - 1.80: 24 Bond restraints: 12911 Sorted by residual: bond pdb=" C3' DA I 131 " pdb=" O3' DA I 131 " ideal model delta sigma weight residual 1.422 1.465 -0.043 3.00e-02 1.11e+03 2.02e+00 bond pdb=" C3' DA I 41 " pdb=" O3' DA I 41 " ideal model delta sigma weight residual 1.422 1.462 -0.040 3.00e-02 1.11e+03 1.80e+00 bond pdb=" C3' DT I 77 " pdb=" O3' DT I 77 " ideal model delta sigma weight residual 1.422 1.462 -0.040 3.00e-02 1.11e+03 1.76e+00 bond pdb=" C3' DT I 32 " pdb=" O3' DT I 32 " ideal model delta sigma weight residual 1.422 1.461 -0.039 3.00e-02 1.11e+03 1.73e+00 bond pdb=" C3' DG I 33 " pdb=" O3' DG I 33 " ideal model delta sigma weight residual 1.422 1.461 -0.039 3.00e-02 1.11e+03 1.73e+00 ... (remaining 12906 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.80: 18219 1.80 - 3.60: 441 3.60 - 5.40: 24 5.40 - 7.20: 5 7.20 - 9.00: 1 Bond angle restraints: 18690 Sorted by residual: angle pdb=" CA ASN G 73 " pdb=" CB ASN G 73 " pdb=" CG ASN G 73 " ideal model delta sigma weight residual 112.60 115.67 -3.07 1.00e+00 1.00e+00 9.40e+00 angle pdb=" C GLY C 37 " pdb=" N ASN C 38 " pdb=" CA ASN C 38 " ideal model delta sigma weight residual 121.54 127.28 -5.74 1.91e+00 2.74e-01 9.04e+00 angle pdb=" N ASN G 73 " pdb=" CA ASN G 73 " pdb=" C ASN G 73 " ideal model delta sigma weight residual 113.16 109.60 3.56 1.24e+00 6.50e-01 8.26e+00 angle pdb=" CB ARG B 23 " pdb=" CG ARG B 23 " pdb=" CD ARG B 23 " ideal model delta sigma weight residual 111.30 117.75 -6.45 2.30e+00 1.89e-01 7.87e+00 angle pdb=" C THR A 80 " pdb=" N ASP A 81 " pdb=" CA ASP A 81 " ideal model delta sigma weight residual 122.82 126.62 -3.80 1.42e+00 4.96e-01 7.17e+00 ... (remaining 18685 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.01: 5451 35.01 - 70.02: 1530 70.02 - 105.03: 28 105.03 - 140.04: 1 140.04 - 175.04: 7 Dihedral angle restraints: 7017 sinusoidal: 4800 harmonic: 2217 Sorted by residual: dihedral pdb=" C4' DT I 32 " pdb=" C3' DT I 32 " pdb=" O3' DT I 32 " pdb=" P DG I 33 " ideal model delta sinusoidal sigma weight residual 220.00 44.96 175.04 1 3.50e+01 8.16e-04 1.56e+01 dihedral pdb=" C4' DG J 4 " pdb=" C3' DG J 4 " pdb=" O3' DG J 4 " pdb=" P DG J 5 " ideal model delta sinusoidal sigma weight residual -140.00 33.09 -173.09 1 3.50e+01 8.16e-04 1.56e+01 dihedral pdb=" C4' DT I 77 " pdb=" C3' DT I 77 " pdb=" O3' DT I 77 " pdb=" P DC I 78 " ideal model delta sinusoidal sigma weight residual -140.00 29.87 -169.87 1 3.50e+01 8.16e-04 1.56e+01 ... (remaining 7014 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.033: 1505 0.033 - 0.065: 485 0.065 - 0.098: 87 0.098 - 0.131: 42 0.131 - 0.163: 6 Chirality restraints: 2125 Sorted by residual: chirality pdb=" CB THR H 119 " pdb=" CA THR H 119 " pdb=" OG1 THR H 119 " pdb=" CG2 THR H 119 " both_signs ideal model delta sigma weight residual False 2.55 2.39 0.16 2.00e-01 2.50e+01 6.66e-01 chirality pdb=" CA ASP A 81 " pdb=" N ASP A 81 " pdb=" C ASP A 81 " pdb=" CB ASP A 81 " both_signs ideal model delta sigma weight residual False 2.51 2.35 0.16 2.00e-01 2.50e+01 6.22e-01 chirality pdb=" CA ASP B 24 " pdb=" N ASP B 24 " pdb=" C ASP B 24 " pdb=" CB ASP B 24 " both_signs ideal model delta sigma weight residual False 2.51 2.36 0.15 2.00e-01 2.50e+01 5.81e-01 ... (remaining 2122 not shown) Planarity restraints: 1345 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA ASN G 73 " 0.010 2.00e-02 2.50e+03 1.93e-02 3.71e+00 pdb=" C ASN G 73 " -0.033 2.00e-02 2.50e+03 pdb=" O ASN G 73 " 0.013 2.00e-02 2.50e+03 pdb=" N LYS G 74 " 0.011 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C LYS E 37 " -0.030 5.00e-02 4.00e+02 4.67e-02 3.48e+00 pdb=" N PRO E 38 " 0.081 5.00e-02 4.00e+02 pdb=" CA PRO E 38 " -0.024 5.00e-02 4.00e+02 pdb=" CD PRO E 38 " -0.026 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CG GLU H 71 " 0.009 2.00e-02 2.50e+03 1.75e-02 3.05e+00 pdb=" CD GLU H 71 " -0.030 2.00e-02 2.50e+03 pdb=" OE1 GLU H 71 " 0.011 2.00e-02 2.50e+03 pdb=" OE2 GLU H 71 " 0.011 2.00e-02 2.50e+03 ... (remaining 1342 not shown) Histogram of nonbonded interaction distances: 2.20 - 2.74: 1260 2.74 - 3.28: 10901 3.28 - 3.82: 25697 3.82 - 4.36: 29975 4.36 - 4.90: 42058 Nonbonded interactions: 109891 Sorted by model distance: nonbonded pdb=" N GLN C 104 " pdb=" OE2 GLU E 94 " model vdw 2.202 3.120 nonbonded pdb=" O HIS F 75 " pdb=" NH2 ARG H 92 " model vdw 2.237 3.120 nonbonded pdb=" OE1 GLU D 76 " pdb=" NH2 ARG D 79 " model vdw 2.238 3.120 nonbonded pdb=" OE1 GLU E 73 " pdb=" ND2 ASN F 25 " model vdw 2.245 3.120 nonbonded pdb=" O HIS B 75 " pdb=" NH1 ARG D 92 " model vdw 2.247 3.120 ... (remaining 109886 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 'A' selection = chain 'E' } ncs_group { reference = chain 'B' selection = chain 'F' } ncs_group { reference = chain 'C' selection = (chain 'G' and resid 10 through 119) } ncs_group { reference = chain 'D' selection = chain 'H' } 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: 3.020 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: 0.380 Check model and map are aligned: 0.080 Set scattering table: 0.100 Process input model: 33.170 Find NCS groups from input model: 0.260 Set up NCS constraints: 0.040 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:13.130 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 50.190 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8248 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 : 0.004 0.045 12911 Z= 0.224 Angle : 0.602 9.002 18690 Z= 0.359 Chirality : 0.035 0.163 2125 Planarity : 0.005 0.060 1345 Dihedral : 29.885 175.045 5587 Min Nonbonded Distance : 2.202 Molprobity Statistics. All-atom Clashscore : 10.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.74 % Favored : 98.26 % Rotamer: Outliers : 3.15 % Allowed : 31.23 % Favored : 65.62 % 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: 2.28 (0.30), residues: 749 helix: 2.15 (0.22), residues: 549 sheet: None (None), residues: 0 loop : -0.28 (0.40), residues: 200 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.004 0.001 HIS B 75 PHE 0.009 0.001 PHE E 67 TYR 0.019 0.001 TYR H 83 ARG 0.016 0.001 ARG H 99 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1498 Ramachandran restraints generated. 749 Oldfield, 0 Emsley, 749 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1498 Ramachandran restraints generated. 749 Oldfield, 0 Emsley, 749 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 201 residues out of total 635 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 181 time to evaluate : 0.842 Fit side-chains REVERT: D 92 ARG cc_start: 0.8694 (OUTLIER) cc_final: 0.7898 (ttm-80) REVERT: H 63 ASN cc_start: 0.8792 (t0) cc_final: 0.8397 (m-40) outliers start: 20 outliers final: 13 residues processed: 196 average time/residue: 1.6915 time to fit residues: 351.0047 Evaluate side-chains 191 residues out of total 635 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 177 time to evaluate : 0.913 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 47 SER Chi-restraints excluded: chain B residue 62 LEU Chi-restraints excluded: chain B residue 95 ARG Chi-restraints excluded: chain B residue 96 THR Chi-restraints excluded: chain C residue 49 VAL Chi-restraints excluded: chain C residue 100 VAL Chi-restraints excluded: chain C residue 101 THR Chi-restraints excluded: chain D residue 92 ARG Chi-restraints excluded: chain D residue 95 GLN Chi-restraints excluded: chain D residue 112 SER Chi-restraints excluded: chain E residue 46 VAL Chi-restraints excluded: chain F residue 96 THR Chi-restraints excluded: chain G residue 18 SER Chi-restraints excluded: chain H residue 106 LEU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 102 random chunks: chunk 86 optimal weight: 2.9990 chunk 77 optimal weight: 2.9990 chunk 42 optimal weight: 0.6980 chunk 26 optimal weight: 0.0000 chunk 52 optimal weight: 0.5980 chunk 41 optimal weight: 0.4980 chunk 79 optimal weight: 1.9990 chunk 30 optimal weight: 1.9990 chunk 48 optimal weight: 2.9990 chunk 59 optimal weight: 0.9980 chunk 92 optimal weight: 2.9990 overall best weight: 0.5584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 68 GLN A 108 ASN B 25 ASN ** B 75 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 108 ASN F 27 GLN F 93 GLN G 73 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8227 moved from start: 0.0838 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 12911 Z= 0.211 Angle : 0.580 7.986 18690 Z= 0.347 Chirality : 0.035 0.156 2125 Planarity : 0.004 0.039 1345 Dihedral : 31.849 174.925 4087 Min Nonbonded Distance : 2.362 Molprobity Statistics. All-atom Clashscore : 8.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.27 % Favored : 97.73 % Rotamer: Outliers : 4.57 % Allowed : 26.50 % Favored : 68.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: 2.46 (0.30), residues: 749 helix: 2.25 (0.22), residues: 555 sheet: None (None), residues: 0 loop : -0.19 (0.40), residues: 194 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.005 0.001 HIS B 75 PHE 0.011 0.001 PHE E 67 TYR 0.014 0.001 TYR H 83 ARG 0.007 0.000 ARG H 99 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1498 Ramachandran restraints generated. 749 Oldfield, 0 Emsley, 749 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1498 Ramachandran restraints generated. 749 Oldfield, 0 Emsley, 749 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 225 residues out of total 635 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 196 time to evaluate : 1.049 Fit side-chains REVERT: A 94 GLU cc_start: 0.8509 (mm-30) cc_final: 0.8207 (mm-30) REVERT: A 120 MET cc_start: 0.8877 (OUTLIER) cc_final: 0.8407 (mtt) REVERT: C 77 ARG cc_start: 0.8708 (OUTLIER) cc_final: 0.7792 (ttp-170) REVERT: C 91 GLU cc_start: 0.8278 (OUTLIER) cc_final: 0.8075 (tt0) REVERT: D 34 LYS cc_start: 0.8608 (mmmm) cc_final: 0.8364 (mppt) REVERT: D 93 GLU cc_start: 0.8386 (mp0) cc_final: 0.8133 (mp0) REVERT: G 104 GLN cc_start: 0.8424 (mm-40) cc_final: 0.8033 (mm110) REVERT: H 63 ASN cc_start: 0.8836 (t0) cc_final: 0.8486 (m-40) outliers start: 29 outliers final: 16 residues processed: 208 average time/residue: 1.6459 time to fit residues: 363.1886 Evaluate side-chains 205 residues out of total 635 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 186 time to evaluate : 0.912 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 90 MET Chi-restraints excluded: chain A residue 120 MET Chi-restraints excluded: chain B residue 62 LEU Chi-restraints excluded: chain B residue 96 THR Chi-restraints excluded: chain C residue 41 GLU Chi-restraints excluded: chain C residue 49 VAL Chi-restraints excluded: chain C residue 77 ARG Chi-restraints excluded: chain C residue 91 GLU Chi-restraints excluded: chain C residue 101 THR Chi-restraints excluded: chain C residue 108 LEU Chi-restraints excluded: chain D residue 33 ARG Chi-restraints excluded: chain D residue 48 VAL Chi-restraints excluded: chain E residue 46 VAL Chi-restraints excluded: chain F residue 92 ARG Chi-restraints excluded: chain F residue 96 THR Chi-restraints excluded: chain G residue 75 LYS Chi-restraints excluded: chain G residue 92 GLU Chi-restraints excluded: chain G residue 99 LYS Chi-restraints excluded: chain G residue 101 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 102 random chunks: chunk 51 optimal weight: 2.9990 chunk 28 optimal weight: 0.9980 chunk 77 optimal weight: 2.9990 chunk 63 optimal weight: 3.9990 chunk 25 optimal weight: 0.9980 chunk 92 optimal weight: 2.9990 chunk 100 optimal weight: 2.9990 chunk 82 optimal weight: 1.9990 chunk 31 optimal weight: 0.6980 chunk 74 optimal weight: 5.9990 chunk 91 optimal weight: 2.9990 overall best weight: 1.5384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 68 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 75 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 84 GLN D 67 ASN D 95 GLN F 27 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8312 moved from start: 0.1173 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.047 12911 Z= 0.364 Angle : 0.634 10.124 18690 Z= 0.374 Chirality : 0.039 0.168 2125 Planarity : 0.005 0.039 1345 Dihedral : 32.290 172.718 4070 Min Nonbonded Distance : 2.506 Molprobity Statistics. All-atom Clashscore : 7.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.14 % Favored : 97.86 % Rotamer: Outliers : 4.73 % Allowed : 27.13 % Favored : 68.14 % 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: 2.21 (0.30), residues: 749 helix: 2.07 (0.22), residues: 555 sheet: None (None), residues: 0 loop : -0.27 (0.40), residues: 194 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.005 0.001 HIS B 75 PHE 0.011 0.002 PHE A 67 TYR 0.015 0.002 TYR H 83 ARG 0.007 0.000 ARG H 99 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1498 Ramachandran restraints generated. 749 Oldfield, 0 Emsley, 749 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1498 Ramachandran restraints generated. 749 Oldfield, 0 Emsley, 749 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 216 residues out of total 635 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 186 time to evaluate : 0.914 Fit side-chains REVERT: A 53 ARG cc_start: 0.8762 (OUTLIER) cc_final: 0.7878 (ttp-110) REVERT: A 59 GLU cc_start: 0.9027 (pm20) cc_final: 0.8811 (pm20) REVERT: B 79 LYS cc_start: 0.9182 (OUTLIER) cc_final: 0.8572 (mtmm) REVERT: C 77 ARG cc_start: 0.8707 (OUTLIER) cc_final: 0.7537 (ttp-170) REVERT: C 91 GLU cc_start: 0.8288 (OUTLIER) cc_final: 0.8087 (tt0) REVERT: C 92 GLU cc_start: 0.8435 (OUTLIER) cc_final: 0.8200 (mt-10) REVERT: C 104 GLN cc_start: 0.8835 (mm-40) cc_final: 0.8620 (mm110) REVERT: D 40 TYR cc_start: 0.9171 (m-80) cc_final: 0.8949 (m-80) REVERT: D 93 GLU cc_start: 0.8544 (mp0) cc_final: 0.8293 (mp0) REVERT: E 59 GLU cc_start: 0.9012 (pm20) cc_final: 0.8736 (pm20) REVERT: G 90 ASP cc_start: 0.8841 (t0) cc_final: 0.8587 (t0) REVERT: H 63 ASN cc_start: 0.8918 (t0) cc_final: 0.8431 (m-40) outliers start: 30 outliers final: 18 residues processed: 202 average time/residue: 1.5720 time to fit residues: 336.3655 Evaluate side-chains 199 residues out of total 635 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 176 time to evaluate : 0.593 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 53 ARG Chi-restraints excluded: chain A residue 76 GLN Chi-restraints excluded: chain B residue 62 LEU Chi-restraints excluded: chain B residue 79 LYS Chi-restraints excluded: chain B residue 96 THR Chi-restraints excluded: chain C residue 41 GLU Chi-restraints excluded: chain C residue 49 VAL Chi-restraints excluded: chain C residue 77 ARG Chi-restraints excluded: chain C residue 91 GLU Chi-restraints excluded: chain C residue 92 GLU Chi-restraints excluded: chain C residue 100 VAL Chi-restraints excluded: chain C residue 101 THR Chi-restraints excluded: chain C residue 108 LEU Chi-restraints excluded: chain D residue 48 VAL Chi-restraints excluded: chain E residue 46 VAL Chi-restraints excluded: chain E residue 64 LYS Chi-restraints excluded: chain E residue 86 SER Chi-restraints excluded: chain F residue 80 THR Chi-restraints excluded: chain F residue 92 ARG Chi-restraints excluded: chain F residue 96 THR Chi-restraints excluded: chain G residue 92 GLU Chi-restraints excluded: chain G residue 99 LYS Chi-restraints excluded: chain G residue 101 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 102 random chunks: chunk 69 optimal weight: 0.5980 chunk 48 optimal weight: 1.9990 chunk 10 optimal weight: 0.6980 chunk 44 optimal weight: 2.9990 chunk 62 optimal weight: 0.6980 chunk 93 optimal weight: 2.9990 chunk 98 optimal weight: 1.9990 chunk 88 optimal weight: 4.9990 chunk 26 optimal weight: 2.9990 chunk 82 optimal weight: 1.9990 chunk 55 optimal weight: 0.8980 overall best weight: 0.9782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 68 GLN B 25 ASN ** B 75 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 63 ASN D 95 GLN F 27 GLN G 24 GLN ** G 73 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 104 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8294 moved from start: 0.1160 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.051 12911 Z= 0.280 Angle : 0.608 9.019 18690 Z= 0.362 Chirality : 0.037 0.157 2125 Planarity : 0.005 0.041 1345 Dihedral : 32.262 173.670 4070 Min Nonbonded Distance : 2.510 Molprobity Statistics. All-atom Clashscore : 7.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.00 % Favored : 98.00 % Rotamer: Outliers : 4.57 % Allowed : 27.13 % Favored : 68.30 % 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: 2.19 (0.30), residues: 749 helix: 2.05 (0.22), residues: 556 sheet: None (None), residues: 0 loop : -0.27 (0.40), residues: 193 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.004 0.001 HIS B 75 PHE 0.011 0.002 PHE E 67 TYR 0.016 0.001 TYR H 83 ARG 0.008 0.000 ARG H 99 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1498 Ramachandran restraints generated. 749 Oldfield, 0 Emsley, 749 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1498 Ramachandran restraints generated. 749 Oldfield, 0 Emsley, 749 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 211 residues out of total 635 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 182 time to evaluate : 1.294 Fit side-chains REVERT: A 53 ARG cc_start: 0.8747 (OUTLIER) cc_final: 0.7882 (ttp-110) REVERT: A 59 GLU cc_start: 0.9031 (pm20) cc_final: 0.8796 (pm20) REVERT: C 77 ARG cc_start: 0.8704 (OUTLIER) cc_final: 0.7533 (ttp-170) REVERT: C 92 GLU cc_start: 0.8403 (OUTLIER) cc_final: 0.8175 (mt-10) REVERT: E 59 GLU cc_start: 0.9037 (pm20) cc_final: 0.8822 (pm20) REVERT: G 73 ASN cc_start: 0.8606 (t160) cc_final: 0.8131 (t0) REVERT: H 63 ASN cc_start: 0.8922 (t0) cc_final: 0.8395 (m-40) outliers start: 29 outliers final: 18 residues processed: 195 average time/residue: 1.4077 time to fit residues: 291.4370 Evaluate side-chains 197 residues out of total 635 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 176 time to evaluate : 0.651 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 53 ARG Chi-restraints excluded: chain A residue 76 GLN Chi-restraints excluded: chain B residue 62 LEU Chi-restraints excluded: chain B residue 96 THR Chi-restraints excluded: chain C residue 41 GLU Chi-restraints excluded: chain C residue 49 VAL Chi-restraints excluded: chain C residue 77 ARG Chi-restraints excluded: chain C residue 92 GLU Chi-restraints excluded: chain C residue 100 VAL Chi-restraints excluded: chain C residue 101 THR Chi-restraints excluded: chain C residue 108 LEU Chi-restraints excluded: chain D residue 48 VAL Chi-restraints excluded: chain E residue 46 VAL Chi-restraints excluded: chain E residue 64 LYS Chi-restraints excluded: chain E residue 86 SER Chi-restraints excluded: chain F residue 80 THR Chi-restraints excluded: chain F residue 92 ARG Chi-restraints excluded: chain F residue 96 THR Chi-restraints excluded: chain G residue 92 GLU Chi-restraints excluded: chain G residue 99 LYS Chi-restraints excluded: chain G residue 101 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 102 random chunks: chunk 1 optimal weight: 0.5980 chunk 73 optimal weight: 0.0770 chunk 40 optimal weight: 0.7980 chunk 84 optimal weight: 2.9990 chunk 68 optimal weight: 0.5980 chunk 0 optimal weight: 2.9990 chunk 50 optimal weight: 0.5980 chunk 88 optimal weight: 4.9990 chunk 24 optimal weight: 2.9990 chunk 33 optimal weight: 0.9980 chunk 19 optimal weight: 1.9990 overall best weight: 0.5338 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 68 GLN B 25 ASN ** B 75 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 95 GLN F 27 GLN G 104 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8278 moved from start: 0.1194 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 12911 Z= 0.221 Angle : 0.607 8.762 18690 Z= 0.360 Chirality : 0.036 0.170 2125 Planarity : 0.004 0.042 1345 Dihedral : 32.252 174.216 4070 Min Nonbonded Distance : 2.511 Molprobity Statistics. All-atom Clashscore : 8.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.14 % Favored : 97.86 % Rotamer: Outliers : 3.63 % Allowed : 28.39 % Favored : 67.98 % 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: 2.28 (0.30), residues: 749 helix: 2.11 (0.22), residues: 556 sheet: None (None), residues: 0 loop : -0.22 (0.40), residues: 193 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.003 0.001 HIS B 75 PHE 0.012 0.002 PHE E 67 TYR 0.016 0.001 TYR H 83 ARG 0.018 0.001 ARG H 99 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1498 Ramachandran restraints generated. 749 Oldfield, 0 Emsley, 749 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1498 Ramachandran restraints generated. 749 Oldfield, 0 Emsley, 749 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 209 residues out of total 635 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 186 time to evaluate : 0.890 Fit side-chains REVERT: A 53 ARG cc_start: 0.8740 (OUTLIER) cc_final: 0.7877 (ttp-110) REVERT: A 59 GLU cc_start: 0.9029 (pm20) cc_final: 0.8792 (pm20) REVERT: C 77 ARG cc_start: 0.8691 (OUTLIER) cc_final: 0.7520 (ttp-170) REVERT: D 34 LYS cc_start: 0.8586 (mmmm) cc_final: 0.8266 (mppt) REVERT: E 59 GLU cc_start: 0.9016 (pm20) cc_final: 0.8732 (pm20) REVERT: G 73 ASN cc_start: 0.8548 (t160) cc_final: 0.8109 (t0) REVERT: H 63 ASN cc_start: 0.8905 (t0) cc_final: 0.8385 (m-40) outliers start: 23 outliers final: 16 residues processed: 195 average time/residue: 1.5283 time to fit residues: 315.9406 Evaluate side-chains 199 residues out of total 635 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 181 time to evaluate : 0.856 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 53 ARG Chi-restraints excluded: chain A residue 76 GLN Chi-restraints excluded: chain B residue 96 THR Chi-restraints excluded: chain C residue 41 GLU Chi-restraints excluded: chain C residue 49 VAL Chi-restraints excluded: chain C residue 77 ARG Chi-restraints excluded: chain C residue 100 VAL Chi-restraints excluded: chain C residue 101 THR Chi-restraints excluded: chain C residue 108 LEU Chi-restraints excluded: chain D residue 48 VAL Chi-restraints excluded: chain E residue 46 VAL Chi-restraints excluded: chain E residue 64 LYS Chi-restraints excluded: chain E residue 86 SER Chi-restraints excluded: chain F residue 92 ARG Chi-restraints excluded: chain F residue 96 THR Chi-restraints excluded: chain G residue 92 GLU Chi-restraints excluded: chain G residue 99 LYS Chi-restraints excluded: chain G residue 101 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 102 random chunks: chunk 57 optimal weight: 1.9990 chunk 24 optimal weight: 0.6980 chunk 98 optimal weight: 2.9990 chunk 81 optimal weight: 1.9990 chunk 45 optimal weight: 0.8980 chunk 8 optimal weight: 0.9980 chunk 32 optimal weight: 2.9990 chunk 51 optimal weight: 0.9980 chunk 95 optimal weight: 1.9990 chunk 11 optimal weight: 0.5980 chunk 56 optimal weight: 2.9990 overall best weight: 0.8380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 68 GLN B 25 ASN ** B 75 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 95 GLN F 27 GLN ** G 73 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 104 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8272 moved from start: 0.1224 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.040 12911 Z= 0.253 Angle : 0.592 7.314 18690 Z= 0.355 Chirality : 0.036 0.161 2125 Planarity : 0.004 0.040 1345 Dihedral : 32.029 174.515 4068 Min Nonbonded Distance : 2.511 Molprobity Statistics. All-atom Clashscore : 7.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.00 % Favored : 98.00 % Rotamer: Outliers : 4.10 % Allowed : 27.92 % Favored : 67.98 % 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: 2.41 (0.30), residues: 749 helix: 2.21 (0.22), residues: 556 sheet: None (None), residues: 0 loop : -0.19 (0.40), residues: 193 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.004 0.001 HIS B 75 PHE 0.011 0.002 PHE E 67 TYR 0.015 0.001 TYR H 83 ARG 0.012 0.000 ARG H 99 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1498 Ramachandran restraints generated. 749 Oldfield, 0 Emsley, 749 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1498 Ramachandran restraints generated. 749 Oldfield, 0 Emsley, 749 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 209 residues out of total 635 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 183 time to evaluate : 0.940 Fit side-chains REVERT: A 53 ARG cc_start: 0.8743 (OUTLIER) cc_final: 0.7884 (ttp-110) REVERT: A 59 GLU cc_start: 0.9030 (pm20) cc_final: 0.8812 (pm20) REVERT: A 120 MET cc_start: 0.8908 (OUTLIER) cc_final: 0.8511 (mtt) REVERT: C 77 ARG cc_start: 0.8708 (OUTLIER) cc_final: 0.7541 (ttp-170) REVERT: D 34 LYS cc_start: 0.8561 (mmmm) cc_final: 0.8350 (mppt) REVERT: D 76 GLU cc_start: 0.8896 (tp30) cc_final: 0.8545 (tp30) REVERT: D 79 ARG cc_start: 0.8770 (mtm-85) cc_final: 0.8297 (mtm-85) REVERT: E 49 ARG cc_start: 0.9040 (OUTLIER) cc_final: 0.8064 (ptp90) REVERT: E 59 GLU cc_start: 0.9047 (pm20) cc_final: 0.8757 (pm20) REVERT: G 73 ASN cc_start: 0.8535 (t160) cc_final: 0.8066 (t0) REVERT: H 63 ASN cc_start: 0.8969 (t0) cc_final: 0.8502 (m-40) outliers start: 26 outliers final: 17 residues processed: 194 average time/residue: 1.6822 time to fit residues: 345.9495 Evaluate side-chains 199 residues out of total 635 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 178 time to evaluate : 0.962 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 53 ARG Chi-restraints excluded: chain A residue 76 GLN Chi-restraints excluded: chain A residue 120 MET Chi-restraints excluded: chain B residue 96 THR Chi-restraints excluded: chain C residue 41 GLU Chi-restraints excluded: chain C residue 49 VAL Chi-restraints excluded: chain C residue 59 THR Chi-restraints excluded: chain C residue 77 ARG Chi-restraints excluded: chain C residue 100 VAL Chi-restraints excluded: chain C residue 101 THR Chi-restraints excluded: chain C residue 108 LEU Chi-restraints excluded: chain D residue 48 VAL Chi-restraints excluded: chain E residue 46 VAL Chi-restraints excluded: chain E residue 49 ARG Chi-restraints excluded: chain E residue 64 LYS Chi-restraints excluded: chain E residue 86 SER Chi-restraints excluded: chain F residue 92 ARG Chi-restraints excluded: chain F residue 96 THR Chi-restraints excluded: chain G residue 92 GLU Chi-restraints excluded: chain G residue 99 LYS Chi-restraints excluded: chain G residue 101 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 102 random chunks: chunk 72 optimal weight: 0.9990 chunk 55 optimal weight: 0.8980 chunk 83 optimal weight: 2.9990 chunk 98 optimal weight: 2.9990 chunk 61 optimal weight: 0.9990 chunk 59 optimal weight: 0.8980 chunk 45 optimal weight: 0.8980 chunk 60 optimal weight: 0.8980 chunk 39 optimal weight: 0.5980 chunk 58 optimal weight: 0.5980 chunk 29 optimal weight: 0.7980 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 68 GLN B 25 ASN ** B 75 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 95 GLN F 27 GLN ** G 73 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 104 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8267 moved from start: 0.1237 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 12911 Z= 0.240 Angle : 0.592 8.221 18690 Z= 0.354 Chirality : 0.036 0.164 2125 Planarity : 0.004 0.053 1345 Dihedral : 32.007 174.861 4068 Min Nonbonded Distance : 2.510 Molprobity Statistics. All-atom Clashscore : 7.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.87 % Favored : 98.13 % Rotamer: Outliers : 3.63 % Allowed : 28.86 % Favored : 67.51 % 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: 2.44 (0.30), residues: 749 helix: 2.23 (0.22), residues: 556 sheet: None (None), residues: 0 loop : -0.17 (0.40), residues: 193 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.004 0.001 HIS B 75 PHE 0.012 0.002 PHE E 67 TYR 0.013 0.001 TYR H 83 ARG 0.013 0.000 ARG H 99 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1498 Ramachandran restraints generated. 749 Oldfield, 0 Emsley, 749 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1498 Ramachandran restraints generated. 749 Oldfield, 0 Emsley, 749 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 203 residues out of total 635 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 180 time to evaluate : 0.968 Fit side-chains REVERT: A 53 ARG cc_start: 0.8743 (OUTLIER) cc_final: 0.7887 (ttp-110) REVERT: A 59 GLU cc_start: 0.9029 (pm20) cc_final: 0.8801 (pm20) REVERT: C 77 ARG cc_start: 0.8705 (OUTLIER) cc_final: 0.7596 (ttp-170) REVERT: D 34 LYS cc_start: 0.8550 (mmmm) cc_final: 0.8328 (mppt) REVERT: D 76 GLU cc_start: 0.8919 (tp30) cc_final: 0.8488 (tp30) REVERT: D 79 ARG cc_start: 0.8767 (mtm-85) cc_final: 0.8263 (mtm-85) REVERT: E 49 ARG cc_start: 0.9042 (OUTLIER) cc_final: 0.8058 (ptp90) REVERT: E 59 GLU cc_start: 0.9042 (pm20) cc_final: 0.8723 (pm20) REVERT: G 73 ASN cc_start: 0.8542 (t160) cc_final: 0.8063 (t0) REVERT: H 63 ASN cc_start: 0.8921 (t0) cc_final: 0.8446 (m-40) outliers start: 23 outliers final: 16 residues processed: 192 average time/residue: 1.6642 time to fit residues: 339.0662 Evaluate side-chains 196 residues out of total 635 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 177 time to evaluate : 0.911 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 53 ARG Chi-restraints excluded: chain A residue 76 GLN Chi-restraints excluded: chain B residue 96 THR Chi-restraints excluded: chain C residue 41 GLU Chi-restraints excluded: chain C residue 49 VAL Chi-restraints excluded: chain C residue 77 ARG Chi-restraints excluded: chain C residue 100 VAL Chi-restraints excluded: chain C residue 101 THR Chi-restraints excluded: chain C residue 108 LEU Chi-restraints excluded: chain D residue 48 VAL Chi-restraints excluded: chain E residue 46 VAL Chi-restraints excluded: chain E residue 49 ARG Chi-restraints excluded: chain E residue 64 LYS Chi-restraints excluded: chain E residue 86 SER Chi-restraints excluded: chain F residue 92 ARG Chi-restraints excluded: chain F residue 96 THR Chi-restraints excluded: chain G residue 92 GLU Chi-restraints excluded: chain G residue 99 LYS Chi-restraints excluded: chain G residue 101 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 102 random chunks: chunk 19 optimal weight: 1.9990 chunk 62 optimal weight: 0.3980 chunk 66 optimal weight: 1.9990 chunk 48 optimal weight: 2.9990 chunk 9 optimal weight: 0.5980 chunk 77 optimal weight: 2.9990 chunk 89 optimal weight: 3.9990 chunk 94 optimal weight: 1.9990 chunk 85 optimal weight: 2.9990 chunk 91 optimal weight: 1.9990 chunk 55 optimal weight: 0.7980 overall best weight: 1.1584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 68 GLN B 25 ASN ** B 75 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 95 GLN F 27 GLN ** G 73 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 104 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8293 moved from start: 0.1306 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.042 12911 Z= 0.304 Angle : 0.615 8.777 18690 Z= 0.366 Chirality : 0.038 0.171 2125 Planarity : 0.004 0.045 1345 Dihedral : 32.070 173.934 4068 Min Nonbonded Distance : 2.507 Molprobity Statistics. All-atom Clashscore : 7.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.00 % Favored : 98.00 % Rotamer: Outliers : 3.94 % Allowed : 29.02 % Favored : 67.03 % 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: 2.35 (0.30), residues: 749 helix: 2.16 (0.22), residues: 556 sheet: None (None), residues: 0 loop : -0.21 (0.40), residues: 193 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.004 0.001 HIS B 75 PHE 0.010 0.002 PHE E 67 TYR 0.014 0.002 TYR H 83 ARG 0.013 0.000 ARG H 99 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1498 Ramachandran restraints generated. 749 Oldfield, 0 Emsley, 749 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1498 Ramachandran restraints generated. 749 Oldfield, 0 Emsley, 749 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 210 residues out of total 635 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 185 time to evaluate : 0.812 Fit side-chains REVERT: A 53 ARG cc_start: 0.8756 (OUTLIER) cc_final: 0.7894 (ttp-110) REVERT: A 59 GLU cc_start: 0.9031 (pm20) cc_final: 0.8789 (pm20) REVERT: C 77 ARG cc_start: 0.8760 (OUTLIER) cc_final: 0.7632 (ttp-170) REVERT: E 49 ARG cc_start: 0.9062 (OUTLIER) cc_final: 0.8094 (ptp90) REVERT: E 59 GLU cc_start: 0.9080 (pm20) cc_final: 0.8783 (pm20) REVERT: G 73 ASN cc_start: 0.8601 (t160) cc_final: 0.8143 (t0) REVERT: H 63 ASN cc_start: 0.8992 (t0) cc_final: 0.8497 (m-40) REVERT: H 71 GLU cc_start: 0.8828 (mm-30) cc_final: 0.8368 (tm-30) outliers start: 25 outliers final: 19 residues processed: 198 average time/residue: 1.7116 time to fit residues: 358.7841 Evaluate side-chains 201 residues out of total 635 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 179 time to evaluate : 0.994 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 53 ARG Chi-restraints excluded: chain A residue 76 GLN Chi-restraints excluded: chain B residue 96 THR Chi-restraints excluded: chain C residue 41 GLU Chi-restraints excluded: chain C residue 49 VAL Chi-restraints excluded: chain C residue 59 THR Chi-restraints excluded: chain C residue 77 ARG Chi-restraints excluded: chain C residue 100 VAL Chi-restraints excluded: chain C residue 101 THR Chi-restraints excluded: chain C residue 108 LEU Chi-restraints excluded: chain D residue 33 ARG Chi-restraints excluded: chain D residue 48 VAL Chi-restraints excluded: chain E residue 46 VAL Chi-restraints excluded: chain E residue 49 ARG Chi-restraints excluded: chain E residue 64 LYS Chi-restraints excluded: chain E residue 86 SER Chi-restraints excluded: chain F residue 80 THR Chi-restraints excluded: chain F residue 92 ARG Chi-restraints excluded: chain F residue 96 THR Chi-restraints excluded: chain G residue 92 GLU Chi-restraints excluded: chain G residue 99 LYS Chi-restraints excluded: chain G residue 101 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 102 random chunks: chunk 39 optimal weight: 0.7980 chunk 71 optimal weight: 1.9990 chunk 28 optimal weight: 0.1980 chunk 82 optimal weight: 1.9990 chunk 86 optimal weight: 1.9990 chunk 91 optimal weight: 2.9990 chunk 60 optimal weight: 0.9990 chunk 96 optimal weight: 1.9990 chunk 59 optimal weight: 0.6980 chunk 45 optimal weight: 0.9980 chunk 67 optimal weight: 0.5980 overall best weight: 0.6580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 68 GLN B 25 ASN ** B 75 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 104 GLN D 95 GLN F 27 GLN ** G 73 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 104 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8282 moved from start: 0.1318 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 12911 Z= 0.242 Angle : 0.615 8.583 18690 Z= 0.365 Chirality : 0.037 0.196 2125 Planarity : 0.004 0.057 1345 Dihedral : 32.098 174.420 4068 Min Nonbonded Distance : 2.449 Molprobity Statistics. All-atom Clashscore : 8.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.74 % Favored : 98.26 % Rotamer: Outliers : 4.42 % Allowed : 29.02 % Favored : 66.56 % 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: 2.40 (0.30), residues: 749 helix: 2.21 (0.22), residues: 556 sheet: None (None), residues: 0 loop : -0.21 (0.40), residues: 193 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.005 0.001 HIS B 75 PHE 0.012 0.002 PHE E 67 TYR 0.019 0.002 TYR H 83 ARG 0.014 0.000 ARG H 99 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1498 Ramachandran restraints generated. 749 Oldfield, 0 Emsley, 749 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1498 Ramachandran restraints generated. 749 Oldfield, 0 Emsley, 749 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 209 residues out of total 635 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 181 time to evaluate : 0.977 Fit side-chains REVERT: A 53 ARG cc_start: 0.8748 (OUTLIER) cc_final: 0.7888 (ttp-110) REVERT: A 59 GLU cc_start: 0.9029 (pm20) cc_final: 0.8787 (pm20) REVERT: B 79 LYS cc_start: 0.9140 (OUTLIER) cc_final: 0.8554 (mtmm) REVERT: C 77 ARG cc_start: 0.8699 (OUTLIER) cc_final: 0.7525 (ttp-170) REVERT: D 33 ARG cc_start: 0.7720 (OUTLIER) cc_final: 0.7100 (mmt-90) REVERT: E 49 ARG cc_start: 0.9050 (OUTLIER) cc_final: 0.8080 (ptp90) REVERT: E 59 GLU cc_start: 0.9078 (pm20) cc_final: 0.8774 (pm20) REVERT: G 73 ASN cc_start: 0.8608 (t160) cc_final: 0.8168 (t0) REVERT: H 63 ASN cc_start: 0.8951 (t0) cc_final: 0.8488 (m-40) REVERT: H 71 GLU cc_start: 0.8823 (mm-30) cc_final: 0.8379 (tm-30) REVERT: H 116 LYS cc_start: 0.8899 (OUTLIER) cc_final: 0.8482 (ptpp) outliers start: 28 outliers final: 19 residues processed: 193 average time/residue: 1.7488 time to fit residues: 357.7811 Evaluate side-chains 204 residues out of total 635 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 179 time to evaluate : 0.899 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 53 ARG Chi-restraints excluded: chain A residue 76 GLN Chi-restraints excluded: chain B residue 79 LYS Chi-restraints excluded: chain B residue 96 THR Chi-restraints excluded: chain C residue 41 GLU Chi-restraints excluded: chain C residue 49 VAL Chi-restraints excluded: chain C residue 59 THR Chi-restraints excluded: chain C residue 77 ARG Chi-restraints excluded: chain C residue 100 VAL Chi-restraints excluded: chain C residue 101 THR Chi-restraints excluded: chain C residue 104 GLN Chi-restraints excluded: chain C residue 108 LEU Chi-restraints excluded: chain D residue 33 ARG Chi-restraints excluded: chain D residue 48 VAL Chi-restraints excluded: chain E residue 46 VAL Chi-restraints excluded: chain E residue 49 ARG Chi-restraints excluded: chain E residue 64 LYS Chi-restraints excluded: chain E residue 86 SER Chi-restraints excluded: chain F residue 80 THR Chi-restraints excluded: chain F residue 92 ARG Chi-restraints excluded: chain F residue 96 THR Chi-restraints excluded: chain G residue 92 GLU Chi-restraints excluded: chain G residue 99 LYS Chi-restraints excluded: chain G residue 101 THR Chi-restraints excluded: chain H residue 116 LYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 102 random chunks: chunk 101 optimal weight: 3.9990 chunk 93 optimal weight: 2.9990 chunk 80 optimal weight: 1.9990 chunk 8 optimal weight: 0.6980 chunk 62 optimal weight: 0.9980 chunk 49 optimal weight: 0.7980 chunk 64 optimal weight: 0.9990 chunk 86 optimal weight: 2.9990 chunk 24 optimal weight: 0.0470 chunk 74 optimal weight: 5.9990 chunk 11 optimal weight: 0.7980 overall best weight: 0.6678 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 68 GLN B 25 ASN ** B 75 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 104 GLN D 95 GLN F 27 GLN ** G 73 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 104 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8273 moved from start: 0.1311 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.050 12911 Z= 0.239 Angle : 0.607 8.268 18690 Z= 0.361 Chirality : 0.036 0.187 2125 Planarity : 0.005 0.062 1345 Dihedral : 32.076 174.825 4068 Min Nonbonded Distance : 2.274 Molprobity Statistics. All-atom Clashscore : 8.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.87 % Favored : 98.13 % Rotamer: Outliers : 4.10 % Allowed : 29.18 % Favored : 66.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: 2.43 (0.30), residues: 749 helix: 2.21 (0.22), residues: 556 sheet: None (None), residues: 0 loop : -0.16 (0.40), residues: 193 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.004 0.001 HIS B 75 PHE 0.013 0.002 PHE E 67 TYR 0.022 0.002 TYR H 83 ARG 0.015 0.000 ARG H 99 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1498 Ramachandran restraints generated. 749 Oldfield, 0 Emsley, 749 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1498 Ramachandran restraints generated. 749 Oldfield, 0 Emsley, 749 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 205 residues out of total 635 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 179 time to evaluate : 0.923 Fit side-chains REVERT: A 53 ARG cc_start: 0.8745 (OUTLIER) cc_final: 0.7884 (ttp-110) REVERT: A 59 GLU cc_start: 0.9029 (pm20) cc_final: 0.8787 (pm20) REVERT: C 77 ARG cc_start: 0.8698 (OUTLIER) cc_final: 0.7529 (ttp-170) REVERT: D 33 ARG cc_start: 0.7667 (OUTLIER) cc_final: 0.7034 (mmt-90) REVERT: D 34 LYS cc_start: 0.8638 (mmmm) cc_final: 0.8373 (mppt) REVERT: E 49 ARG cc_start: 0.9046 (OUTLIER) cc_final: 0.8091 (ptp90) REVERT: E 59 GLU cc_start: 0.9061 (pm20) cc_final: 0.8758 (pm20) REVERT: G 73 ASN cc_start: 0.8614 (t160) cc_final: 0.8175 (t0) REVERT: H 63 ASN cc_start: 0.8926 (t0) cc_final: 0.8465 (m-40) REVERT: H 71 GLU cc_start: 0.8830 (mm-30) cc_final: 0.8380 (tm-30) REVERT: H 116 LYS cc_start: 0.8897 (OUTLIER) cc_final: 0.8478 (ptpp) outliers start: 26 outliers final: 18 residues processed: 191 average time/residue: 1.6515 time to fit residues: 334.3661 Evaluate side-chains 203 residues out of total 635 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 180 time to evaluate : 0.913 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 53 ARG Chi-restraints excluded: chain A residue 76 GLN Chi-restraints excluded: chain B residue 96 THR Chi-restraints excluded: chain C residue 41 GLU Chi-restraints excluded: chain C residue 49 VAL Chi-restraints excluded: chain C residue 59 THR Chi-restraints excluded: chain C residue 77 ARG Chi-restraints excluded: chain C residue 100 VAL Chi-restraints excluded: chain C residue 101 THR Chi-restraints excluded: chain C residue 108 LEU Chi-restraints excluded: chain D residue 33 ARG Chi-restraints excluded: chain D residue 48 VAL Chi-restraints excluded: chain E residue 46 VAL Chi-restraints excluded: chain E residue 49 ARG Chi-restraints excluded: chain E residue 64 LYS Chi-restraints excluded: chain E residue 86 SER Chi-restraints excluded: chain F residue 80 THR Chi-restraints excluded: chain F residue 92 ARG Chi-restraints excluded: chain F residue 96 THR Chi-restraints excluded: chain G residue 92 GLU Chi-restraints excluded: chain G residue 99 LYS Chi-restraints excluded: chain G residue 101 THR Chi-restraints excluded: chain H residue 116 LYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 102 random chunks: chunk 22 optimal weight: 0.0980 chunk 81 optimal weight: 1.9990 chunk 33 optimal weight: 1.9990 chunk 83 optimal weight: 2.9990 chunk 10 optimal weight: 0.5980 chunk 14 optimal weight: 1.9990 chunk 71 optimal weight: 1.9990 chunk 4 optimal weight: 0.5980 chunk 58 optimal weight: 0.6980 chunk 92 optimal weight: 1.9990 chunk 54 optimal weight: 0.1980 overall best weight: 0.4380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 25 ASN ** B 75 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 104 GLN D 95 GLN F 27 GLN ** G 73 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 104 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3553 r_free = 0.3553 target = 0.103349 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3239 r_free = 0.3239 target = 0.082004 restraints weight = 18826.056| |-----------------------------------------------------------------------------| r_work (start): 0.3219 rms_B_bonded: 1.24 r_work: 0.3058 rms_B_bonded: 2.52 restraints_weight: 0.5000 r_work: 0.2932 rms_B_bonded: 4.08 restraints_weight: 0.2500 r_work (final): 0.2932 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8402 moved from start: 0.1308 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.046 12911 Z= 0.218 Angle : 0.609 8.161 18690 Z= 0.361 Chirality : 0.036 0.219 2125 Planarity : 0.005 0.062 1345 Dihedral : 32.075 175.005 4068 Min Nonbonded Distance : 2.511 Molprobity Statistics. All-atom Clashscore : 8.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.74 % Favored : 98.26 % Rotamer: Outliers : 3.94 % Allowed : 29.18 % Favored : 66.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: 2.46 (0.30), residues: 749 helix: 2.23 (0.22), residues: 556 sheet: None (None), residues: 0 loop : -0.12 (0.41), residues: 193 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.004 0.001 HIS B 75 PHE 0.014 0.002 PHE E 67 TYR 0.016 0.001 TYR H 83 ARG 0.015 0.000 ARG H 99 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5091.20 seconds wall clock time: 95 minutes 24.30 seconds (5724.30 seconds total)