Starting phenix.real_space_refine on Tue Jul 29 23:13:47 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8guk_34275/07_2025/8guk_34275.cif Found real_map, /net/cci-nas-00/data/ceres_data/8guk_34275/07_2025/8guk_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/cci-nas-00/data/ceres_data/8guk_34275/07_2025/8guk_34275.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8guk_34275/07_2025/8guk_34275.map" model { file = "/net/cci-nas-00/data/ceres_data/8guk_34275/07_2025/8guk_34275.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8guk_34275/07_2025/8guk_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): 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5711/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: 9.08, per 1000 atoms: 0.75 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: 3.65 Conformation dependent library (CDL) restraints added in 1.1 seconds 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: 6.49 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: 4.39 Time building geometry restraints manager: 3.82 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: 9.650 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: 0.020 Extract box with map and model: 0.420 Check model and map are aligned: 0.080 Set scattering table: 0.100 Process input model: 37.210 Find NCS groups from input model: 0.320 Set up NCS constraints: 0.070 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: 0.010 Load rotamer database and sin/cos tables:15.480 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 63.360 ------------------------------------------------------------------------------- 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= 0.182 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 Details of bonding type rmsd hydrogen bonds : bond 0.09278 ( 799) hydrogen bonds : angle 3.78834 ( 1992) covalent geometry : bond 0.00407 (12911) covalent geometry : angle 0.60212 (18690) *********************** 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 to be fit. rotamer outliers: 20 poor density : 181 time to evaluate : 0.852 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: 1.8273 time to fit residues: 379.2695 Evaluate side-chains 191 residues out of total 635 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 177 time to evaluate : 1.592 ------------------------------------------------------------------------------- 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: 0.8980 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: 0.6384 ------------------------------------------------------------------------------- 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** 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: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3577 r_free = 0.3577 target = 0.104462 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.3275 r_free = 0.3275 target = 0.083307 restraints weight = 19305.032| |-----------------------------------------------------------------------------| r_work (start): 0.3253 rms_B_bonded: 1.26 r_work: 0.3098 rms_B_bonded: 2.55 restraints_weight: 0.5000 r_work: 0.2974 rms_B_bonded: 4.12 restraints_weight: 0.2500 r_work (final): 0.2974 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8409 moved from start: 0.0849 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.048 12911 Z= 0.182 Angle : 0.582 8.219 18690 Z= 0.348 Chirality : 0.035 0.156 2125 Planarity : 0.004 0.040 1345 Dihedral : 31.867 175.234 4087 Min Nonbonded Distance : 2.361 Molprobity Statistics. All-atom Clashscore : 8.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.00 % Favored : 98.00 % Rotamer: Outliers : 5.05 % Allowed : 25.55 % Favored : 69.40 % 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: 2.23 (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 0.004 0.001 HIS B 75 PHE 0.011 0.001 PHE E 67 TYR 0.014 0.001 TYR H 83 ARG 0.008 0.000 ARG H 99 Details of bonding type rmsd hydrogen bonds : bond 0.03712 ( 799) hydrogen bonds : angle 3.11914 ( 1992) covalent geometry : bond 0.00403 (12911) covalent geometry : angle 0.58170 (18690) *********************** 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 228 residues out of total 635 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 196 time to evaluate : 2.611 Fit side-chains REVERT: A 120 MET cc_start: 0.8749 (OUTLIER) cc_final: 0.8210 (mtt) REVERT: C 77 ARG cc_start: 0.8555 (OUTLIER) cc_final: 0.7701 (ttp-170) REVERT: D 34 LYS cc_start: 0.8711 (mmmm) cc_final: 0.8434 (mppt) REVERT: D 40 TYR cc_start: 0.9035 (m-80) cc_final: 0.8828 (m-80) REVERT: D 93 GLU cc_start: 0.8236 (mp0) cc_final: 0.7966 (mp0) REVERT: E 59 GLU cc_start: 0.8927 (pm20) cc_final: 0.8660 (pm20) REVERT: F 22 LEU cc_start: 0.6507 (OUTLIER) cc_final: 0.6250 (tp) REVERT: G 104 GLN cc_start: 0.8423 (mm-40) cc_final: 0.8083 (mm110) REVERT: H 63 ASN cc_start: 0.8754 (t0) cc_final: 0.8458 (m-40) outliers start: 32 outliers final: 19 residues processed: 211 average time/residue: 2.3308 time to fit residues: 523.6858 Evaluate side-chains 206 residues out of total 635 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 184 time to evaluate : 0.879 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 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 D residue 55 SER Chi-restraints excluded: chain D residue 88 THR Chi-restraints excluded: chain E residue 46 VAL Chi-restraints excluded: chain E residue 86 SER Chi-restraints excluded: chain F residue 22 LEU 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 5 optimal weight: 0.5980 chunk 57 optimal weight: 0.9990 chunk 40 optimal weight: 0.0010 chunk 54 optimal weight: 5.9990 chunk 43 optimal weight: 0.5980 chunk 88 optimal weight: 4.9990 chunk 7 optimal weight: 1.9990 chunk 20 optimal weight: 1.9990 chunk 75 optimal weight: 3.9990 chunk 58 optimal weight: 1.9990 chunk 70 optimal weight: 0.8980 overall best weight: 0.6188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 68 GLN ** 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: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3582 r_free = 0.3582 target = 0.104738 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3283 r_free = 0.3283 target = 0.083754 restraints weight = 19462.529| |-----------------------------------------------------------------------------| r_work (start): 0.3253 rms_B_bonded: 1.25 r_work: 0.3096 rms_B_bonded: 2.55 restraints_weight: 0.5000 r_work: 0.2973 rms_B_bonded: 4.12 restraints_weight: 0.2500 r_work (final): 0.2973 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8406 moved from start: 0.1056 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 12911 Z= 0.178 Angle : 0.576 8.177 18690 Z= 0.345 Chirality : 0.035 0.162 2125 Planarity : 0.004 0.040 1345 Dihedral : 31.827 174.442 4071 Min Nonbonded Distance : 2.511 Molprobity Statistics. All-atom Clashscore : 7.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.27 % Favored : 97.73 % Rotamer: Outliers : 4.26 % Allowed : 27.29 % Favored : 68.45 % 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: 2.53 (0.30), residues: 749 helix: 2.29 (0.22), residues: 555 sheet: None (None), residues: 0 loop : -0.13 (0.41), residues: 194 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 0.015 0.001 TYR H 83 ARG 0.009 0.000 ARG H 99 Details of bonding type rmsd hydrogen bonds : bond 0.03549 ( 799) hydrogen bonds : angle 3.02147 ( 1992) covalent geometry : bond 0.00395 (12911) covalent geometry : angle 0.57551 (18690) *********************** 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 224 residues out of total 635 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 197 time to evaluate : 0.921 Fit side-chains REVERT: A 59 GLU cc_start: 0.9020 (pm20) cc_final: 0.8820 (pm20) REVERT: A 94 GLU cc_start: 0.8614 (mm-30) cc_final: 0.8240 (mm-30) REVERT: A 120 MET cc_start: 0.8780 (OUTLIER) cc_final: 0.8321 (mtt) REVERT: C 77 ARG cc_start: 0.8526 (OUTLIER) cc_final: 0.7581 (ttp-170) REVERT: D 93 GLU cc_start: 0.8224 (mp0) cc_final: 0.7926 (mp0) REVERT: G 90 ASP cc_start: 0.8822 (t0) cc_final: 0.8600 (t0) REVERT: H 63 ASN cc_start: 0.8760 (t0) cc_final: 0.8415 (m-40) outliers start: 27 outliers final: 17 residues processed: 210 average time/residue: 1.6110 time to fit residues: 360.7933 Evaluate side-chains 202 residues out of total 635 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 183 time to evaluate : 1.013 ------------------------------------------------------------------------------- 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 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 D residue 55 SER 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 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 36 optimal weight: 2.9990 chunk 56 optimal weight: 0.9980 chunk 4 optimal weight: 0.7980 chunk 92 optimal weight: 2.9990 chunk 73 optimal weight: 1.9990 chunk 8 optimal weight: 1.9990 chunk 91 optimal weight: 2.9990 chunk 31 optimal weight: 0.7980 chunk 19 optimal weight: 1.9990 chunk 44 optimal weight: 0.8980 chunk 6 optimal weight: 0.5980 overall best weight: 0.8180 ------------------------------------------------------------------------------- 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** F 27 GLN G 24 GLN ** G 73 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 = 0.3565 r_free = 0.3565 target = 0.103668 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3263 r_free = 0.3263 target = 0.082456 restraints weight = 19337.387| |-----------------------------------------------------------------------------| r_work (start): 0.3230 rms_B_bonded: 1.24 r_work: 0.3072 rms_B_bonded: 2.54 restraints_weight: 0.5000 r_work: 0.2948 rms_B_bonded: 4.10 restraints_weight: 0.2500 r_work (final): 0.2948 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8425 moved from start: 0.1142 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= 0.199 Angle : 0.584 8.525 18690 Z= 0.349 Chirality : 0.036 0.164 2125 Planarity : 0.004 0.038 1345 Dihedral : 31.907 174.139 4071 Min Nonbonded Distance : 2.509 Molprobity Statistics. All-atom Clashscore : 8.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.14 % Favored : 97.86 % Rotamer: Outliers : 4.26 % Allowed : 28.08 % Favored : 67.67 % 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: 2.54 (0.30), residues: 749 helix: 2.30 (0.22), residues: 555 sheet: None (None), residues: 0 loop : -0.13 (0.40), residues: 194 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.004 0.001 HIS B 75 PHE 0.009 0.002 PHE E 67 TYR 0.016 0.001 TYR H 83 ARG 0.010 0.000 ARG H 99 Details of bonding type rmsd hydrogen bonds : bond 0.03744 ( 799) hydrogen bonds : angle 3.04000 ( 1992) covalent geometry : bond 0.00446 (12911) covalent geometry : angle 0.58419 (18690) *********************** 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 215 residues out of total 635 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 188 time to evaluate : 1.820 Fit side-chains REVERT: A 53 ARG cc_start: 0.8747 (OUTLIER) cc_final: 0.7905 (ttp-110) REVERT: A 59 GLU cc_start: 0.9033 (pm20) cc_final: 0.8780 (pm20) REVERT: B 79 LYS cc_start: 0.9219 (OUTLIER) cc_final: 0.8654 (mtmm) REVERT: C 77 ARG cc_start: 0.8545 (OUTLIER) cc_final: 0.7621 (ttp-170) REVERT: D 40 TYR cc_start: 0.9042 (m-80) cc_final: 0.8824 (m-80) REVERT: D 93 GLU cc_start: 0.8246 (mp0) cc_final: 0.7972 (mp0) REVERT: E 59 GLU cc_start: 0.8941 (pm20) cc_final: 0.8606 (pm20) REVERT: F 68 ASP cc_start: 0.9158 (m-30) cc_final: 0.8924 (m-30) REVERT: F 92 ARG cc_start: 0.9041 (OUTLIER) cc_final: 0.8758 (mtp-110) REVERT: G 73 ASN cc_start: 0.8798 (t160) cc_final: 0.8255 (t0) REVERT: H 63 ASN cc_start: 0.8851 (t0) cc_final: 0.8457 (m-40) outliers start: 27 outliers final: 17 residues processed: 199 average time/residue: 2.3520 time to fit residues: 497.5531 Evaluate side-chains 200 residues out of total 635 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 179 time to evaluate : 1.191 ------------------------------------------------------------------------------- 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 77 ASP 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 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=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 102 random chunks: chunk 31 optimal weight: 0.6980 chunk 91 optimal weight: 2.9990 chunk 0 optimal weight: 3.9990 chunk 64 optimal weight: 2.9990 chunk 23 optimal weight: 3.9990 chunk 60 optimal weight: 0.8980 chunk 14 optimal weight: 1.9990 chunk 17 optimal weight: 5.9990 chunk 6 optimal weight: 0.5980 chunk 98 optimal weight: 2.9990 chunk 49 optimal weight: 0.5980 overall best weight: 0.9582 ------------------------------------------------------------------------------- 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** ** E 113 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 27 GLN ** G 73 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 = 0.3549 r_free = 0.3549 target = 0.102812 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3228 r_free = 0.3228 target = 0.081299 restraints weight = 18943.794| |-----------------------------------------------------------------------------| r_work (start): 0.3211 rms_B_bonded: 1.24 r_work: 0.3050 rms_B_bonded: 2.54 restraints_weight: 0.5000 r_work: 0.2924 rms_B_bonded: 4.09 restraints_weight: 0.2500 r_work (final): 0.2924 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8409 moved from start: 0.1273 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.039 12911 Z= 0.215 Angle : 0.594 8.940 18690 Z= 0.355 Chirality : 0.036 0.172 2125 Planarity : 0.004 0.042 1345 Dihedral : 31.986 174.267 4071 Min Nonbonded Distance : 2.508 Molprobity Statistics. All-atom Clashscore : 7.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.00 % Favored : 98.00 % Rotamer: Outliers : 3.79 % Allowed : 28.39 % Favored : 67.82 % 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: 2.49 (0.30), residues: 749 helix: 2.24 (0.22), residues: 556 sheet: None (None), residues: 0 loop : -0.10 (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 0.017 0.002 TYR H 83 ARG 0.012 0.000 ARG H 99 Details of bonding type rmsd hydrogen bonds : bond 0.03906 ( 799) hydrogen bonds : angle 3.06589 ( 1992) covalent geometry : bond 0.00484 (12911) covalent geometry : angle 0.59447 (18690) *********************** 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 207 residues out of total 635 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 183 time to evaluate : 0.858 Fit side-chains REVERT: A 53 ARG cc_start: 0.8745 (OUTLIER) cc_final: 0.7889 (ttp-110) REVERT: A 59 GLU cc_start: 0.9011 (pm20) cc_final: 0.8715 (pm20) REVERT: C 77 ARG cc_start: 0.8475 (OUTLIER) cc_final: 0.7405 (ttp-170) REVERT: D 33 ARG cc_start: 0.7610 (OUTLIER) cc_final: 0.6976 (mmt-90) REVERT: D 93 GLU cc_start: 0.8295 (mp0) cc_final: 0.7980 (mp0) REVERT: E 59 GLU cc_start: 0.8965 (pm20) cc_final: 0.8649 (pm20) REVERT: G 73 ASN cc_start: 0.8664 (t160) cc_final: 0.8213 (t0) REVERT: H 63 ASN cc_start: 0.8862 (t0) cc_final: 0.8444 (m-40) outliers start: 24 outliers final: 16 residues processed: 195 average time/residue: 1.9120 time to fit residues: 395.8077 Evaluate side-chains 195 residues out of total 635 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 176 time to evaluate : 0.859 ------------------------------------------------------------------------------- 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 33 ARG 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 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 46 optimal weight: 1.9990 chunk 77 optimal weight: 2.9990 chunk 14 optimal weight: 1.9990 chunk 76 optimal weight: 2.9990 chunk 65 optimal weight: 0.9980 chunk 68 optimal weight: 0.5980 chunk 73 optimal weight: 2.9990 chunk 38 optimal weight: 0.5980 chunk 83 optimal weight: 2.9990 chunk 84 optimal weight: 2.9990 chunk 27 optimal weight: 0.8980 overall best weight: 1.0182 ------------------------------------------------------------------------------- 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** ** E 113 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** 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: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3548 r_free = 0.3548 target = 0.102674 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3226 r_free = 0.3226 target = 0.081117 restraints weight = 19197.385| |-----------------------------------------------------------------------------| r_work (start): 0.3202 rms_B_bonded: 1.26 r_work: 0.3040 rms_B_bonded: 2.55 restraints_weight: 0.5000 r_work: 0.2914 rms_B_bonded: 4.11 restraints_weight: 0.2500 r_work (final): 0.2914 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8415 moved from start: 0.1304 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.039 12911 Z= 0.223 Angle : 0.599 8.908 18690 Z= 0.358 Chirality : 0.037 0.177 2125 Planarity : 0.004 0.038 1345 Dihedral : 31.994 174.523 4069 Min Nonbonded Distance : 2.515 Molprobity Statistics. All-atom Clashscore : 7.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.87 % Favored : 98.13 % Rotamer: Outliers : 4.10 % Allowed : 28.55 % Favored : 67.35 % 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: 2.45 (0.30), residues: 749 helix: 2.22 (0.22), residues: 556 sheet: None (None), residues: 0 loop : -0.10 (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 0.018 0.002 TYR H 83 ARG 0.012 0.000 ARG H 99 Details of bonding type rmsd hydrogen bonds : bond 0.03976 ( 799) hydrogen bonds : angle 3.09164 ( 1992) covalent geometry : bond 0.00501 (12911) covalent geometry : angle 0.59910 (18690) *********************** 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 211 residues out of total 635 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 185 time to evaluate : 0.828 Fit side-chains REVERT: A 53 ARG cc_start: 0.8744 (OUTLIER) cc_final: 0.7885 (ttp-110) REVERT: A 59 GLU cc_start: 0.9006 (pm20) cc_final: 0.8678 (pm20) REVERT: C 77 ARG cc_start: 0.8484 (OUTLIER) cc_final: 0.7366 (ttp-170) REVERT: D 93 GLU cc_start: 0.8289 (OUTLIER) cc_final: 0.7967 (mp0) REVERT: E 59 GLU cc_start: 0.8968 (pm20) cc_final: 0.8697 (pm20) REVERT: G 73 ASN cc_start: 0.8665 (t160) cc_final: 0.8183 (t0) REVERT: H 63 ASN cc_start: 0.8849 (t0) cc_final: 0.8362 (m-40) outliers start: 26 outliers final: 18 residues processed: 197 average time/residue: 1.6285 time to fit residues: 340.8591 Evaluate side-chains 196 residues out of total 635 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 175 time to evaluate : 0.836 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 53 ARG Chi-restraints excluded: chain A residue 64 LYS 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 48 VAL Chi-restraints excluded: chain D residue 93 GLU 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 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 57 optimal weight: 0.8980 chunk 39 optimal weight: 0.4980 chunk 89 optimal weight: 3.9990 chunk 44 optimal weight: 0.6980 chunk 22 optimal weight: 0.9980 chunk 95 optimal weight: 1.9990 chunk 84 optimal weight: 2.9990 chunk 85 optimal weight: 2.9990 chunk 6 optimal weight: 0.1980 chunk 36 optimal weight: 0.9990 chunk 72 optimal weight: 0.9980 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** ** E 113 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 27 GLN ** G 73 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 104 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3553 r_free = 0.3553 target = 0.102981 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3235 r_free = 0.3235 target = 0.081548 restraints weight = 19046.556| |-----------------------------------------------------------------------------| r_work (start): 0.3214 rms_B_bonded: 1.23 r_work: 0.3052 rms_B_bonded: 2.52 restraints_weight: 0.5000 r_work: 0.2927 rms_B_bonded: 4.07 restraints_weight: 0.2500 r_work (final): 0.2927 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8405 moved from start: 0.1335 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.052 12911 Z= 0.193 Angle : 0.601 9.309 18690 Z= 0.358 Chirality : 0.036 0.193 2125 Planarity : 0.004 0.050 1345 Dihedral : 32.008 174.852 4069 Min Nonbonded Distance : 2.518 Molprobity Statistics. All-atom Clashscore : 7.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.87 % Favored : 98.13 % Rotamer: Outliers : 3.94 % Allowed : 29.81 % Favored : 66.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: 2.49 (0.30), residues: 749 helix: 2.23 (0.22), residues: 556 sheet: None (None), residues: 0 loop : -0.05 (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 0.020 0.001 TYR H 83 ARG 0.015 0.000 ARG H 99 Details of bonding type rmsd hydrogen bonds : bond 0.03891 ( 799) hydrogen bonds : angle 3.08745 ( 1992) covalent geometry : bond 0.00430 (12911) covalent geometry : angle 0.60144 (18690) *********************** 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 208 residues out of total 635 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 183 time to evaluate : 0.810 Fit side-chains REVERT: A 53 ARG cc_start: 0.8738 (OUTLIER) cc_final: 0.7881 (ttp-110) REVERT: A 59 GLU cc_start: 0.9010 (pm20) cc_final: 0.8701 (pm20) REVERT: B 79 LYS cc_start: 0.9170 (OUTLIER) cc_final: 0.8596 (mtmm) REVERT: C 77 ARG cc_start: 0.8476 (OUTLIER) cc_final: 0.7355 (ttp-170) REVERT: D 93 GLU cc_start: 0.8282 (OUTLIER) cc_final: 0.7959 (mp0) REVERT: E 59 GLU cc_start: 0.8965 (pm20) cc_final: 0.8606 (pm20) REVERT: G 73 ASN cc_start: 0.8672 (t160) cc_final: 0.8189 (t0) REVERT: H 63 ASN cc_start: 0.8836 (t0) cc_final: 0.8395 (m-40) outliers start: 25 outliers final: 17 residues processed: 191 average time/residue: 1.5830 time to fit residues: 321.1064 Evaluate side-chains 197 residues out of total 635 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 176 time to evaluate : 0.859 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 53 ARG Chi-restraints excluded: chain A residue 64 LYS 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 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 D residue 93 GLU 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=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 102 random chunks: chunk 27 optimal weight: 0.0010 chunk 82 optimal weight: 1.9990 chunk 53 optimal weight: 1.9990 chunk 4 optimal weight: 0.8980 chunk 78 optimal weight: 2.9990 chunk 93 optimal weight: 2.9990 chunk 23 optimal weight: 2.9990 chunk 51 optimal weight: 0.6980 chunk 33 optimal weight: 0.7980 chunk 44 optimal weight: 0.9980 chunk 94 optimal weight: 1.9990 overall best weight: 0.6786 ------------------------------------------------------------------------------- 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** ** E 113 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 27 GLN ** G 73 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 104 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3556 r_free = 0.3556 target = 0.103208 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3238 r_free = 0.3238 target = 0.081752 restraints weight = 19125.887| |-----------------------------------------------------------------------------| r_work (start): 0.3218 rms_B_bonded: 1.24 r_work: 0.3056 rms_B_bonded: 2.53 restraints_weight: 0.5000 r_work: 0.2930 rms_B_bonded: 4.10 restraints_weight: 0.2500 r_work (final): 0.2930 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8402 moved from start: 0.1356 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.056 12911 Z= 0.193 Angle : 0.600 9.362 18690 Z= 0.357 Chirality : 0.036 0.178 2125 Planarity : 0.005 0.060 1345 Dihedral : 31.986 175.001 4069 Min Nonbonded Distance : 2.463 Molprobity Statistics. All-atom Clashscore : 7.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.74 % Favored : 98.26 % Rotamer: Outliers : 4.42 % Allowed : 29.50 % Favored : 66.09 % 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: 2.48 (0.30), residues: 749 helix: 2.22 (0.22), residues: 556 sheet: None (None), residues: 0 loop : -0.02 (0.40), 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 0.023 0.001 TYR H 83 ARG 0.015 0.001 ARG H 99 Details of bonding type rmsd hydrogen bonds : bond 0.03738 ( 799) hydrogen bonds : angle 3.07660 ( 1992) covalent geometry : bond 0.00430 (12911) covalent geometry : angle 0.60035 (18690) *********************** 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 211 residues out of total 635 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 183 time to evaluate : 0.860 Fit side-chains REVERT: A 53 ARG cc_start: 0.8736 (OUTLIER) cc_final: 0.7876 (ttp-110) REVERT: A 59 GLU cc_start: 0.9023 (pm20) cc_final: 0.8708 (pm20) REVERT: B 79 LYS cc_start: 0.9173 (OUTLIER) cc_final: 0.8602 (mtmm) REVERT: C 77 ARG cc_start: 0.8480 (OUTLIER) cc_final: 0.7361 (ttp-170) REVERT: D 76 GLU cc_start: 0.8824 (tp30) cc_final: 0.8558 (tp30) REVERT: D 93 GLU cc_start: 0.8278 (OUTLIER) cc_final: 0.7955 (mp0) REVERT: E 49 ARG cc_start: 0.8963 (OUTLIER) cc_final: 0.8019 (ptp90) REVERT: E 59 GLU cc_start: 0.8962 (pm20) cc_final: 0.8279 (pm20) REVERT: G 73 ASN cc_start: 0.8671 (t160) cc_final: 0.8192 (t0) REVERT: H 63 ASN cc_start: 0.8845 (t0) cc_final: 0.8389 (m-40) REVERT: H 116 LYS cc_start: 0.8925 (OUTLIER) cc_final: 0.8534 (ptpp) outliers start: 28 outliers final: 17 residues processed: 193 average time/residue: 1.6258 time to fit residues: 333.6155 Evaluate side-chains 201 residues out of total 635 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 178 time to evaluate : 0.893 ------------------------------------------------------------------------------- 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 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 D residue 93 GLU 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 96 THR Chi-restraints excluded: chain G residue 74 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 Chi-restraints excluded: chain H residue 116 LYS Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 102 random chunks: chunk 73 optimal weight: 0.9990 chunk 34 optimal weight: 0.9990 chunk 30 optimal weight: 2.9990 chunk 25 optimal weight: 0.9980 chunk 22 optimal weight: 0.2980 chunk 98 optimal weight: 2.9990 chunk 35 optimal weight: 0.6980 chunk 77 optimal weight: 2.9990 chunk 43 optimal weight: 0.6980 chunk 40 optimal weight: 0.0980 chunk 60 optimal weight: 0.3980 overall best weight: 0.4380 ------------------------------------------------------------------------------- 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** ** E 113 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 27 GLN ** G 73 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 104 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3564 r_free = 0.3564 target = 0.103696 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3247 r_free = 0.3247 target = 0.082274 restraints weight = 19051.112| |-----------------------------------------------------------------------------| r_work (start): 0.3226 rms_B_bonded: 1.24 r_work: 0.3064 rms_B_bonded: 2.53 restraints_weight: 0.5000 r_work: 0.2939 rms_B_bonded: 4.08 restraints_weight: 0.2500 r_work (final): 0.2939 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8393 moved from start: 0.1344 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.055 12911 Z= 0.177 Angle : 0.602 9.432 18690 Z= 0.357 Chirality : 0.036 0.190 2125 Planarity : 0.005 0.066 1345 Dihedral : 31.985 175.351 4069 Min Nonbonded Distance : 2.463 Molprobity Statistics. All-atom Clashscore : 8.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.74 % Favored : 98.26 % Rotamer: Outliers : 3.94 % Allowed : 29.97 % Favored : 66.09 % 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: 2.49 (0.30), residues: 749 helix: 2.22 (0.22), residues: 556 sheet: None (None), residues: 0 loop : -0.01 (0.41), residues: 193 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.003 0.001 HIS F 75 PHE 0.015 0.002 PHE E 67 TYR 0.025 0.001 TYR H 83 ARG 0.013 0.000 ARG H 99 Details of bonding type rmsd hydrogen bonds : bond 0.03664 ( 799) hydrogen bonds : angle 3.07604 ( 1992) covalent geometry : bond 0.00392 (12911) covalent geometry : angle 0.60169 (18690) *********************** 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 211 residues out of total 635 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 186 time to evaluate : 1.066 Fit side-chains REVERT: A 53 ARG cc_start: 0.8731 (OUTLIER) cc_final: 0.7876 (ttp-110) REVERT: A 59 GLU cc_start: 0.9019 (pm20) cc_final: 0.8701 (pm20) REVERT: A 120 MET cc_start: 0.8745 (mtt) cc_final: 0.8053 (mtt) REVERT: B 79 LYS cc_start: 0.9163 (OUTLIER) cc_final: 0.8588 (mtmm) REVERT: C 77 ARG cc_start: 0.8473 (OUTLIER) cc_final: 0.7351 (ttp-170) REVERT: D 93 GLU cc_start: 0.8273 (OUTLIER) cc_final: 0.7947 (mp0) REVERT: E 49 ARG cc_start: 0.8961 (OUTLIER) cc_final: 0.8051 (ptp90) REVERT: E 59 GLU cc_start: 0.8960 (pm20) cc_final: 0.8273 (pm20) REVERT: G 73 ASN cc_start: 0.8676 (t160) cc_final: 0.8205 (t0) REVERT: H 63 ASN cc_start: 0.8832 (t0) cc_final: 0.8390 (m-40) REVERT: H 116 LYS cc_start: 0.8918 (OUTLIER) cc_final: 0.8525 (ptpp) outliers start: 25 outliers final: 15 residues processed: 196 average time/residue: 1.7605 time to fit residues: 366.6294 Evaluate side-chains 202 residues out of total 635 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 181 time to evaluate : 0.829 ------------------------------------------------------------------------------- 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 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 D residue 93 GLU 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 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 2 optimal weight: 2.9990 chunk 7 optimal weight: 1.9990 chunk 1 optimal weight: 0.9980 chunk 50 optimal weight: 1.9990 chunk 69 optimal weight: 2.9990 chunk 45 optimal weight: 0.9990 chunk 3 optimal weight: 0.7980 chunk 74 optimal weight: 5.9990 chunk 13 optimal weight: 0.7980 chunk 23 optimal weight: 2.9990 chunk 77 optimal weight: 2.9990 overall best weight: 1.1184 ------------------------------------------------------------------------------- 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** ** E 113 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 27 GLN ** G 73 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 104 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3539 r_free = 0.3539 target = 0.102114 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3220 r_free = 0.3220 target = 0.080635 restraints weight = 18908.752| |-----------------------------------------------------------------------------| r_work (start): 0.3196 rms_B_bonded: 1.24 r_work: 0.3035 rms_B_bonded: 2.51 restraints_weight: 0.5000 r_work: 0.2908 rms_B_bonded: 4.05 restraints_weight: 0.2500 r_work (final): 0.2908 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8420 moved from start: 0.1423 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.053 12911 Z= 0.239 Angle : 0.622 10.331 18690 Z= 0.368 Chirality : 0.038 0.184 2125 Planarity : 0.005 0.051 1345 Dihedral : 32.006 174.202 4069 Min Nonbonded Distance : 2.462 Molprobity Statistics. All-atom Clashscore : 7.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.87 % Favored : 98.13 % Rotamer: Outliers : 3.94 % Allowed : 30.13 % Favored : 65.93 % 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: 2.38 (0.30), residues: 749 helix: 2.14 (0.22), residues: 556 sheet: None (None), residues: 0 loop : -0.06 (0.40), residues: 193 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.003 0.001 HIS F 75 PHE 0.015 0.002 PHE E 67 TYR 0.028 0.002 TYR H 83 ARG 0.016 0.001 ARG H 99 Details of bonding type rmsd hydrogen bonds : bond 0.04270 ( 799) hydrogen bonds : angle 3.14015 ( 1992) covalent geometry : bond 0.00539 (12911) covalent geometry : angle 0.62219 (18690) ********************** 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 206 residues out of total 635 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 181 time to evaluate : 1.114 Fit side-chains REVERT: A 53 ARG cc_start: 0.8756 (OUTLIER) cc_final: 0.7908 (ttp-110) REVERT: A 59 GLU cc_start: 0.9015 (pm20) cc_final: 0.8769 (pm20) REVERT: B 79 LYS cc_start: 0.9167 (OUTLIER) cc_final: 0.8606 (mtmm) REVERT: C 77 ARG cc_start: 0.8495 (OUTLIER) cc_final: 0.7334 (ttp-170) REVERT: D 93 GLU cc_start: 0.8288 (OUTLIER) cc_final: 0.7968 (mp0) REVERT: E 49 ARG cc_start: 0.8978 (OUTLIER) cc_final: 0.8106 (ptp90) REVERT: E 59 GLU cc_start: 0.8960 (pm20) cc_final: 0.8269 (pm20) REVERT: G 73 ASN cc_start: 0.8617 (t160) cc_final: 0.8128 (t0) REVERT: H 63 ASN cc_start: 0.8897 (t0) cc_final: 0.8443 (m-40) REVERT: H 116 LYS cc_start: 0.8925 (OUTLIER) cc_final: 0.8542 (ptpp) outliers start: 25 outliers final: 18 residues processed: 191 average time/residue: 2.4456 time to fit residues: 494.4879 Evaluate side-chains 200 residues out of total 635 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 176 time to evaluate : 0.939 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 53 ARG Chi-restraints excluded: chain A residue 64 LYS Chi-restraints excluded: chain A residue 76 GLN Chi-restraints excluded: chain A residue 77 ASP 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 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 D residue 93 GLU 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 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 3 optimal weight: 0.5980 chunk 65 optimal weight: 0.6980 chunk 22 optimal weight: 0.0670 chunk 74 optimal weight: 5.9990 chunk 36 optimal weight: 0.9990 chunk 78 optimal weight: 2.9990 chunk 62 optimal weight: 0.5980 chunk 29 optimal weight: 0.5980 chunk 72 optimal weight: 0.7980 chunk 56 optimal weight: 0.5980 chunk 1 optimal weight: 0.7980 overall best weight: 0.4918 ------------------------------------------------------------------------------- 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** ** E 113 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 27 GLN ** G 73 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 104 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3549 r_free = 0.3549 target = 0.102793 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3230 r_free = 0.3230 target = 0.081330 restraints weight = 18965.903| |-----------------------------------------------------------------------------| r_work (start): 0.3209 rms_B_bonded: 1.23 r_work: 0.3046 rms_B_bonded: 2.53 restraints_weight: 0.5000 r_work: 0.2920 rms_B_bonded: 4.07 restraints_weight: 0.2500 r_work (final): 0.2920 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8405 moved from start: 0.1406 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= 0.185 Angle : 0.617 10.134 18690 Z= 0.365 Chirality : 0.036 0.213 2125 Planarity : 0.005 0.059 1345 Dihedral : 32.040 175.050 4069 Min Nonbonded Distance : 2.543 Molprobity Statistics. All-atom Clashscore : 8.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.00 % Favored : 98.00 % Rotamer: Outliers : 3.94 % Allowed : 30.13 % Favored : 65.93 % 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: 2.45 (0.30), residues: 749 helix: 2.20 (0.22), residues: 556 sheet: None (None), residues: 0 loop : -0.06 (0.41), residues: 193 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.004 0.001 HIS F 75 PHE 0.018 0.002 PHE E 67 TYR 0.025 0.002 TYR H 83 ARG 0.014 0.001 ARG H 99 Details of bonding type rmsd hydrogen bonds : bond 0.04064 ( 799) hydrogen bonds : angle 3.12204 ( 1992) covalent geometry : bond 0.00412 (12911) covalent geometry : angle 0.61663 (18690) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 10629.52 seconds wall clock time: 191 minutes 55.97 seconds (11515.97 seconds total)