Starting phenix.real_space_refine on Tue Jun 10 08:36:05 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9k40_62036/06_2025/9k40_62036.cif Found real_map, /net/cci-nas-00/data/ceres_data/9k40_62036/06_2025/9k40_62036.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.15 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9k40_62036/06_2025/9k40_62036.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9k40_62036/06_2025/9k40_62036.map" model { file = "/net/cci-nas-00/data/ceres_data/9k40_62036/06_2025/9k40_62036.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9k40_62036/06_2025/9k40_62036.cif" } resolution = 3.15 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= 0.000 sd= 0.040 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 289 5.49 5 S 12 5.16 5 C 6575 2.51 5 N 2168 2.21 5 O 2780 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 18 residue(s): 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/chem_data/mon_lib" Total number of atoms: 11824 Number of models: 1 Model: "" Number of chains: 10 Chain: "A" Number of atoms: 783 Number of conformers: 1 Conformer: "" Number of residues, atoms: 96, 783 Classifications: {'peptide': 96} Link IDs: {'PTRANS': 3, 'TRANS': 92} Chain: "B" Number of atoms: 644 Number of conformers: 1 Conformer: "" Number of residues, atoms: 80, 644 Classifications: {'peptide': 80} Link IDs: {'PTRANS': 1, 'TRANS': 78} Chain: "C" Number of atoms: 783 Number of conformers: 1 Conformer: "" Number of residues, atoms: 104, 783 Classifications: {'peptide': 104} Link IDs: {'PTRANS': 5, 'TRANS': 98} Chain: "D" Number of atoms: 731 Number of conformers: 1 Conformer: "" Number of residues, atoms: 93, 731 Classifications: {'peptide': 93} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 3, 'TRANS': 89} Chain: "E" Number of atoms: 783 Number of conformers: 1 Conformer: "" Number of residues, atoms: 96, 783 Classifications: {'peptide': 96} Link IDs: {'PTRANS': 3, 'TRANS': 92} Chain: "F" Number of atoms: 644 Number of conformers: 1 Conformer: "" Number of residues, atoms: 80, 644 Classifications: {'peptide': 80} Link IDs: {'PTRANS': 1, 'TRANS': 78} Chain: "G" Number of atoms: 783 Number of conformers: 1 Conformer: "" Number of residues, atoms: 104, 783 Classifications: {'peptide': 104} Link IDs: {'PTRANS': 5, 'TRANS': 98} Chain: "H" Number of atoms: 731 Number of conformers: 1 Conformer: "" Number of residues, atoms: 93, 731 Classifications: {'peptide': 93} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 3, 'TRANS': 89} Chain: "I" Number of atoms: 2950 Number of conformers: 1 Conformer: "" Number of residues, atoms: 145, 2950 Classifications: {'DNA': 145} Link IDs: {'rna3p': 144} Chain: "J" Number of atoms: 2992 Number of conformers: 1 Conformer: "" Number of residues, atoms: 145, 2992 Classifications: {'DNA': 145} Modifications used: {'5*END': 1} Link IDs: {'rna3p': 144} Time building chain proxies: 8.24, per 1000 atoms: 0.70 Number of scatterers: 11824 At special positions: 0 Unit cell: (104.5, 119.9, 115.5, 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 12 16.00 P 289 15.00 O 2780 8.00 N 2168 7.00 C 6575 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: 2.66 Conformation dependent library (CDL) restraints added in 874.0 milliseconds 1460 Ramachandran restraints generated. 730 Oldfield, 0 Emsley, 730 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1396 Finding SS restraints... Secondary structure from input PDB file: 35 helices and 10 sheets defined 74.1% alpha, 2.7% beta 144 base pairs and 251 stacking pairs defined. Time for finding SS restraints: 5.45 Creating SS restraints... Processing helix chain 'A' and resid 44 through 57 removed outlier: 3.632A pdb=" N LYS A 56 " --> pdb=" O ARG A 52 " (cutoff:3.500A) removed outlier: 3.647A pdb=" N SER A 57 " --> pdb=" O LYS A 53 " (cutoff:3.500A) Processing helix chain 'A' and resid 63 through 77 removed outlier: 3.890A pdb=" N ASP A 77 " --> pdb=" O GLU A 73 " (cutoff:3.500A) 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: 3.503A pdb=" N ALA B 76 " --> pdb=" O TYR B 72 " (cutoff:3.500A) Processing helix chain 'B' and resid 82 through 93 removed outlier: 3.536A pdb=" N VAL B 86 " --> pdb=" O THR B 82 " (cutoff:3.500A) removed outlier: 3.605A pdb=" N GLN B 93 " --> pdb=" O ALA B 89 " (cutoff:3.500A) Processing helix chain 'C' and resid 17 through 22 Processing helix chain 'C' and resid 27 through 38 Processing helix chain 'C' and resid 47 through 74 Processing helix chain 'C' and resid 80 through 91 Processing helix chain 'C' and resid 91 through 98 Processing helix chain 'C' and resid 113 through 117 Processing helix chain 'D' and resid 60 through 72 Processing helix chain 'D' and resid 78 through 107 Processing helix chain 'D' and resid 113 through 125 Processing helix chain 'D' and resid 126 through 147 removed outlier: 3.715A pdb=" N SER D 147 " --> pdb=" O LYS D 143 " (cutoff:3.500A) Processing helix chain 'E' and resid 44 through 57 removed outlier: 3.570A pdb=" N LYS E 56 " --> pdb=" O ARG E 52 " (cutoff:3.500A) removed outlier: 3.576A pdb=" N SER E 57 " --> pdb=" O LYS E 53 " (cutoff:3.500A) Processing helix chain 'E' and resid 63 through 77 removed outlier: 3.832A pdb=" N ASP E 77 " --> pdb=" O GLU E 73 " (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 30 through 41 Processing helix chain 'F' and resid 49 through 76 removed outlier: 3.552A pdb=" N ALA F 76 " --> pdb=" O TYR F 72 " (cutoff:3.500A) Processing helix chain 'F' and resid 82 through 93 removed outlier: 3.541A pdb=" N VAL F 86 " --> pdb=" O THR F 82 " (cutoff:3.500A) removed outlier: 3.643A pdb=" N GLN F 93 " --> pdb=" O ALA F 89 " (cutoff:3.500A) Processing helix chain 'G' and resid 17 through 22 Processing helix chain 'G' and resid 27 through 38 Processing helix chain 'G' and resid 47 through 75 Processing helix chain 'G' and resid 80 through 91 Processing helix chain 'G' and resid 91 through 98 Processing helix chain 'G' and resid 113 through 117 Processing helix chain 'H' and resid 60 through 72 Processing helix chain 'H' and resid 78 through 107 Processing helix chain 'H' and resid 113 through 125 Processing helix chain 'H' and resid 126 through 147 Processing sheet with id=AA1, first strand: chain 'A' and resid 83 through 84 removed outlier: 7.035A 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 43 through 44 removed outlier: 6.851A pdb=" N ARG C 43 " --> pdb=" O ILE D 112 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA4 Processing sheet with id=AA5, first strand: chain 'C' and resid 78 through 79 Processing sheet with id=AA6, first strand: chain 'C' and resid 102 through 103 removed outlier: 7.092A pdb=" N THR C 102 " --> pdb=" O TYR F 98 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA6 Processing sheet with id=AA7, first strand: chain 'E' and resid 83 through 84 removed outlier: 7.035A 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 43 through 44 removed outlier: 6.985A pdb=" N ARG G 43 " --> pdb=" O ILE H 112 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA9 Processing sheet with id=AB1, first strand: chain 'G' and resid 78 through 79 408 hydrogen bonds defined for protein. 1203 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 346 hydrogen bonds 692 hydrogen bond angles 0 basepair planarities 144 basepair parallelities 251 stacking parallelities Total time for adding SS restraints: 4.35 Time building geometry restraints manager: 3.24 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: 2039 1.33 - 1.45: 4192 1.45 - 1.57: 5799 1.57 - 1.69: 577 1.69 - 1.80: 22 Bond restraints: 12629 Sorted by residual: bond pdb=" O3' DG I -26 " pdb=" P DT I -25 " ideal model delta sigma weight residual 1.607 1.657 -0.050 1.50e-02 4.44e+03 1.11e+01 bond pdb=" O3' DA J -46 " pdb=" P DA J -45 " ideal model delta sigma weight residual 1.607 1.655 -0.048 1.50e-02 4.44e+03 1.04e+01 bond pdb=" O3' DC J -24 " pdb=" P DC J -23 " ideal model delta sigma weight residual 1.607 1.654 -0.047 1.50e-02 4.44e+03 1.00e+01 bond pdb=" O3' DT J -36 " pdb=" P DG J -35 " ideal model delta sigma weight residual 1.607 1.654 -0.047 1.50e-02 4.44e+03 1.00e+01 bond pdb=" O3' DA J -49 " pdb=" P DG J -48 " ideal model delta sigma weight residual 1.607 1.644 -0.037 1.50e-02 4.44e+03 6.14e+00 ... (remaining 12624 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.43: 17597 1.43 - 2.86: 639 2.86 - 4.28: 48 4.28 - 5.71: 15 5.71 - 7.14: 4 Bond angle restraints: 18303 Sorted by residual: angle pdb=" N ASN F 25 " pdb=" CA ASN F 25 " pdb=" C ASN F 25 " ideal model delta sigma weight residual 112.92 106.83 6.09 1.23e+00 6.61e-01 2.45e+01 angle pdb=" O3' DG J -37 " pdb=" C3' DG J -37 " pdb=" C2' DG J -37 " ideal model delta sigma weight residual 111.50 105.24 6.26 1.50e+00 4.44e-01 1.74e+01 angle pdb=" N GLY D 127 " pdb=" CA GLY D 127 " pdb=" C GLY D 127 " ideal model delta sigma weight residual 111.02 118.16 -7.14 1.86e+00 2.89e-01 1.47e+01 angle pdb=" N GLY H 127 " pdb=" CA GLY H 127 " pdb=" C GLY H 127 " ideal model delta sigma weight residual 111.34 118.26 -6.92 1.82e+00 3.02e-01 1.45e+01 angle pdb=" N ILE F 26 " pdb=" CA ILE F 26 " pdb=" C ILE F 26 " ideal model delta sigma weight residual 111.09 106.72 4.37 1.25e+00 6.40e-01 1.22e+01 ... (remaining 18298 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 18.21: 4295 18.21 - 36.42: 1209 36.42 - 54.64: 1118 54.64 - 72.85: 287 72.85 - 91.06: 22 Dihedral angle restraints: 6931 sinusoidal: 4773 harmonic: 2158 Sorted by residual: dihedral pdb=" CA ASN G 69 " pdb=" CB ASN G 69 " pdb=" CG ASN G 69 " pdb=" OD1 ASN G 69 " ideal model delta sinusoidal sigma weight residual 120.00 -173.40 -66.60 2 2.00e+01 2.50e-03 1.01e+01 dihedral pdb=" CA PRO H 126 " pdb=" C PRO H 126 " pdb=" N GLY H 127 " pdb=" CA GLY H 127 " ideal model delta harmonic sigma weight residual 180.00 164.14 15.86 0 5.00e+00 4.00e-02 1.01e+01 dihedral pdb=" CA PRO D 126 " pdb=" C PRO D 126 " pdb=" N GLY D 127 " pdb=" CA GLY D 127 " ideal model delta harmonic sigma weight residual 180.00 164.51 15.49 0 5.00e+00 4.00e-02 9.60e+00 ... (remaining 6928 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.044: 1723 0.044 - 0.088: 300 0.088 - 0.132: 55 0.132 - 0.176: 10 0.176 - 0.220: 1 Chirality restraints: 2089 Sorted by residual: chirality pdb=" C3' DG J -37 " pdb=" C4' DG J -37 " pdb=" O3' DG J -37 " pdb=" C2' DG J -37 " both_signs ideal model delta sigma weight residual False -2.66 -2.88 0.22 2.00e-01 2.50e+01 1.21e+00 chirality pdb=" C3' DC J -26 " pdb=" C4' DC J -26 " pdb=" O3' DC J -26 " pdb=" C2' DC J -26 " both_signs ideal model delta sigma weight residual False -2.66 -2.83 0.17 2.00e-01 2.50e+01 7.36e-01 chirality pdb=" C3' DG J -47 " pdb=" C4' DG J -47 " pdb=" O3' DG J -47 " pdb=" C2' DG J -47 " both_signs ideal model delta sigma weight residual False -2.66 -2.82 0.16 2.00e-01 2.50e+01 6.67e-01 ... (remaining 2086 not shown) Planarity restraints: 1310 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA ASN G 74 " 0.011 2.00e-02 2.50e+03 2.18e-02 4.74e+00 pdb=" C ASN G 74 " -0.038 2.00e-02 2.50e+03 pdb=" O ASN G 74 " 0.014 2.00e-02 2.50e+03 pdb=" N LYS G 75 " 0.013 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C LEU D 125 " -0.028 5.00e-02 4.00e+02 4.23e-02 2.86e+00 pdb=" N PRO D 126 " 0.073 5.00e-02 4.00e+02 pdb=" CA PRO D 126 " -0.022 5.00e-02 4.00e+02 pdb=" CD PRO D 126 " -0.023 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C LEU H 125 " 0.027 5.00e-02 4.00e+02 4.15e-02 2.76e+00 pdb=" N PRO H 126 " -0.072 5.00e-02 4.00e+02 pdb=" CA PRO H 126 " 0.021 5.00e-02 4.00e+02 pdb=" CD PRO H 126 " 0.023 5.00e-02 4.00e+02 ... (remaining 1307 not shown) Histogram of nonbonded interaction distances: 2.22 - 2.75: 1553 2.75 - 3.29: 10323 3.29 - 3.83: 23082 3.83 - 4.36: 27355 4.36 - 4.90: 39301 Nonbonded interactions: 101614 Sorted by model distance: nonbonded pdb=" OG SER G 19 " pdb=" O PHE G 26 " model vdw 2.219 3.040 nonbonded pdb=" NH2 ARG C 33 " pdb=" OE1 GLU D 58 " model vdw 2.282 3.120 nonbonded pdb=" OD2 ASP A 106 " pdb=" NH1 ARG A 131 " model vdw 2.295 3.120 nonbonded pdb=" OD2 ASP E 106 " pdb=" NH1 ARG E 131 " model vdw 2.310 3.120 nonbonded pdb=" OG1 THR F 73 " pdb=" OD2 ASP F 85 " model vdw 2.334 3.040 ... (remaining 101609 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' } 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=0.00 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: 1.360 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: 0.440 Check model and map are aligned: 0.080 Set scattering table: 0.100 Process input model: 33.350 Find NCS groups from input model: 0.230 Set up NCS constraints: 0.050 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.690 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 38.310 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8090 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 0.050 12629 Z= 0.189 Angle : 0.606 7.139 18303 Z= 0.375 Chirality : 0.036 0.220 2089 Planarity : 0.004 0.042 1310 Dihedral : 28.829 91.058 5535 Min Nonbonded Distance : 2.219 Molprobity Statistics. All-atom Clashscore : 7.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.96 % Favored : 99.04 % Rotamer: Outliers : 0.65 % Allowed : 11.33 % Favored : 88.03 % 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: 2.72 (0.30), residues: 730 helix: 2.37 (0.22), residues: 534 sheet: None (None), residues: 0 loop : 0.25 (0.39), residues: 196 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.002 0.001 HIS D 72 PHE 0.008 0.001 PHE H 88 TYR 0.019 0.001 TYR F 98 ARG 0.006 0.001 ARG C 72 Details of bonding type rmsd hydrogen bonds : bond 0.11525 ( 754) hydrogen bonds : angle 3.89656 ( 1895) covalent geometry : bond 0.00396 (12629) covalent geometry : angle 0.60648 (18303) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1460 Ramachandran restraints generated. 730 Oldfield, 0 Emsley, 730 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1460 Ramachandran restraints generated. 730 Oldfield, 0 Emsley, 730 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 232 residues out of total 618 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 228 time to evaluate : 0.960 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 4 outliers final: 0 residues processed: 230 average time/residue: 0.2843 time to fit residues: 89.2789 Evaluate side-chains 196 residues out of total 618 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 196 time to evaluate : 0.968 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 84 optimal weight: 8.9990 chunk 75 optimal weight: 6.9990 chunk 42 optimal weight: 0.8980 chunk 25 optimal weight: 8.9990 chunk 51 optimal weight: 3.9990 chunk 40 optimal weight: 2.9990 chunk 78 optimal weight: 4.9990 chunk 30 optimal weight: 3.9990 chunk 47 optimal weight: 0.7980 chunk 58 optimal weight: 1.9990 chunk 90 optimal weight: 4.9990 overall best weight: 2.1386 ------------------------------------------------------------------------------- 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 B 93 GLN C 83 HIS D 86 ASN E 68 GLN F 75 HIS G 69 ASN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3560 r_free = 0.3560 target = 0.066996 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.2976 r_free = 0.2976 target = 0.046435 restraints weight = 49985.146| |-----------------------------------------------------------------------------| r_work (start): 0.2896 rms_B_bonded: 2.27 r_work: 0.2715 rms_B_bonded: 4.36 restraints_weight: 0.5000 r_work (final): 0.2715 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8736 moved from start: 0.1937 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.032 12629 Z= 0.218 Angle : 0.601 6.215 18303 Z= 0.363 Chirality : 0.036 0.160 2089 Planarity : 0.004 0.036 1310 Dihedral : 31.759 89.890 4071 Min Nonbonded Distance : 2.495 Molprobity Statistics. All-atom Clashscore : 6.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.10 % Favored : 98.90 % Rotamer: Outliers : 2.59 % Allowed : 15.53 % Favored : 81.88 % 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: 3.10 (0.30), residues: 730 helix: 2.71 (0.21), residues: 544 sheet: None (None), residues: 0 loop : 0.05 (0.41), residues: 186 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.005 0.001 HIS H 72 PHE 0.009 0.001 PHE E 67 TYR 0.013 0.002 TYR H 63 ARG 0.005 0.000 ARG D 122 Details of bonding type rmsd hydrogen bonds : bond 0.04936 ( 754) hydrogen bonds : angle 3.04803 ( 1895) covalent geometry : bond 0.00484 (12629) covalent geometry : angle 0.60147 (18303) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1460 Ramachandran restraints generated. 730 Oldfield, 0 Emsley, 730 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1460 Ramachandran restraints generated. 730 Oldfield, 0 Emsley, 730 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 215 residues out of total 618 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 199 time to evaluate : 0.900 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 53 LYS cc_start: 0.9466 (tttm) cc_final: 0.9233 (tttm) REVERT: A 59 GLU cc_start: 0.8489 (pt0) cc_final: 0.8226 (pm20) REVERT: A 73 GLU cc_start: 0.8997 (tp30) cc_final: 0.8790 (tp30) REVERT: A 81 ASP cc_start: 0.8647 (t0) cc_final: 0.8437 (t0) REVERT: B 84 MET cc_start: 0.9063 (mmm) cc_final: 0.8535 (mmm) REVERT: C 65 GLU cc_start: 0.8753 (tp30) cc_final: 0.8458 (tp30) REVERT: C 92 GLU cc_start: 0.9025 (tp30) cc_final: 0.8782 (tp30) REVERT: D 91 ASP cc_start: 0.9339 (t0) cc_final: 0.9132 (t0) REVERT: E 53 LYS cc_start: 0.9453 (tttm) cc_final: 0.9221 (tttm) REVERT: E 59 GLU cc_start: 0.8507 (OUTLIER) cc_final: 0.8274 (pm20) REVERT: F 84 MET cc_start: 0.8982 (mmm) cc_final: 0.8116 (mmm) REVERT: G 21 LYS cc_start: 0.9430 (mmmt) cc_final: 0.8999 (tptm) REVERT: G 91 ASP cc_start: 0.8272 (t0) cc_final: 0.7878 (t70) REVERT: H 94 GLU cc_start: 0.9043 (tp30) cc_final: 0.8689 (tp30) REVERT: H 98 GLN cc_start: 0.8995 (mm-40) cc_final: 0.8429 (mm-40) REVERT: H 102 LYS cc_start: 0.9361 (OUTLIER) cc_final: 0.9036 (mtpt) REVERT: H 128 GLU cc_start: 0.8445 (tp30) cc_final: 0.7926 (tp30) outliers start: 16 outliers final: 12 residues processed: 208 average time/residue: 0.2608 time to fit residues: 74.2821 Evaluate side-chains 204 residues out of total 618 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 190 time to evaluate : 0.836 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 80 THR Chi-restraints excluded: chain A residue 87 SER Chi-restraints excluded: chain C residue 101 VAL Chi-restraints excluded: chain D residue 86 ASN Chi-restraints excluded: chain D residue 138 THR Chi-restraints excluded: chain E residue 58 THR Chi-restraints excluded: chain E residue 59 GLU Chi-restraints excluded: chain E residue 80 THR Chi-restraints excluded: chain E residue 87 SER Chi-restraints excluded: chain F residue 96 THR Chi-restraints excluded: chain F residue 97 LEU Chi-restraints excluded: chain H residue 102 LYS Chi-restraints excluded: chain H residue 121 VAL Chi-restraints excluded: chain H residue 138 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 48 optimal weight: 2.9990 chunk 76 optimal weight: 6.9990 chunk 51 optimal weight: 2.9990 chunk 59 optimal weight: 3.9990 chunk 62 optimal weight: 5.9990 chunk 23 optimal weight: 0.6980 chunk 5 optimal weight: 0.9980 chunk 67 optimal weight: 0.9990 chunk 33 optimal weight: 0.7980 chunk 81 optimal weight: 5.9990 chunk 93 optimal weight: 4.9990 overall best weight: 1.2984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 86 ASN D 132 HIS E 68 GLN H 132 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3571 r_free = 0.3571 target = 0.067477 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.2993 r_free = 0.2993 target = 0.046764 restraints weight = 50386.748| |-----------------------------------------------------------------------------| r_work (start): 0.2910 rms_B_bonded: 2.26 r_work: 0.2727 rms_B_bonded: 4.45 restraints_weight: 0.5000 r_work (final): 0.2727 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8732 moved from start: 0.2237 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.024 12629 Z= 0.167 Angle : 0.568 6.477 18303 Z= 0.346 Chirality : 0.034 0.150 2089 Planarity : 0.004 0.040 1310 Dihedral : 31.718 88.933 4071 Min Nonbonded Distance : 2.498 Molprobity Statistics. All-atom Clashscore : 7.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.51 % Favored : 98.49 % Rotamer: Outliers : 2.59 % Allowed : 18.12 % Favored : 79.29 % 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: 3.48 (0.30), residues: 730 helix: 3.00 (0.21), residues: 542 sheet: None (None), residues: 0 loop : 0.15 (0.41), residues: 188 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.002 0.001 HIS E 39 PHE 0.006 0.001 PHE A 67 TYR 0.016 0.002 TYR F 88 ARG 0.005 0.000 ARG D 105 Details of bonding type rmsd hydrogen bonds : bond 0.04046 ( 754) hydrogen bonds : angle 2.87506 ( 1895) covalent geometry : bond 0.00365 (12629) covalent geometry : angle 0.56753 (18303) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1460 Ramachandran restraints generated. 730 Oldfield, 0 Emsley, 730 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1460 Ramachandran restraints generated. 730 Oldfield, 0 Emsley, 730 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 221 residues out of total 618 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 205 time to evaluate : 0.847 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 53 LYS cc_start: 0.9456 (tttm) cc_final: 0.9235 (tttm) REVERT: A 59 GLU cc_start: 0.8550 (OUTLIER) cc_final: 0.8262 (pm20) REVERT: A 73 GLU cc_start: 0.8982 (tp30) cc_final: 0.8773 (tp30) REVERT: A 81 ASP cc_start: 0.8733 (t0) cc_final: 0.8444 (t0) REVERT: B 84 MET cc_start: 0.9095 (mmm) cc_final: 0.8543 (mmm) REVERT: B 88 TYR cc_start: 0.9470 (m-10) cc_final: 0.8699 (m-10) REVERT: C 65 GLU cc_start: 0.8726 (tp30) cc_final: 0.8396 (tp30) REVERT: D 91 ASP cc_start: 0.9333 (t0) cc_final: 0.9118 (t0) REVERT: E 53 LYS cc_start: 0.9420 (tttm) cc_final: 0.9180 (tttm) REVERT: E 59 GLU cc_start: 0.8500 (pt0) cc_final: 0.8291 (pm20) REVERT: E 81 ASP cc_start: 0.8794 (m-30) cc_final: 0.8465 (t0) REVERT: G 21 LYS cc_start: 0.9443 (mmmt) cc_final: 0.8943 (tptm) REVERT: G 79 ILE cc_start: 0.9347 (OUTLIER) cc_final: 0.9015 (mm) REVERT: G 91 ASP cc_start: 0.8160 (t0) cc_final: 0.7817 (t70) outliers start: 16 outliers final: 10 residues processed: 210 average time/residue: 0.2772 time to fit residues: 79.2194 Evaluate side-chains 209 residues out of total 618 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 197 time to evaluate : 0.955 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 59 GLU Chi-restraints excluded: chain A residue 80 THR Chi-restraints excluded: chain A residue 87 SER Chi-restraints excluded: chain B residue 24 ASP Chi-restraints excluded: chain B residue 96 THR Chi-restraints excluded: chain B residue 97 LEU Chi-restraints excluded: chain C residue 101 VAL Chi-restraints excluded: chain E residue 58 THR Chi-restraints excluded: chain F residue 96 THR Chi-restraints excluded: chain F residue 97 LEU Chi-restraints excluded: chain G residue 39 LYS Chi-restraints excluded: chain G residue 79 ILE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 87 optimal weight: 10.0000 chunk 59 optimal weight: 3.9990 chunk 50 optimal weight: 3.9990 chunk 4 optimal weight: 0.0980 chunk 67 optimal weight: 3.9990 chunk 31 optimal weight: 3.9990 chunk 79 optimal weight: 4.9990 chunk 95 optimal weight: 5.9990 chunk 23 optimal weight: 0.4980 chunk 19 optimal weight: 0.7980 chunk 8 optimal weight: 0.5980 overall best weight: 1.1982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 68 GLN E 68 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3570 r_free = 0.3570 target = 0.067164 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.2998 r_free = 0.2998 target = 0.046692 restraints weight = 50078.326| |-----------------------------------------------------------------------------| r_work (start): 0.2918 rms_B_bonded: 2.30 r_work: 0.2739 rms_B_bonded: 4.37 restraints_weight: 0.5000 r_work (final): 0.2739 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8727 moved from start: 0.2726 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.027 12629 Z= 0.163 Angle : 0.571 6.682 18303 Z= 0.346 Chirality : 0.034 0.147 2089 Planarity : 0.004 0.039 1310 Dihedral : 31.601 89.975 4071 Min Nonbonded Distance : 2.516 Molprobity Statistics. All-atom Clashscore : 7.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.78 % Favored : 98.22 % Rotamer: Outliers : 2.10 % Allowed : 17.96 % Favored : 79.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 3.63 (0.30), residues: 730 helix: 3.13 (0.21), residues: 544 sheet: None (None), residues: 0 loop : 0.09 (0.41), residues: 186 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.003 0.001 HIS F 75 PHE 0.006 0.001 PHE A 67 TYR 0.026 0.002 TYR F 88 ARG 0.005 0.000 ARG H 122 Details of bonding type rmsd hydrogen bonds : bond 0.03907 ( 754) hydrogen bonds : angle 2.80366 ( 1895) covalent geometry : bond 0.00354 (12629) covalent geometry : angle 0.57131 (18303) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1460 Ramachandran restraints generated. 730 Oldfield, 0 Emsley, 730 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1460 Ramachandran restraints generated. 730 Oldfield, 0 Emsley, 730 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 216 residues out of total 618 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 203 time to evaluate : 0.845 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 53 LYS cc_start: 0.9485 (tttm) cc_final: 0.9258 (tttm) REVERT: A 59 GLU cc_start: 0.8609 (OUTLIER) cc_final: 0.8326 (pm20) REVERT: A 73 GLU cc_start: 0.8960 (tp30) cc_final: 0.8718 (tp30) REVERT: A 81 ASP cc_start: 0.8861 (t0) cc_final: 0.8534 (t0) REVERT: A 94 GLU cc_start: 0.9067 (mm-30) cc_final: 0.8832 (mt-10) REVERT: B 84 MET cc_start: 0.9069 (mmm) cc_final: 0.8510 (mmm) REVERT: C 65 GLU cc_start: 0.8723 (tp30) cc_final: 0.8336 (tp30) REVERT: D 91 ASP cc_start: 0.9334 (t0) cc_final: 0.9129 (t0) REVERT: D 94 GLU cc_start: 0.9160 (tp30) cc_final: 0.8412 (tp30) REVERT: D 98 GLN cc_start: 0.9250 (mm-40) cc_final: 0.8551 (mm-40) REVERT: D 143 LYS cc_start: 0.9673 (OUTLIER) cc_final: 0.9279 (tttp) REVERT: E 53 LYS cc_start: 0.9428 (tttm) cc_final: 0.9165 (tttm) REVERT: E 81 ASP cc_start: 0.8861 (m-30) cc_final: 0.8529 (t0) REVERT: E 94 GLU cc_start: 0.9106 (mm-30) cc_final: 0.8851 (mt-10) REVERT: F 84 MET cc_start: 0.9024 (mmm) cc_final: 0.8582 (mmm) REVERT: F 88 TYR cc_start: 0.9269 (m-10) cc_final: 0.8823 (m-10) REVERT: G 21 LYS cc_start: 0.9460 (mmmt) cc_final: 0.9081 (tptm) REVERT: G 91 ASP cc_start: 0.8059 (t0) cc_final: 0.7552 (t70) REVERT: G 92 GLU cc_start: 0.8937 (tp30) cc_final: 0.8712 (tp30) REVERT: G 93 GLU cc_start: 0.9277 (mp0) cc_final: 0.8952 (mp0) REVERT: H 94 GLU cc_start: 0.9205 (tp30) cc_final: 0.8519 (tp30) REVERT: H 98 GLN cc_start: 0.9237 (mm-40) cc_final: 0.8622 (mm-40) outliers start: 13 outliers final: 7 residues processed: 207 average time/residue: 0.2653 time to fit residues: 74.6972 Evaluate side-chains 202 residues out of total 618 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 193 time to evaluate : 0.846 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 59 GLU Chi-restraints excluded: chain A residue 87 SER Chi-restraints excluded: chain B residue 24 ASP Chi-restraints excluded: chain B residue 96 THR Chi-restraints excluded: chain D residue 143 LYS Chi-restraints excluded: chain E residue 118 THR Chi-restraints excluded: chain E residue 122 LYS Chi-restraints excluded: chain F residue 96 THR Chi-restraints excluded: chain F residue 97 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 92 optimal weight: 4.9990 chunk 80 optimal weight: 4.9990 chunk 41 optimal weight: 0.9980 chunk 86 optimal weight: 10.0000 chunk 45 optimal weight: 1.9990 chunk 51 optimal weight: 1.9990 chunk 49 optimal weight: 0.9990 chunk 50 optimal weight: 0.9990 chunk 79 optimal weight: 3.9990 chunk 24 optimal weight: 8.9990 chunk 10 optimal weight: 2.9990 overall best weight: 1.3988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 68 GLN G 74 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3555 r_free = 0.3555 target = 0.066337 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.2978 r_free = 0.2978 target = 0.046016 restraints weight = 50666.374| |-----------------------------------------------------------------------------| r_work (start): 0.2903 rms_B_bonded: 2.32 r_work: 0.2721 rms_B_bonded: 4.39 restraints_weight: 0.5000 r_work (final): 0.2721 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8751 moved from start: 0.3101 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.030 12629 Z= 0.171 Angle : 0.576 7.325 18303 Z= 0.348 Chirality : 0.034 0.148 2089 Planarity : 0.004 0.041 1310 Dihedral : 31.645 88.722 4071 Min Nonbonded Distance : 2.420 Molprobity Statistics. All-atom Clashscore : 7.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.78 % Favored : 98.22 % Rotamer: Outliers : 2.43 % Allowed : 18.93 % Favored : 78.64 % 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: 3.69 (0.30), residues: 730 helix: 3.19 (0.21), residues: 544 sheet: None (None), residues: 0 loop : 0.04 (0.42), residues: 186 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.003 0.001 HIS F 75 PHE 0.007 0.001 PHE H 93 TYR 0.022 0.002 TYR F 88 ARG 0.006 0.000 ARG H 122 Details of bonding type rmsd hydrogen bonds : bond 0.04066 ( 754) hydrogen bonds : angle 2.78225 ( 1895) covalent geometry : bond 0.00375 (12629) covalent geometry : angle 0.57620 (18303) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1460 Ramachandran restraints generated. 730 Oldfield, 0 Emsley, 730 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1460 Ramachandran restraints generated. 730 Oldfield, 0 Emsley, 730 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 218 residues out of total 618 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 203 time to evaluate : 0.813 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 53 LYS cc_start: 0.9494 (tttm) cc_final: 0.9272 (tttm) REVERT: A 59 GLU cc_start: 0.8613 (OUTLIER) cc_final: 0.8334 (pm20) REVERT: A 73 GLU cc_start: 0.8962 (tp30) cc_final: 0.8692 (tp30) REVERT: A 81 ASP cc_start: 0.8852 (t0) cc_final: 0.8544 (t0) REVERT: A 94 GLU cc_start: 0.9077 (mm-30) cc_final: 0.8838 (mt-10) REVERT: B 84 MET cc_start: 0.9123 (mmm) cc_final: 0.8601 (mmm) REVERT: B 88 TYR cc_start: 0.9400 (m-10) cc_final: 0.8729 (m-10) REVERT: C 65 GLU cc_start: 0.8752 (tp30) cc_final: 0.8365 (tp30) REVERT: D 91 ASP cc_start: 0.9334 (t0) cc_final: 0.9134 (t0) REVERT: D 94 GLU cc_start: 0.9182 (tp30) cc_final: 0.8588 (tp30) REVERT: D 98 GLN cc_start: 0.9284 (mm-40) cc_final: 0.8663 (mm-40) REVERT: D 143 LYS cc_start: 0.9685 (OUTLIER) cc_final: 0.9315 (tttp) REVERT: E 53 LYS cc_start: 0.9452 (tttm) cc_final: 0.9183 (tttm) REVERT: E 59 GLU cc_start: 0.8753 (pm20) cc_final: 0.8473 (pm20) REVERT: E 73 GLU cc_start: 0.8890 (tp30) cc_final: 0.8652 (tp30) REVERT: E 81 ASP cc_start: 0.8864 (m-30) cc_final: 0.8571 (t0) REVERT: E 94 GLU cc_start: 0.9072 (mm-30) cc_final: 0.8835 (mt-10) REVERT: F 84 MET cc_start: 0.9050 (mmm) cc_final: 0.8680 (mmm) REVERT: F 88 TYR cc_start: 0.9187 (m-10) cc_final: 0.8955 (m-10) REVERT: G 21 LYS cc_start: 0.9440 (mmmt) cc_final: 0.8999 (tptm) REVERT: G 74 ASN cc_start: 0.8751 (OUTLIER) cc_final: 0.8405 (t0) REVERT: G 92 GLU cc_start: 0.9015 (tp30) cc_final: 0.8794 (tp30) REVERT: H 94 GLU cc_start: 0.9208 (tp30) cc_final: 0.8540 (tp30) REVERT: H 98 GLN cc_start: 0.9354 (mm-40) cc_final: 0.8700 (mm-40) outliers start: 15 outliers final: 9 residues processed: 210 average time/residue: 0.2600 time to fit residues: 75.0931 Evaluate side-chains 207 residues out of total 618 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 195 time to evaluate : 0.907 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 59 GLU Chi-restraints excluded: chain A residue 80 THR Chi-restraints excluded: chain A residue 87 SER Chi-restraints excluded: chain B residue 24 ASP Chi-restraints excluded: chain B residue 96 THR Chi-restraints excluded: chain B residue 97 LEU Chi-restraints excluded: chain D residue 143 LYS Chi-restraints excluded: chain E residue 118 THR Chi-restraints excluded: chain F residue 96 THR Chi-restraints excluded: chain F residue 97 LEU Chi-restraints excluded: chain G residue 74 ASN Chi-restraints excluded: chain H residue 62 ILE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 23 optimal weight: 3.9990 chunk 37 optimal weight: 2.9990 chunk 11 optimal weight: 0.8980 chunk 44 optimal weight: 0.9990 chunk 82 optimal weight: 6.9990 chunk 5 optimal weight: 0.6980 chunk 28 optimal weight: 2.9990 chunk 49 optimal weight: 1.9990 chunk 16 optimal weight: 0.9990 chunk 2 optimal weight: 2.9990 chunk 94 optimal weight: 3.9990 overall best weight: 1.1186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 70 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3556 r_free = 0.3556 target = 0.066249 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.2990 r_free = 0.2990 target = 0.046080 restraints weight = 50766.156| |-----------------------------------------------------------------------------| r_work (start): 0.2918 rms_B_bonded: 2.29 r_work: 0.2738 rms_B_bonded: 4.35 restraints_weight: 0.5000 r_work (final): 0.2738 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8737 moved from start: 0.3386 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 12629 Z= 0.159 Angle : 0.575 7.449 18303 Z= 0.347 Chirality : 0.034 0.158 2089 Planarity : 0.004 0.035 1310 Dihedral : 31.529 88.600 4071 Min Nonbonded Distance : 2.497 Molprobity Statistics. All-atom Clashscore : 8.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.05 % Favored : 97.95 % Rotamer: Outliers : 2.27 % Allowed : 20.06 % Favored : 77.67 % 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: 3.69 (0.30), residues: 730 helix: 3.17 (0.21), residues: 546 sheet: None (None), residues: 0 loop : 0.08 (0.43), residues: 184 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.003 0.001 HIS D 132 PHE 0.007 0.001 PHE E 67 TYR 0.014 0.002 TYR C 51 ARG 0.006 0.000 ARG D 122 Details of bonding type rmsd hydrogen bonds : bond 0.03834 ( 754) hydrogen bonds : angle 2.76318 ( 1895) covalent geometry : bond 0.00346 (12629) covalent geometry : angle 0.57477 (18303) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1460 Ramachandran restraints generated. 730 Oldfield, 0 Emsley, 730 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1460 Ramachandran restraints generated. 730 Oldfield, 0 Emsley, 730 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 219 residues out of total 618 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 205 time to evaluate : 0.920 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 53 LYS cc_start: 0.9494 (tttm) cc_final: 0.9277 (tttm) REVERT: A 59 GLU cc_start: 0.8642 (OUTLIER) cc_final: 0.8369 (pm20) REVERT: A 73 GLU cc_start: 0.9025 (tp30) cc_final: 0.8752 (tp30) REVERT: A 81 ASP cc_start: 0.8871 (t0) cc_final: 0.8535 (t0) REVERT: A 94 GLU cc_start: 0.9062 (mm-30) cc_final: 0.8832 (mt-10) REVERT: C 65 GLU cc_start: 0.8663 (tp30) cc_final: 0.8266 (tp30) REVERT: D 94 GLU cc_start: 0.9253 (tp30) cc_final: 0.8546 (tp30) REVERT: D 98 GLN cc_start: 0.9375 (mm-40) cc_final: 0.8664 (mm-40) REVERT: D 143 LYS cc_start: 0.9685 (OUTLIER) cc_final: 0.9314 (tttp) REVERT: E 53 LYS cc_start: 0.9436 (tttm) cc_final: 0.9185 (tttm) REVERT: E 59 GLU cc_start: 0.8752 (pm20) cc_final: 0.8516 (pm20) REVERT: E 73 GLU cc_start: 0.8902 (tp30) cc_final: 0.8505 (tp30) REVERT: E 81 ASP cc_start: 0.8875 (m-30) cc_final: 0.8623 (t0) REVERT: E 94 GLU cc_start: 0.9061 (mm-30) cc_final: 0.8829 (mt-10) REVERT: F 84 MET cc_start: 0.9085 (mmm) cc_final: 0.8548 (mmm) REVERT: F 88 TYR cc_start: 0.9282 (m-10) cc_final: 0.8790 (m-10) REVERT: G 21 LYS cc_start: 0.9391 (mmmt) cc_final: 0.8927 (tptm) REVERT: G 65 GLU cc_start: 0.8774 (tp30) cc_final: 0.8567 (tp30) REVERT: G 91 ASP cc_start: 0.8216 (t70) cc_final: 0.7935 (t70) REVERT: G 93 GLU cc_start: 0.9317 (mp0) cc_final: 0.9115 (mp0) REVERT: H 94 GLU cc_start: 0.9131 (tp30) cc_final: 0.8344 (tp30) REVERT: H 98 GLN cc_start: 0.9411 (mm-40) cc_final: 0.8614 (mm-40) outliers start: 14 outliers final: 8 residues processed: 211 average time/residue: 0.2711 time to fit residues: 79.2406 Evaluate side-chains 204 residues out of total 618 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 194 time to evaluate : 1.028 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 59 GLU Chi-restraints excluded: chain A residue 80 THR Chi-restraints excluded: chain A residue 87 SER Chi-restraints excluded: chain B residue 24 ASP Chi-restraints excluded: chain B residue 96 THR Chi-restraints excluded: chain B residue 97 LEU Chi-restraints excluded: chain D residue 143 LYS Chi-restraints excluded: chain E residue 118 THR Chi-restraints excluded: chain F residue 97 LEU Chi-restraints excluded: chain H residue 62 ILE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 87 optimal weight: 10.0000 chunk 98 optimal weight: 7.9990 chunk 28 optimal weight: 0.8980 chunk 93 optimal weight: 4.9990 chunk 50 optimal weight: 0.0970 chunk 48 optimal weight: 3.9990 chunk 55 optimal weight: 0.7980 chunk 84 optimal weight: 7.9990 chunk 54 optimal weight: 3.9990 chunk 45 optimal weight: 6.9990 chunk 40 optimal weight: 0.9990 overall best weight: 1.3582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 68 GLN G 74 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3543 r_free = 0.3543 target = 0.065430 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.2973 r_free = 0.2973 target = 0.045362 restraints weight = 50544.607| |-----------------------------------------------------------------------------| r_work (start): 0.2900 rms_B_bonded: 2.27 r_work: 0.2721 rms_B_bonded: 4.28 restraints_weight: 0.5000 r_work (final): 0.2721 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8752 moved from start: 0.3595 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.031 12629 Z= 0.171 Angle : 0.591 11.417 18303 Z= 0.351 Chirality : 0.034 0.167 2089 Planarity : 0.004 0.035 1310 Dihedral : 31.604 88.596 4071 Min Nonbonded Distance : 2.454 Molprobity Statistics. All-atom Clashscore : 8.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.78 % Favored : 98.22 % Rotamer: Outliers : 2.75 % Allowed : 20.23 % Favored : 77.02 % 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: 3.62 (0.30), residues: 730 helix: 3.13 (0.21), residues: 546 sheet: None (None), residues: 0 loop : 0.02 (0.43), residues: 184 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.003 0.001 HIS F 75 PHE 0.007 0.001 PHE D 88 TYR 0.013 0.002 TYR B 88 ARG 0.007 0.000 ARG D 122 Details of bonding type rmsd hydrogen bonds : bond 0.04107 ( 754) hydrogen bonds : angle 2.84066 ( 1895) covalent geometry : bond 0.00375 (12629) covalent geometry : angle 0.59053 (18303) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1460 Ramachandran restraints generated. 730 Oldfield, 0 Emsley, 730 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1460 Ramachandran restraints generated. 730 Oldfield, 0 Emsley, 730 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 219 residues out of total 618 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 202 time to evaluate : 0.966 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 53 LYS cc_start: 0.9491 (tttm) cc_final: 0.9256 (tttm) REVERT: A 59 GLU cc_start: 0.8620 (OUTLIER) cc_final: 0.8343 (pm20) REVERT: A 73 GLU cc_start: 0.8951 (tp30) cc_final: 0.8544 (tp30) REVERT: A 81 ASP cc_start: 0.8866 (t0) cc_final: 0.8520 (t0) REVERT: A 94 GLU cc_start: 0.9049 (mm-30) cc_final: 0.8813 (mt-10) REVERT: B 84 MET cc_start: 0.9221 (mmm) cc_final: 0.8429 (mmm) REVERT: B 88 TYR cc_start: 0.9482 (m-10) cc_final: 0.8875 (m-10) REVERT: C 65 GLU cc_start: 0.8671 (tp30) cc_final: 0.8285 (tp30) REVERT: D 59 THR cc_start: 0.9310 (OUTLIER) cc_final: 0.9041 (p) REVERT: D 94 GLU cc_start: 0.9213 (tp30) cc_final: 0.8418 (tp30) REVERT: D 98 GLN cc_start: 0.9431 (mm-40) cc_final: 0.8576 (mm-40) REVERT: D 132 HIS cc_start: 0.9093 (OUTLIER) cc_final: 0.8770 (m90) REVERT: D 143 LYS cc_start: 0.9684 (OUTLIER) cc_final: 0.9311 (tttp) REVERT: E 53 LYS cc_start: 0.9445 (tttm) cc_final: 0.9177 (tttm) REVERT: E 59 GLU cc_start: 0.8719 (pm20) cc_final: 0.8432 (pm20) REVERT: E 81 ASP cc_start: 0.8861 (m-30) cc_final: 0.8617 (t0) REVERT: E 94 GLU cc_start: 0.9067 (mm-30) cc_final: 0.8829 (mt-10) REVERT: F 84 MET cc_start: 0.9157 (mmm) cc_final: 0.8564 (mmm) REVERT: F 88 TYR cc_start: 0.9369 (m-10) cc_final: 0.8797 (m-10) REVERT: G 21 LYS cc_start: 0.9392 (mmmt) cc_final: 0.8890 (tptm) REVERT: G 65 GLU cc_start: 0.8770 (tp30) cc_final: 0.8535 (tp30) REVERT: G 74 ASN cc_start: 0.8963 (OUTLIER) cc_final: 0.8590 (t0) REVERT: G 91 ASP cc_start: 0.8149 (t70) cc_final: 0.7896 (t70) REVERT: H 94 GLU cc_start: 0.9119 (tp30) cc_final: 0.8232 (tp30) REVERT: H 98 GLN cc_start: 0.9441 (mm-40) cc_final: 0.8558 (mm-40) REVERT: H 128 GLU cc_start: 0.8265 (tp30) cc_final: 0.7932 (tp30) outliers start: 17 outliers final: 11 residues processed: 211 average time/residue: 0.2832 time to fit residues: 82.8065 Evaluate side-chains 213 residues out of total 618 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 197 time to evaluate : 0.920 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 59 GLU Chi-restraints excluded: chain A residue 61 LEU Chi-restraints excluded: chain A residue 80 THR Chi-restraints excluded: chain A residue 87 SER Chi-restraints excluded: chain B residue 24 ASP Chi-restraints excluded: chain B residue 96 THR Chi-restraints excluded: chain B residue 97 LEU Chi-restraints excluded: chain C residue 101 VAL Chi-restraints excluded: chain D residue 59 THR Chi-restraints excluded: chain D residue 132 HIS Chi-restraints excluded: chain D residue 143 LYS Chi-restraints excluded: chain E residue 118 THR Chi-restraints excluded: chain F residue 97 LEU Chi-restraints excluded: chain G residue 74 ASN Chi-restraints excluded: chain H residue 57 VAL Chi-restraints excluded: chain H residue 62 ILE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 45 optimal weight: 5.9990 chunk 53 optimal weight: 10.0000 chunk 80 optimal weight: 4.9990 chunk 27 optimal weight: 5.9990 chunk 90 optimal weight: 6.9990 chunk 26 optimal weight: 2.9990 chunk 15 optimal weight: 4.9990 chunk 57 optimal weight: 4.9990 chunk 32 optimal weight: 0.9980 chunk 5 optimal weight: 0.8980 chunk 88 optimal weight: 7.9990 overall best weight: 2.9786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 39 HIS A 68 GLN E 68 GLN G 74 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3483 r_free = 0.3483 target = 0.062696 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.2885 r_free = 0.2885 target = 0.042402 restraints weight = 51498.618| |-----------------------------------------------------------------------------| r_work (start): 0.2813 rms_B_bonded: 2.30 r_work: 0.2628 rms_B_bonded: 4.30 restraints_weight: 0.5000 r_work (final): 0.2628 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8840 moved from start: 0.3893 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.039 12629 Z= 0.275 Angle : 0.654 10.099 18303 Z= 0.385 Chirality : 0.037 0.176 2089 Planarity : 0.004 0.033 1310 Dihedral : 32.161 88.290 4071 Min Nonbonded Distance : 2.491 Molprobity Statistics. All-atom Clashscore : 8.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.05 % Favored : 97.95 % Rotamer: Outliers : 2.91 % Allowed : 20.06 % Favored : 77.02 % 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: 3.36 (0.30), residues: 730 helix: 2.94 (0.21), residues: 546 sheet: None (None), residues: 0 loop : -0.06 (0.42), residues: 184 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.004 0.001 HIS B 75 PHE 0.009 0.002 PHE H 93 TYR 0.023 0.002 TYR B 88 ARG 0.007 0.001 ARG C 72 Details of bonding type rmsd hydrogen bonds : bond 0.05827 ( 754) hydrogen bonds : angle 3.22922 ( 1895) covalent geometry : bond 0.00615 (12629) covalent geometry : angle 0.65443 (18303) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1460 Ramachandran restraints generated. 730 Oldfield, 0 Emsley, 730 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1460 Ramachandran restraints generated. 730 Oldfield, 0 Emsley, 730 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 209 residues out of total 618 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 191 time to evaluate : 1.056 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 59 GLU cc_start: 0.8722 (OUTLIER) cc_final: 0.8472 (pm20) REVERT: A 76 GLN cc_start: 0.9270 (OUTLIER) cc_final: 0.9037 (pp30) REVERT: A 81 ASP cc_start: 0.8899 (t0) cc_final: 0.8585 (t0) REVERT: B 84 MET cc_start: 0.9229 (mmm) cc_final: 0.8275 (mmm) REVERT: C 65 GLU cc_start: 0.8757 (tp30) cc_final: 0.8336 (tp30) REVERT: D 94 GLU cc_start: 0.9213 (tp30) cc_final: 0.8437 (tp30) REVERT: D 98 GLN cc_start: 0.9426 (mm-40) cc_final: 0.8540 (mm-40) REVERT: D 128 GLU cc_start: 0.8648 (tp30) cc_final: 0.7993 (tp30) REVERT: D 132 HIS cc_start: 0.9154 (OUTLIER) cc_final: 0.8919 (m170) REVERT: D 136 GLU cc_start: 0.9302 (mm-30) cc_final: 0.9011 (mm-30) REVERT: D 143 LYS cc_start: 0.9680 (OUTLIER) cc_final: 0.9277 (tttp) REVERT: E 53 LYS cc_start: 0.9429 (tttm) cc_final: 0.9135 (tttm) REVERT: E 59 GLU cc_start: 0.8851 (pm20) cc_final: 0.8411 (pm20) REVERT: E 73 GLU cc_start: 0.9003 (tp30) cc_final: 0.8603 (tp30) REVERT: G 21 LYS cc_start: 0.9378 (mmmt) cc_final: 0.8843 (tptm) REVERT: G 65 GLU cc_start: 0.8783 (tp30) cc_final: 0.8571 (tp30) REVERT: G 74 ASN cc_start: 0.9188 (OUTLIER) cc_final: 0.8676 (t0) REVERT: G 93 GLU cc_start: 0.9301 (mp0) cc_final: 0.8820 (pm20) REVERT: H 56 ASN cc_start: 0.8814 (m-40) cc_final: 0.8207 (t0) REVERT: H 94 GLU cc_start: 0.9099 (tp30) cc_final: 0.8672 (tp30) REVERT: H 128 GLU cc_start: 0.8468 (tp30) cc_final: 0.8104 (tp30) outliers start: 18 outliers final: 9 residues processed: 199 average time/residue: 0.2701 time to fit residues: 73.3602 Evaluate side-chains 202 residues out of total 618 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 188 time to evaluate : 0.850 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 59 GLU Chi-restraints excluded: chain A residue 76 GLN Chi-restraints excluded: chain A residue 80 THR Chi-restraints excluded: chain B residue 24 ASP Chi-restraints excluded: chain B residue 96 THR Chi-restraints excluded: chain B residue 97 LEU Chi-restraints excluded: chain D residue 132 HIS Chi-restraints excluded: chain D residue 143 LYS Chi-restraints excluded: chain E residue 118 THR Chi-restraints excluded: chain F residue 96 THR Chi-restraints excluded: chain F residue 97 LEU Chi-restraints excluded: chain G residue 74 ASN Chi-restraints excluded: chain H residue 62 ILE Chi-restraints excluded: chain H residue 121 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 71 optimal weight: 0.9990 chunk 65 optimal weight: 3.9990 chunk 62 optimal weight: 7.9990 chunk 38 optimal weight: 1.9990 chunk 81 optimal weight: 5.9990 chunk 13 optimal weight: 0.7980 chunk 54 optimal weight: 0.9990 chunk 99 optimal weight: 10.0000 chunk 49 optimal weight: 0.6980 chunk 46 optimal weight: 1.9990 chunk 57 optimal weight: 0.8980 overall best weight: 0.8784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 68 GLN D 70 GLN E 68 GLN G 74 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3538 r_free = 0.3538 target = 0.064709 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.2965 r_free = 0.2965 target = 0.044914 restraints weight = 50873.407| |-----------------------------------------------------------------------------| r_work (start): 0.2893 rms_B_bonded: 2.33 r_work: 0.2710 rms_B_bonded: 4.37 restraints_weight: 0.5000 r_work (final): 0.2710 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8770 moved from start: 0.4028 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 12629 Z= 0.157 Angle : 0.609 10.150 18303 Z= 0.360 Chirality : 0.034 0.169 2089 Planarity : 0.004 0.035 1310 Dihedral : 31.642 88.987 4071 Min Nonbonded Distance : 2.385 Molprobity Statistics. All-atom Clashscore : 8.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.05 % Favored : 97.95 % Rotamer: Outliers : 2.10 % Allowed : 22.17 % Favored : 75.73 % 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: 3.51 (0.30), residues: 730 helix: 3.09 (0.21), residues: 544 sheet: None (None), residues: 0 loop : -0.11 (0.42), residues: 186 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.002 0.001 HIS B 75 PHE 0.007 0.001 PHE A 67 TYR 0.015 0.002 TYR F 88 ARG 0.006 0.000 ARG H 122 Details of bonding type rmsd hydrogen bonds : bond 0.03759 ( 754) hydrogen bonds : angle 2.85208 ( 1895) covalent geometry : bond 0.00341 (12629) covalent geometry : angle 0.60934 (18303) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1460 Ramachandran restraints generated. 730 Oldfield, 0 Emsley, 730 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1460 Ramachandran restraints generated. 730 Oldfield, 0 Emsley, 730 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 216 residues out of total 618 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 203 time to evaluate : 0.860 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 59 GLU cc_start: 0.8672 (OUTLIER) cc_final: 0.8387 (pm20) REVERT: A 73 GLU cc_start: 0.8972 (tp30) cc_final: 0.8768 (tp30) REVERT: A 76 GLN cc_start: 0.9213 (OUTLIER) cc_final: 0.8997 (pp30) REVERT: A 81 ASP cc_start: 0.8943 (t0) cc_final: 0.8627 (t0) REVERT: B 84 MET cc_start: 0.9100 (mmm) cc_final: 0.8539 (mmm) REVERT: B 88 TYR cc_start: 0.9402 (m-10) cc_final: 0.8969 (m-10) REVERT: C 65 GLU cc_start: 0.8661 (tp30) cc_final: 0.8232 (tp30) REVERT: D 94 GLU cc_start: 0.9191 (tp30) cc_final: 0.8357 (tp30) REVERT: D 98 GLN cc_start: 0.9424 (mm-40) cc_final: 0.8486 (mm-40) REVERT: D 128 GLU cc_start: 0.8306 (tp30) cc_final: 0.7332 (tp30) REVERT: D 132 HIS cc_start: 0.9098 (OUTLIER) cc_final: 0.8646 (m170) REVERT: D 136 GLU cc_start: 0.9299 (mm-30) cc_final: 0.9008 (mm-30) REVERT: D 143 LYS cc_start: 0.9677 (OUTLIER) cc_final: 0.9302 (tttp) REVERT: E 53 LYS cc_start: 0.9471 (tttm) cc_final: 0.9223 (tttm) REVERT: E 59 GLU cc_start: 0.8755 (pm20) cc_final: 0.8402 (pm20) REVERT: E 94 GLU cc_start: 0.9078 (mm-30) cc_final: 0.8855 (mt-10) REVERT: F 84 MET cc_start: 0.9082 (mmm) cc_final: 0.8863 (mmm) REVERT: F 88 TYR cc_start: 0.9255 (m-10) cc_final: 0.8953 (m-10) REVERT: G 21 LYS cc_start: 0.9396 (mmmt) cc_final: 0.8892 (tptm) REVERT: G 65 GLU cc_start: 0.8766 (tp30) cc_final: 0.8519 (tp30) REVERT: G 74 ASN cc_start: 0.9078 (OUTLIER) cc_final: 0.8421 (t0) REVERT: G 91 ASP cc_start: 0.8312 (t70) cc_final: 0.7454 (t70) REVERT: G 93 GLU cc_start: 0.9259 (mp0) cc_final: 0.8716 (pm20) REVERT: H 94 GLU cc_start: 0.9084 (tp30) cc_final: 0.8160 (tp30) REVERT: H 98 GLN cc_start: 0.9407 (mm-40) cc_final: 0.8401 (mm-40) REVERT: H 128 GLU cc_start: 0.8302 (tp30) cc_final: 0.7953 (tp30) outliers start: 13 outliers final: 6 residues processed: 210 average time/residue: 0.2612 time to fit residues: 75.4861 Evaluate side-chains 212 residues out of total 618 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 201 time to evaluate : 0.846 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 59 GLU Chi-restraints excluded: chain A residue 76 GLN Chi-restraints excluded: chain A residue 80 THR Chi-restraints excluded: chain B residue 24 ASP Chi-restraints excluded: chain B residue 96 THR Chi-restraints excluded: chain B residue 97 LEU Chi-restraints excluded: chain D residue 132 HIS Chi-restraints excluded: chain D residue 143 LYS Chi-restraints excluded: chain F residue 97 LEU Chi-restraints excluded: chain G residue 74 ASN Chi-restraints excluded: chain H residue 62 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 40 optimal weight: 0.0980 chunk 28 optimal weight: 0.9990 chunk 33 optimal weight: 0.8980 chunk 19 optimal weight: 4.9990 chunk 3 optimal weight: 0.8980 chunk 13 optimal weight: 2.9990 chunk 6 optimal weight: 0.9980 chunk 32 optimal weight: 6.9990 chunk 29 optimal weight: 9.9990 chunk 62 optimal weight: 10.0000 chunk 45 optimal weight: 1.9990 overall best weight: 0.7782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 68 GLN E 68 GLN G 74 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3556 r_free = 0.3556 target = 0.065458 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.2991 r_free = 0.2991 target = 0.045607 restraints weight = 50442.193| |-----------------------------------------------------------------------------| r_work (start): 0.2914 rms_B_bonded: 2.34 r_work: 0.2730 rms_B_bonded: 4.42 restraints_weight: 0.5000 r_work (final): 0.2730 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8756 moved from start: 0.4243 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 12629 Z= 0.153 Angle : 0.613 12.692 18303 Z= 0.359 Chirality : 0.034 0.177 2089 Planarity : 0.004 0.034 1310 Dihedral : 31.528 88.302 4071 Min Nonbonded Distance : 2.449 Molprobity Statistics. All-atom Clashscore : 8.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.19 % Favored : 97.81 % Rotamer: Outliers : 2.10 % Allowed : 23.46 % Favored : 74.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: 3.47 (0.31), residues: 730 helix: 3.06 (0.21), residues: 546 sheet: None (None), residues: 0 loop : -0.15 (0.42), residues: 184 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.003 0.001 HIS B 75 PHE 0.007 0.001 PHE A 67 TYR 0.016 0.002 TYR F 88 ARG 0.009 0.000 ARG H 122 Details of bonding type rmsd hydrogen bonds : bond 0.03761 ( 754) hydrogen bonds : angle 2.84984 ( 1895) covalent geometry : bond 0.00332 (12629) covalent geometry : angle 0.61264 (18303) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1460 Ramachandran restraints generated. 730 Oldfield, 0 Emsley, 730 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1460 Ramachandran restraints generated. 730 Oldfield, 0 Emsley, 730 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 223 residues out of total 618 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 210 time to evaluate : 0.831 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 59 GLU cc_start: 0.8676 (OUTLIER) cc_final: 0.8400 (pm20) REVERT: A 76 GLN cc_start: 0.9226 (OUTLIER) cc_final: 0.9007 (pp30) REVERT: A 81 ASP cc_start: 0.8906 (t0) cc_final: 0.8619 (t0) REVERT: B 84 MET cc_start: 0.9120 (mmm) cc_final: 0.8510 (mmm) REVERT: B 88 TYR cc_start: 0.9421 (m-10) cc_final: 0.8967 (m-10) REVERT: C 65 GLU cc_start: 0.8634 (tp30) cc_final: 0.8218 (tp30) REVERT: C 93 GLU cc_start: 0.9086 (mm-30) cc_final: 0.8841 (mp0) REVERT: D 58 GLU cc_start: 0.8554 (tp30) cc_final: 0.8280 (tp30) REVERT: D 94 GLU cc_start: 0.9203 (tp30) cc_final: 0.8353 (tp30) REVERT: D 98 GLN cc_start: 0.9426 (mm-40) cc_final: 0.8434 (mm-40) REVERT: D 128 GLU cc_start: 0.8266 (tp30) cc_final: 0.6996 (tp30) REVERT: D 132 HIS cc_start: 0.9062 (OUTLIER) cc_final: 0.8573 (m170) REVERT: D 136 GLU cc_start: 0.9289 (mm-30) cc_final: 0.9008 (mm-30) REVERT: D 143 LYS cc_start: 0.9678 (OUTLIER) cc_final: 0.9425 (tttm) REVERT: E 53 LYS cc_start: 0.9472 (tttm) cc_final: 0.9230 (tttm) REVERT: E 59 GLU cc_start: 0.8763 (pm20) cc_final: 0.8473 (pm20) REVERT: E 73 GLU cc_start: 0.9008 (tp30) cc_final: 0.8627 (tp30) REVERT: E 94 GLU cc_start: 0.9065 (mm-30) cc_final: 0.8858 (mt-10) REVERT: G 21 LYS cc_start: 0.9373 (mmmt) cc_final: 0.8872 (tptm) REVERT: G 65 GLU cc_start: 0.8668 (tp30) cc_final: 0.8381 (tp30) REVERT: G 74 ASN cc_start: 0.8854 (OUTLIER) cc_final: 0.8408 (t0) REVERT: G 75 LYS cc_start: 0.9245 (mtmm) cc_final: 0.9042 (mtmm) REVERT: G 91 ASP cc_start: 0.8281 (t70) cc_final: 0.7391 (t70) REVERT: G 93 GLU cc_start: 0.9253 (mp0) cc_final: 0.8692 (pm20) REVERT: H 56 ASN cc_start: 0.8969 (m-40) cc_final: 0.8412 (t0) REVERT: H 94 GLU cc_start: 0.9111 (tp30) cc_final: 0.8414 (tp30) REVERT: H 98 GLN cc_start: 0.9396 (mm-40) cc_final: 0.8717 (mm-40) REVERT: H 106 TYR cc_start: 0.8249 (m-10) cc_final: 0.7810 (m-10) REVERT: H 128 GLU cc_start: 0.8252 (tp30) cc_final: 0.7888 (tp30) outliers start: 13 outliers final: 6 residues processed: 216 average time/residue: 0.2714 time to fit residues: 80.4257 Evaluate side-chains 215 residues out of total 618 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 204 time to evaluate : 0.804 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 59 GLU Chi-restraints excluded: chain A residue 76 GLN Chi-restraints excluded: chain A residue 80 THR Chi-restraints excluded: chain B residue 24 ASP Chi-restraints excluded: chain B residue 96 THR Chi-restraints excluded: chain B residue 97 LEU Chi-restraints excluded: chain D residue 132 HIS Chi-restraints excluded: chain D residue 143 LYS Chi-restraints excluded: chain F residue 97 LEU Chi-restraints excluded: chain G residue 74 ASN Chi-restraints excluded: chain H residue 62 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 5 optimal weight: 4.9990 chunk 10 optimal weight: 2.9990 chunk 0 optimal weight: 9.9990 chunk 97 optimal weight: 5.9990 chunk 49 optimal weight: 4.9990 chunk 85 optimal weight: 10.0000 chunk 90 optimal weight: 6.9990 chunk 63 optimal weight: 0.9980 chunk 37 optimal weight: 5.9990 chunk 66 optimal weight: 1.9990 chunk 84 optimal weight: 6.9990 overall best weight: 3.1988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 55 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 68 GLN E 68 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3485 r_free = 0.3485 target = 0.062624 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.2890 r_free = 0.2890 target = 0.042351 restraints weight = 51121.255| |-----------------------------------------------------------------------------| r_work (start): 0.2815 rms_B_bonded: 2.32 r_work: 0.2631 rms_B_bonded: 4.31 restraints_weight: 0.5000 r_work (final): 0.2631 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8841 moved from start: 0.4267 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.036 12629 Z= 0.281 Angle : 0.658 12.539 18303 Z= 0.387 Chirality : 0.037 0.181 2089 Planarity : 0.004 0.035 1310 Dihedral : 32.067 89.345 4071 Min Nonbonded Distance : 2.441 Molprobity Statistics. All-atom Clashscore : 8.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.05 % Favored : 97.95 % Rotamer: Outliers : 2.59 % Allowed : 22.82 % Favored : 74.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 3.20 (0.30), residues: 730 helix: 2.86 (0.21), residues: 548 sheet: None (None), residues: 0 loop : -0.32 (0.42), residues: 182 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.004 0.001 HIS F 75 PHE 0.009 0.002 PHE H 93 TYR 0.041 0.003 TYR F 88 ARG 0.007 0.001 ARG H 122 Details of bonding type rmsd hydrogen bonds : bond 0.05687 ( 754) hydrogen bonds : angle 3.26090 ( 1895) covalent geometry : bond 0.00631 (12629) covalent geometry : angle 0.65796 (18303) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5859.65 seconds wall clock time: 100 minutes 40.61 seconds (6040.61 seconds total)