Starting phenix.real_space_refine on Wed May 14 09:28:38 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8g86_29837/05_2025/8g86_29837.cif Found real_map, /net/cci-nas-00/data/ceres_data/8g86_29837/05_2025/8g86_29837.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.3 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8g86_29837/05_2025/8g86_29837.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8g86_29837/05_2025/8g86_29837.map" model { file = "/net/cci-nas-00/data/ceres_data/8g86_29837/05_2025/8g86_29837.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8g86_29837/05_2025/8g86_29837.cif" } resolution = 2.3 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= 0.002 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 290 5.49 5 S 12 5.16 5 C 6637 2.51 5 N 2229 2.21 5 O 2804 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 16 residue(s): 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/chem_data/mon_lib" Total number of atoms: 11972 Number of models: 1 Model: "" Number of chains: 10 Chain: "A" Number of atoms: 802 Number of conformers: 1 Conformer: "" Number of residues, atoms: 97, 802 Classifications: {'peptide': 97} Link IDs: {'PTRANS': 3, 'TRANS': 93} Chain: "B" Number of atoms: 646 Number of conformers: 1 Conformer: "" Number of residues, atoms: 81, 646 Classifications: {'peptide': 81} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 79} Chain: "C" Number of atoms: 834 Number of conformers: 1 Conformer: "" Number of residues, atoms: 108, 834 Classifications: {'peptide': 108} Link IDs: {'PTRANS': 5, 'TRANS': 102} Chain: "D" Number of atoms: 736 Number of conformers: 1 Conformer: "" Number of residues, atoms: 94, 736 Classifications: {'peptide': 94} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 2, 'TRANS': 91} Chain: "E" Number of atoms: 791 Number of conformers: 1 Conformer: "" Number of residues, atoms: 96, 791 Classifications: {'peptide': 96} Link IDs: {'PTRANS': 3, 'TRANS': 92} Chain: "F" Number of atoms: 648 Number of conformers: 1 Conformer: "" Number of residues, atoms: 81, 648 Classifications: {'peptide': 81} Link IDs: {'PTRANS': 1, 'TRANS': 79} Chain: "G" Number of atoms: 834 Number of conformers: 1 Conformer: "" Number of residues, atoms: 108, 834 Classifications: {'peptide': 108} Link IDs: {'PTRANS': 5, 'TRANS': 102} Chain: "H" Number of atoms: 736 Number of conformers: 1 Conformer: "" Number of residues, atoms: 94, 736 Classifications: {'peptide': 94} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 2, 'TRANS': 91} 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: 2995 Number of conformers: 1 Conformer: "" Number of residues, atoms: 145, 2995 Classifications: {'DNA': 145} Link IDs: {'rna3p': 144} Time building chain proxies: 7.73, per 1000 atoms: 0.65 Number of scatterers: 11972 At special positions: 0 Unit cell: (74.865, 116.725, 114.31, 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 290 15.00 O 2804 8.00 N 2229 7.00 C 6637 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: 2.75 Conformation dependent library (CDL) restraints added in 892.4 milliseconds 1486 Ramachandran restraints generated. 743 Oldfield, 0 Emsley, 743 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1424 Finding SS restraints... Secondary structure from input PDB file: 36 helices and 10 sheets defined 73.4% alpha, 2.9% beta 134 base pairs and 275 stacking pairs defined. Time for finding SS restraints: 6.30 Creating SS restraints... Processing helix chain 'A' and resid 44 through 57 Processing helix chain 'A' and resid 63 through 77 removed outlier: 4.145A 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 25 through 29 Processing helix chain 'B' and resid 30 through 41 Processing helix chain 'B' and resid 49 through 76 Processing helix chain 'B' and resid 82 through 93 Processing helix chain 'C' and resid 16 through 22 Processing helix chain 'C' and resid 26 through 36 Processing helix chain 'C' and resid 45 through 73 removed outlier: 4.236A 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 34 through 46 Processing helix chain 'D' and resid 52 through 81 Processing helix chain 'D' and resid 87 through 99 Processing helix chain 'D' and resid 100 through 122 Processing helix chain 'E' and resid 44 through 55 Processing helix chain 'E' and resid 63 through 76 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 removed outlier: 3.829A pdb=" N GLN F 27 " --> pdb=" O ASP F 24 " (cutoff:3.500A) Processing helix chain 'F' and resid 30 through 41 Processing helix chain 'F' and resid 49 through 76 Processing helix chain 'F' and resid 82 through 93 Processing helix chain 'G' and resid 16 through 21 Processing helix chain 'G' and resid 26 through 37 Processing helix chain 'G' and resid 45 through 73 removed outlier: 4.387A 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 34 through 46 Processing helix chain 'H' and resid 52 through 81 Processing helix chain 'H' and resid 87 through 99 Processing helix chain 'H' and resid 100 through 121 Processing sheet with id=AA1, first strand: chain 'A' and resid 83 through 84 removed outlier: 7.003A 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 96 through 98 removed outlier: 6.691A pdb=" N THR B 96 " --> pdb=" O THR G 101 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA3 Processing sheet with id=AA4, first strand: chain 'C' and resid 42 through 43 removed outlier: 7.144A pdb=" N ARG C 42 " --> pdb=" O ILE D 86 " (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 101 through 102 removed outlier: 6.769A pdb=" N THR C 101 " --> 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: 6.764A 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: 7.057A pdb=" N ARG G 42 " --> pdb=" O ILE H 86 " (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 78 417 hydrogen bonds defined for protein. 1227 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 319 hydrogen bonds 634 hydrogen bond angles 0 basepair planarities 134 basepair parallelities 275 stacking parallelities Total time for adding SS restraints: 4.57 Time building geometry restraints manager: 3.28 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.33: 2227 1.33 - 1.45: 4184 1.45 - 1.57: 5764 1.57 - 1.69: 578 1.69 - 1.81: 22 Bond restraints: 12775 Sorted by residual: bond pdb=" C3' DT I 20 " pdb=" O3' DT I 20 " ideal model delta sigma weight residual 1.422 1.460 -0.038 3.00e-02 1.11e+03 1.62e+00 bond pdb=" C3' DT J 41 " pdb=" C2' DT J 41 " ideal model delta sigma weight residual 1.525 1.543 -0.018 2.00e-02 2.50e+03 8.20e-01 bond pdb=" C3' DC I 52 " pdb=" O3' DC I 52 " ideal model delta sigma weight residual 1.422 1.449 -0.027 3.00e-02 1.11e+03 8.07e-01 bond pdb=" C3' DC I -22 " pdb=" C2' DC I -22 " ideal model delta sigma weight residual 1.525 1.543 -0.018 2.00e-02 2.50e+03 8.00e-01 bond pdb=" C3' DG I 68 " pdb=" C2' DG I 68 " ideal model delta sigma weight residual 1.525 1.543 -0.018 2.00e-02 2.50e+03 7.94e-01 ... (remaining 12770 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.41: 17993 1.41 - 2.83: 482 2.83 - 4.24: 14 4.24 - 5.65: 6 5.65 - 7.06: 3 Bond angle restraints: 18498 Sorted by residual: angle pdb=" N GLY D 101 " pdb=" CA GLY D 101 " pdb=" C GLY D 101 " ideal model delta sigma weight residual 113.18 118.43 -5.25 2.37e+00 1.78e-01 4.91e+00 angle pdb=" CA LEU F 22 " pdb=" CB LEU F 22 " pdb=" CG LEU F 22 " ideal model delta sigma weight residual 116.30 123.36 -7.06 3.50e+00 8.16e-02 4.07e+00 angle pdb=" N GLY H 101 " pdb=" CA GLY H 101 " pdb=" C GLY H 101 " ideal model delta sigma weight residual 113.18 117.81 -4.63 2.37e+00 1.78e-01 3.82e+00 angle pdb=" C3' DA I 29 " pdb=" C2' DA I 29 " pdb=" C1' DA I 29 " ideal model delta sigma weight residual 101.60 104.30 -2.70 1.50e+00 4.44e-01 3.24e+00 angle pdb=" C3' DT I 20 " pdb=" O3' DT I 20 " pdb=" P DG I 21 " ideal model delta sigma weight residual 120.20 122.87 -2.67 1.50e+00 4.44e-01 3.17e+00 ... (remaining 18493 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.88: 5664 35.88 - 71.77: 1344 71.77 - 107.65: 13 107.65 - 143.53: 0 143.53 - 179.41: 1 Dihedral angle restraints: 7022 sinusoidal: 4817 harmonic: 2205 Sorted by residual: dihedral pdb=" C4' DT I 20 " pdb=" C3' DT I 20 " pdb=" O3' DT I 20 " pdb=" P DG I 21 " ideal model delta sinusoidal sigma weight residual -140.00 39.41 -179.41 1 3.50e+01 8.16e-04 1.57e+01 dihedral pdb=" CA ASP A 77 " pdb=" CB ASP A 77 " pdb=" CG ASP A 77 " pdb=" OD1 ASP A 77 " ideal model delta sinusoidal sigma weight residual -30.00 -88.37 58.37 1 2.00e+01 2.50e-03 1.14e+01 dihedral pdb=" CB GLU F 74 " pdb=" CG GLU F 74 " pdb=" CD GLU F 74 " pdb=" OE1 GLU F 74 " ideal model delta sinusoidal sigma weight residual 0.00 -88.78 88.78 1 3.00e+01 1.11e-03 1.04e+01 ... (remaining 7019 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.026: 1457 0.026 - 0.052: 505 0.052 - 0.078: 103 0.078 - 0.104: 24 0.104 - 0.130: 20 Chirality restraints: 2109 Sorted by residual: chirality pdb=" CA ILE B 29 " pdb=" N ILE B 29 " pdb=" C ILE B 29 " pdb=" CB ILE B 29 " both_signs ideal model delta sigma weight residual False 2.43 2.56 -0.13 2.00e-01 2.50e+01 4.21e-01 chirality pdb=" CA ILE A 62 " pdb=" N ILE A 62 " pdb=" C ILE A 62 " pdb=" CB ILE A 62 " both_signs ideal model delta sigma weight residual False 2.43 2.56 -0.13 2.00e-01 2.50e+01 4.02e-01 chirality pdb=" CA ILE F 29 " pdb=" N ILE F 29 " pdb=" C ILE F 29 " pdb=" CB ILE F 29 " both_signs ideal model delta sigma weight residual False 2.43 2.56 -0.12 2.00e-01 2.50e+01 3.88e-01 ... (remaining 2106 not shown) Planarity restraints: 1335 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ILE G 79 " 0.031 5.00e-02 4.00e+02 4.72e-02 3.57e+00 pdb=" N PRO G 80 " -0.082 5.00e-02 4.00e+02 pdb=" CA PRO G 80 " 0.024 5.00e-02 4.00e+02 pdb=" CD PRO G 80 " 0.026 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ILE C 79 " 0.030 5.00e-02 4.00e+02 4.52e-02 3.27e+00 pdb=" N PRO C 80 " -0.078 5.00e-02 4.00e+02 pdb=" CA PRO C 80 " 0.023 5.00e-02 4.00e+02 pdb=" CD PRO C 80 " 0.025 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C LEU A 65 " 0.022 5.00e-02 4.00e+02 3.38e-02 1.82e+00 pdb=" N PRO A 66 " -0.058 5.00e-02 4.00e+02 pdb=" CA PRO A 66 " 0.017 5.00e-02 4.00e+02 pdb=" CD PRO A 66 " 0.019 5.00e-02 4.00e+02 ... (remaining 1332 not shown) Histogram of nonbonded interaction distances: 2.29 - 2.81: 2611 2.81 - 3.33: 10262 3.33 - 3.85: 24101 3.85 - 4.38: 30291 4.38 - 4.90: 40295 Nonbonded interactions: 107560 Sorted by model distance: nonbonded pdb=" OG SER C 18 " pdb=" O PHE C 25 " model vdw 2.287 3.040 nonbonded pdb=" NH1 ARG E 72 " pdb=" OP1 DT J -23 " model vdw 2.328 3.120 nonbonded pdb=" NH2 ARG C 20 " pdb=" OP1 DC I -42 " model vdw 2.386 3.120 nonbonded pdb=" O2 DC I -42 " pdb=" N2 DG J 42 " model vdw 2.395 3.120 nonbonded pdb=" O2 DC I -51 " pdb=" N2 DG J 51 " model vdw 2.425 2.496 ... (remaining 107555 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' and resid 38 through 133) selection = chain 'E' } ncs_group { reference = (chain 'B' and resid 22 through 101) selection = (chain 'F' and resid 22 through 101) } 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=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: 2.630 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: 0.090 Set scattering table: 0.110 Process input model: 33.570 Find NCS groups from input model: 0.250 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: 0.010 Load rotamer database and sin/cos tables:11.820 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 48.980 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8034 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 : 0.003 0.038 12775 Z= 0.153 Angle : 0.502 7.065 18498 Z= 0.305 Chirality : 0.029 0.130 2109 Planarity : 0.003 0.047 1335 Dihedral : 27.264 179.413 5598 Min Nonbonded Distance : 2.287 Molprobity Statistics. All-atom Clashscore : 6.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.94 % Favored : 99.06 % Rotamer: Outliers : 0.95 % Allowed : 16.30 % Favored : 82.75 % 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: 1.60 (0.28), residues: 743 helix: 1.47 (0.20), residues: 551 sheet: None (None), residues: 0 loop : 0.04 (0.39), residues: 192 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.004 0.001 HIS B 75 PHE 0.008 0.001 PHE E 67 TYR 0.010 0.001 TYR B 51 ARG 0.003 0.000 ARG H 83 Details of bonding type rmsd hydrogen bonds : bond 0.23805 ( 736) hydrogen bonds : angle 8.65357 ( 1861) covalent geometry : bond 0.00326 (12775) covalent geometry : angle 0.50160 (18498) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1486 Ramachandran restraints generated. 743 Oldfield, 0 Emsley, 743 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1486 Ramachandran restraints generated. 743 Oldfield, 0 Emsley, 743 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 166 residues out of total 632 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 160 time to evaluate : 0.884 Fit side-chains REVERT: A 40 ARG cc_start: 0.8006 (mtp85) cc_final: 0.7789 (mtp85) REVERT: A 120 MET cc_start: 0.8545 (mtt) cc_final: 0.8326 (mtp) REVERT: B 79 LYS cc_start: 0.8392 (mtpt) cc_final: 0.8095 (mtmm) REVERT: C 110 ASN cc_start: 0.8575 (t0) cc_final: 0.8350 (t0) REVERT: D 73 GLU cc_start: 0.8617 (tp30) cc_final: 0.8383 (tp30) REVERT: D 113 LYS cc_start: 0.8106 (ttmp) cc_final: 0.7756 (ttpp) REVERT: E 59 GLU cc_start: 0.8053 (pm20) cc_final: 0.7844 (pm20) REVERT: F 27 GLN cc_start: 0.8276 (mm110) cc_final: 0.7981 (mm110) REVERT: G 15 LYS cc_start: 0.7400 (mtpt) cc_final: 0.6751 (tttt) REVERT: G 71 ARG cc_start: 0.7091 (ttp-110) cc_final: 0.6668 (ttm-80) REVERT: G 75 LYS cc_start: 0.8044 (mmtm) cc_final: 0.7803 (mmtp) REVERT: H 54 LYS cc_start: 0.8614 (tptt) cc_final: 0.8385 (mmmm) outliers start: 6 outliers final: 2 residues processed: 163 average time/residue: 1.8613 time to fit residues: 319.1723 Evaluate side-chains 142 residues out of total 632 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 140 time to evaluate : 0.795 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 46 VAL Chi-restraints excluded: chain A residue 118 THR Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 84 optimal weight: 7.9990 chunk 75 optimal weight: 5.9990 chunk 42 optimal weight: 2.9990 chunk 25 optimal weight: 0.9980 chunk 51 optimal weight: 5.9990 chunk 40 optimal weight: 0.6980 chunk 78 optimal weight: 3.9990 chunk 30 optimal weight: 3.9990 chunk 47 optimal weight: 6.9990 chunk 58 optimal weight: 0.9990 chunk 90 optimal weight: 5.9990 overall best weight: 1.9386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 76 GLN C 104 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4088 r_free = 0.4088 target = 0.176328 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3604 r_free = 0.3604 target = 0.134643 restraints weight = 10508.711| |-----------------------------------------------------------------------------| r_work (start): 0.3574 rms_B_bonded: 0.92 r_work: 0.3376 rms_B_bonded: 2.24 restraints_weight: 0.5000 r_work: 0.3232 rms_B_bonded: 3.58 restraints_weight: 0.2500 r_work (final): 0.3232 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8218 moved from start: 0.2581 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.052 12775 Z= 0.223 Angle : 0.628 8.107 18498 Z= 0.376 Chirality : 0.037 0.148 2109 Planarity : 0.005 0.042 1335 Dihedral : 30.866 178.974 4097 Min Nonbonded Distance : 2.131 Molprobity Statistics. All-atom Clashscore : 6.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.35 % Favored : 98.65 % Rotamer: Outliers : 4.27 % Allowed : 15.66 % Favored : 80.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.44 (0.29), residues: 743 helix: 2.18 (0.21), residues: 557 sheet: None (None), residues: 0 loop : -0.09 (0.39), residues: 186 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.006 0.001 HIS B 75 PHE 0.013 0.002 PHE A 67 TYR 0.014 0.002 TYR B 51 ARG 0.006 0.001 ARG E 42 Details of bonding type rmsd hydrogen bonds : bond 0.06343 ( 736) hydrogen bonds : angle 3.18374 ( 1861) covalent geometry : bond 0.00492 (12775) covalent geometry : angle 0.62837 (18498) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1486 Ramachandran restraints generated. 743 Oldfield, 0 Emsley, 743 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1486 Ramachandran restraints generated. 743 Oldfield, 0 Emsley, 743 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 181 residues out of total 632 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 154 time to evaluate : 0.940 Fit side-chains REVERT: A 59 GLU cc_start: 0.8542 (pm20) cc_final: 0.8331 (pm20) REVERT: A 131 ARG cc_start: 0.8485 (OUTLIER) cc_final: 0.7463 (mtp180) REVERT: B 79 LYS cc_start: 0.8784 (mtpt) cc_final: 0.8416 (mtmm) REVERT: C 36 LYS cc_start: 0.8544 (mmtm) cc_final: 0.8258 (mmpt) REVERT: D 102 GLU cc_start: 0.7776 (OUTLIER) cc_final: 0.7436 (tp30) REVERT: D 113 LYS cc_start: 0.8552 (OUTLIER) cc_final: 0.7970 (tttm) REVERT: E 59 GLU cc_start: 0.8498 (pm20) cc_final: 0.8181 (pm20) REVERT: F 27 GLN cc_start: 0.8549 (mm110) cc_final: 0.8239 (mm110) REVERT: F 77 LYS cc_start: 0.8519 (OUTLIER) cc_final: 0.8156 (mtpt) REVERT: F 93 GLN cc_start: 0.8246 (OUTLIER) cc_final: 0.7743 (mt0) REVERT: G 15 LYS cc_start: 0.7604 (mtpt) cc_final: 0.6892 (tttt) REVERT: G 71 ARG cc_start: 0.7470 (ttp-110) cc_final: 0.6975 (ttm-80) REVERT: G 75 LYS cc_start: 0.8469 (mmtm) cc_final: 0.8197 (mmtt) REVERT: G 95 LYS cc_start: 0.8725 (OUTLIER) cc_final: 0.8395 (tmtm) outliers start: 27 outliers final: 9 residues processed: 165 average time/residue: 2.0040 time to fit residues: 347.5517 Evaluate side-chains 161 residues out of total 632 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 146 time to evaluate : 0.827 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 46 VAL Chi-restraints excluded: chain A residue 118 THR Chi-restraints excluded: chain A residue 131 ARG Chi-restraints excluded: chain B residue 47 SER Chi-restraints excluded: chain B residue 77 LYS Chi-restraints excluded: chain C residue 64 GLU Chi-restraints excluded: chain D residue 102 GLU Chi-restraints excluded: chain D residue 113 LYS Chi-restraints excluded: chain F residue 77 LYS Chi-restraints excluded: chain F residue 93 GLN Chi-restraints excluded: chain F residue 96 THR Chi-restraints excluded: chain G residue 41 GLU Chi-restraints excluded: chain G residue 76 THR Chi-restraints excluded: chain G residue 95 LYS Chi-restraints excluded: chain H residue 85 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 59 optimal weight: 0.0060 chunk 2 optimal weight: 3.9990 chunk 0 optimal weight: 5.9990 chunk 54 optimal weight: 0.9980 chunk 76 optimal weight: 7.9990 chunk 23 optimal weight: 3.9990 chunk 83 optimal weight: 5.9990 chunk 9 optimal weight: 0.4980 chunk 16 optimal weight: 0.7980 chunk 36 optimal weight: 7.9990 chunk 51 optimal weight: 5.9990 overall best weight: 1.2598 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 76 GLN C 104 GLN D 44 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4098 r_free = 0.4098 target = 0.177386 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3616 r_free = 0.3616 target = 0.135846 restraints weight = 10712.518| |-----------------------------------------------------------------------------| r_work (start): 0.3587 rms_B_bonded: 0.91 r_work: 0.3391 rms_B_bonded: 2.25 restraints_weight: 0.5000 r_work: 0.3247 rms_B_bonded: 3.60 restraints_weight: 0.2500 r_work (final): 0.3247 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8193 moved from start: 0.2670 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 12775 Z= 0.177 Angle : 0.580 7.750 18498 Z= 0.351 Chirality : 0.034 0.134 2109 Planarity : 0.004 0.040 1335 Dihedral : 30.681 178.942 4097 Min Nonbonded Distance : 2.090 Molprobity Statistics. All-atom Clashscore : 6.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.21 % Favored : 98.79 % Rotamer: Outliers : 3.01 % Allowed : 16.61 % Favored : 80.38 % 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: 2.71 (0.29), residues: 743 helix: 2.40 (0.21), residues: 557 sheet: None (None), residues: 0 loop : -0.09 (0.40), residues: 186 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.003 0.001 HIS B 75 PHE 0.013 0.001 PHE A 67 TYR 0.011 0.002 TYR B 51 ARG 0.004 0.000 ARG E 72 Details of bonding type rmsd hydrogen bonds : bond 0.05497 ( 736) hydrogen bonds : angle 3.04533 ( 1861) covalent geometry : bond 0.00387 (12775) covalent geometry : angle 0.57988 (18498) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1486 Ramachandran restraints generated. 743 Oldfield, 0 Emsley, 743 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1486 Ramachandran restraints generated. 743 Oldfield, 0 Emsley, 743 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 164 residues out of total 632 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 145 time to evaluate : 0.865 Fit side-chains REVERT: A 59 GLU cc_start: 0.8550 (pm20) cc_final: 0.8307 (pm20) REVERT: A 131 ARG cc_start: 0.8487 (OUTLIER) cc_final: 0.7520 (mtp180) REVERT: B 79 LYS cc_start: 0.8795 (mtpt) cc_final: 0.8433 (mtmm) REVERT: C 36 LYS cc_start: 0.8511 (mmtm) cc_final: 0.8222 (mmpt) REVERT: D 102 GLU cc_start: 0.7725 (tp30) cc_final: 0.7485 (mm-30) REVERT: D 113 LYS cc_start: 0.8541 (ttmp) cc_final: 0.7957 (tttm) REVERT: F 27 GLN cc_start: 0.8578 (mm110) cc_final: 0.8251 (mm110) REVERT: F 77 LYS cc_start: 0.8495 (OUTLIER) cc_final: 0.8133 (mtpt) REVERT: F 93 GLN cc_start: 0.8243 (mt0) cc_final: 0.8030 (mt0) REVERT: G 15 LYS cc_start: 0.7602 (mtpt) cc_final: 0.6952 (tttt) REVERT: G 71 ARG cc_start: 0.7486 (ttp-110) cc_final: 0.7146 (ttm110) REVERT: G 75 LYS cc_start: 0.8446 (mmtm) cc_final: 0.8215 (mmtm) REVERT: G 95 LYS cc_start: 0.8696 (OUTLIER) cc_final: 0.8380 (tmtm) REVERT: H 105 LYS cc_start: 0.8117 (mtmm) cc_final: 0.7508 (mmtt) outliers start: 19 outliers final: 11 residues processed: 152 average time/residue: 1.9840 time to fit residues: 316.7246 Evaluate side-chains 158 residues out of total 632 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 144 time to evaluate : 0.892 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 46 VAL Chi-restraints excluded: chain A residue 131 ARG Chi-restraints excluded: chain B residue 47 SER Chi-restraints excluded: chain B residue 77 LYS Chi-restraints excluded: chain C residue 64 GLU Chi-restraints excluded: chain D residue 109 SER Chi-restraints excluded: chain E residue 77 ASP Chi-restraints excluded: chain F residue 77 LYS Chi-restraints excluded: chain F residue 96 THR Chi-restraints excluded: chain G residue 41 GLU Chi-restraints excluded: chain G residue 76 THR Chi-restraints excluded: chain G residue 95 LYS Chi-restraints excluded: chain H residue 85 THR Chi-restraints excluded: chain H residue 109 SER Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 44 optimal weight: 3.9990 chunk 93 optimal weight: 4.9990 chunk 76 optimal weight: 7.9990 chunk 8 optimal weight: 3.9990 chunk 75 optimal weight: 5.9990 chunk 53 optimal weight: 0.6980 chunk 22 optimal weight: 6.9990 chunk 62 optimal weight: 4.9990 chunk 95 optimal weight: 4.9990 chunk 28 optimal weight: 0.8980 chunk 9 optimal weight: 0.7980 overall best weight: 2.0784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 76 GLN C 104 GLN D 44 GLN E 76 GLN H 44 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4068 r_free = 0.4068 target = 0.175019 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3579 r_free = 0.3579 target = 0.132315 restraints weight = 10650.813| |-----------------------------------------------------------------------------| r_work (start): 0.3536 rms_B_bonded: 0.92 r_work: 0.3336 rms_B_bonded: 2.25 restraints_weight: 0.5000 r_work: 0.3192 rms_B_bonded: 3.58 restraints_weight: 0.2500 r_work (final): 0.3192 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8225 moved from start: 0.2960 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.060 12775 Z= 0.229 Angle : 0.609 7.516 18498 Z= 0.364 Chirality : 0.036 0.143 2109 Planarity : 0.005 0.041 1335 Dihedral : 30.726 176.981 4096 Min Nonbonded Distance : 2.085 Molprobity Statistics. All-atom Clashscore : 6.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.21 % Favored : 98.79 % Rotamer: Outliers : 3.16 % Allowed : 16.46 % Favored : 80.38 % 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: 2.55 (0.29), residues: 743 helix: 2.29 (0.21), residues: 558 sheet: None (None), residues: 0 loop : -0.16 (0.40), residues: 185 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.005 0.001 HIS B 75 PHE 0.014 0.002 PHE A 67 TYR 0.012 0.002 TYR B 51 ARG 0.006 0.001 ARG E 72 Details of bonding type rmsd hydrogen bonds : bond 0.06190 ( 736) hydrogen bonds : angle 3.08221 ( 1861) covalent geometry : bond 0.00514 (12775) covalent geometry : angle 0.60902 (18498) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1486 Ramachandran restraints generated. 743 Oldfield, 0 Emsley, 743 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1486 Ramachandran restraints generated. 743 Oldfield, 0 Emsley, 743 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 169 residues out of total 632 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 149 time to evaluate : 0.905 Fit side-chains REVERT: A 59 GLU cc_start: 0.8527 (pm20) cc_final: 0.8277 (pm20) REVERT: A 131 ARG cc_start: 0.8481 (OUTLIER) cc_final: 0.7522 (mtp180) REVERT: B 79 LYS cc_start: 0.8785 (mtpt) cc_final: 0.8402 (mtmm) REVERT: C 36 LYS cc_start: 0.8509 (mmtm) cc_final: 0.8213 (mmpt) REVERT: C 92 GLU cc_start: 0.8270 (mt-10) cc_final: 0.8055 (mt-10) REVERT: E 133 GLU cc_start: 0.7359 (OUTLIER) cc_final: 0.7159 (mt-10) REVERT: F 27 GLN cc_start: 0.8628 (mm110) cc_final: 0.8375 (mm110) REVERT: F 77 LYS cc_start: 0.8501 (OUTLIER) cc_final: 0.8119 (mtpt) REVERT: F 93 GLN cc_start: 0.8273 (mt0) cc_final: 0.8051 (mt0) REVERT: G 15 LYS cc_start: 0.7683 (mtpt) cc_final: 0.6986 (tttt) REVERT: G 71 ARG cc_start: 0.7604 (ttp-110) cc_final: 0.7392 (tmm-80) REVERT: G 75 LYS cc_start: 0.8445 (mmtm) cc_final: 0.8169 (mmtt) REVERT: G 95 LYS cc_start: 0.8719 (OUTLIER) cc_final: 0.8442 (tmtm) REVERT: H 105 LYS cc_start: 0.8210 (mtmm) cc_final: 0.7621 (mmtt) outliers start: 20 outliers final: 8 residues processed: 156 average time/residue: 1.9334 time to fit residues: 317.3840 Evaluate side-chains 156 residues out of total 632 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 144 time to evaluate : 0.832 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 46 VAL Chi-restraints excluded: chain A residue 131 ARG Chi-restraints excluded: chain B residue 47 SER Chi-restraints excluded: chain C residue 64 GLU Chi-restraints excluded: chain D residue 109 SER Chi-restraints excluded: chain E residue 133 GLU Chi-restraints excluded: chain F residue 77 LYS Chi-restraints excluded: chain F residue 96 THR Chi-restraints excluded: chain G residue 76 THR Chi-restraints excluded: chain G residue 95 LYS Chi-restraints excluded: chain H residue 85 THR Chi-restraints excluded: chain H residue 109 SER Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 53 optimal weight: 0.0060 chunk 35 optimal weight: 0.9980 chunk 83 optimal weight: 6.9990 chunk 76 optimal weight: 7.9990 chunk 73 optimal weight: 10.0000 chunk 20 optimal weight: 3.9990 chunk 6 optimal weight: 0.7980 chunk 19 optimal weight: 2.9990 chunk 37 optimal weight: 4.9990 chunk 74 optimal weight: 5.9990 chunk 32 optimal weight: 0.6980 overall best weight: 1.0998 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 76 GLN C 104 GLN E 68 GLN H 44 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4086 r_free = 0.4086 target = 0.176289 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3605 r_free = 0.3605 target = 0.134861 restraints weight = 10617.138| |-----------------------------------------------------------------------------| r_work (start): 0.3575 rms_B_bonded: 0.91 r_work: 0.3377 rms_B_bonded: 2.24 restraints_weight: 0.5000 r_work: 0.3231 rms_B_bonded: 3.59 restraints_weight: 0.2500 r_work (final): 0.3231 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8207 moved from start: 0.3015 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.046 12775 Z= 0.176 Angle : 0.581 7.468 18498 Z= 0.351 Chirality : 0.034 0.134 2109 Planarity : 0.004 0.039 1335 Dihedral : 30.707 177.106 4096 Min Nonbonded Distance : 2.092 Molprobity Statistics. All-atom Clashscore : 6.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.94 % Favored : 99.06 % Rotamer: Outliers : 3.01 % Allowed : 16.77 % Favored : 80.22 % 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: 2.65 (0.29), residues: 743 helix: 2.37 (0.21), residues: 558 sheet: None (None), residues: 0 loop : -0.16 (0.39), residues: 185 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.004 0.001 HIS B 75 PHE 0.013 0.001 PHE A 67 TYR 0.012 0.001 TYR B 51 ARG 0.003 0.000 ARG E 42 Details of bonding type rmsd hydrogen bonds : bond 0.05698 ( 736) hydrogen bonds : angle 3.06057 ( 1861) covalent geometry : bond 0.00380 (12775) covalent geometry : angle 0.58144 (18498) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1486 Ramachandran restraints generated. 743 Oldfield, 0 Emsley, 743 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1486 Ramachandran restraints generated. 743 Oldfield, 0 Emsley, 743 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 163 residues out of total 632 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 144 time to evaluate : 0.835 Fit side-chains REVERT: A 59 GLU cc_start: 0.8554 (pm20) cc_final: 0.8316 (pm20) REVERT: A 131 ARG cc_start: 0.8467 (OUTLIER) cc_final: 0.7565 (mtp180) REVERT: B 79 LYS cc_start: 0.8799 (mtpt) cc_final: 0.8437 (mtmm) REVERT: C 36 LYS cc_start: 0.8519 (mmtm) cc_final: 0.8227 (mmpt) REVERT: C 92 GLU cc_start: 0.8221 (mt-10) cc_final: 0.7982 (mt-10) REVERT: D 82 LYS cc_start: 0.8614 (mmtp) cc_final: 0.8265 (mtmm) REVERT: F 27 GLN cc_start: 0.8596 (mm110) cc_final: 0.8257 (mm110) REVERT: F 77 LYS cc_start: 0.8500 (OUTLIER) cc_final: 0.8136 (mtpt) REVERT: F 93 GLN cc_start: 0.8228 (OUTLIER) cc_final: 0.7997 (mt0) REVERT: G 15 LYS cc_start: 0.7692 (mtpt) cc_final: 0.6949 (tttt) REVERT: G 75 LYS cc_start: 0.8431 (mmtm) cc_final: 0.8151 (mmtt) REVERT: G 95 LYS cc_start: 0.8700 (OUTLIER) cc_final: 0.8404 (tmtm) REVERT: H 105 LYS cc_start: 0.8194 (mtmm) cc_final: 0.7592 (mmtt) outliers start: 19 outliers final: 8 residues processed: 150 average time/residue: 1.9679 time to fit residues: 310.4499 Evaluate side-chains 155 residues out of total 632 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 143 time to evaluate : 0.879 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 46 VAL Chi-restraints excluded: chain A residue 56 LYS Chi-restraints excluded: chain A residue 131 ARG Chi-restraints excluded: chain B residue 47 SER Chi-restraints excluded: chain C residue 64 GLU Chi-restraints excluded: chain C residue 95 LYS Chi-restraints excluded: chain F residue 77 LYS Chi-restraints excluded: chain F residue 93 GLN Chi-restraints excluded: chain F residue 96 THR Chi-restraints excluded: chain G residue 76 THR Chi-restraints excluded: chain G residue 95 LYS Chi-restraints excluded: chain H residue 85 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 48 optimal weight: 0.7980 chunk 12 optimal weight: 2.9990 chunk 19 optimal weight: 2.9990 chunk 96 optimal weight: 5.9990 chunk 37 optimal weight: 4.9990 chunk 41 optimal weight: 2.9990 chunk 82 optimal weight: 7.9990 chunk 36 optimal weight: 6.9990 chunk 34 optimal weight: 0.0870 chunk 54 optimal weight: 4.9990 chunk 83 optimal weight: 6.9990 overall best weight: 1.9764 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 76 GLN C 104 GLN E 68 GLN E 76 GLN H 44 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4070 r_free = 0.4070 target = 0.175330 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3580 r_free = 0.3580 target = 0.132465 restraints weight = 10794.998| |-----------------------------------------------------------------------------| r_work (start): 0.3539 rms_B_bonded: 0.93 r_work: 0.3337 rms_B_bonded: 2.27 restraints_weight: 0.5000 r_work: 0.3191 rms_B_bonded: 3.63 restraints_weight: 0.2500 r_work (final): 0.3191 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8225 moved from start: 0.3210 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.053 12775 Z= 0.216 Angle : 0.605 8.347 18498 Z= 0.361 Chirality : 0.036 0.136 2109 Planarity : 0.004 0.043 1335 Dihedral : 30.723 177.330 4096 Min Nonbonded Distance : 2.103 Molprobity Statistics. All-atom Clashscore : 6.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.94 % Favored : 99.06 % Rotamer: Outliers : 3.32 % Allowed : 15.98 % Favored : 80.70 % 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 (0.29), residues: 743 helix: 2.28 (0.21), residues: 558 sheet: None (None), residues: 0 loop : -0.20 (0.40), residues: 185 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.005 0.001 HIS B 75 PHE 0.013 0.002 PHE A 67 TYR 0.012 0.002 TYR F 51 ARG 0.005 0.001 ARG E 42 Details of bonding type rmsd hydrogen bonds : bond 0.06037 ( 736) hydrogen bonds : angle 3.04313 ( 1861) covalent geometry : bond 0.00483 (12775) covalent geometry : angle 0.60484 (18498) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1486 Ramachandran restraints generated. 743 Oldfield, 0 Emsley, 743 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1486 Ramachandran restraints generated. 743 Oldfield, 0 Emsley, 743 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 170 residues out of total 632 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 149 time to evaluate : 0.811 Fit side-chains revert: symmetry clash REVERT: A 59 GLU cc_start: 0.8524 (pm20) cc_final: 0.8292 (pm20) REVERT: A 131 ARG cc_start: 0.8465 (OUTLIER) cc_final: 0.7525 (mtp180) REVERT: B 52 GLU cc_start: 0.8571 (OUTLIER) cc_final: 0.7689 (mp0) REVERT: B 79 LYS cc_start: 0.8769 (mtpt) cc_final: 0.8395 (mtmm) REVERT: C 36 LYS cc_start: 0.8511 (mmtm) cc_final: 0.8221 (mmpt) REVERT: C 92 GLU cc_start: 0.8275 (mt-10) cc_final: 0.8046 (mt-10) REVERT: D 82 LYS cc_start: 0.8638 (mmtp) cc_final: 0.8296 (mtmm) REVERT: D 102 GLU cc_start: 0.7736 (mm-30) cc_final: 0.7414 (mm-30) REVERT: F 27 GLN cc_start: 0.8643 (mm110) cc_final: 0.8388 (mm110) REVERT: F 77 LYS cc_start: 0.8511 (OUTLIER) cc_final: 0.8135 (mtpt) REVERT: F 93 GLN cc_start: 0.8281 (mt0) cc_final: 0.7801 (mt0) REVERT: G 15 LYS cc_start: 0.7710 (mtpt) cc_final: 0.6951 (tttt) REVERT: G 75 LYS cc_start: 0.8431 (mmtm) cc_final: 0.8173 (mmtt) REVERT: G 95 LYS cc_start: 0.8702 (OUTLIER) cc_final: 0.8412 (tmtm) REVERT: H 105 LYS cc_start: 0.8173 (mtmm) cc_final: 0.7574 (mmtt) outliers start: 21 outliers final: 8 residues processed: 155 average time/residue: 1.8793 time to fit residues: 306.6443 Evaluate side-chains 155 residues out of total 632 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 143 time to evaluate : 0.879 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 46 VAL Chi-restraints excluded: chain A residue 118 THR Chi-restraints excluded: chain A residue 131 ARG Chi-restraints excluded: chain B residue 47 SER Chi-restraints excluded: chain B residue 52 GLU Chi-restraints excluded: chain C residue 64 GLU Chi-restraints excluded: chain D residue 109 SER Chi-restraints excluded: chain F residue 77 LYS Chi-restraints excluded: chain F residue 96 THR Chi-restraints excluded: chain G residue 76 THR Chi-restraints excluded: chain G residue 95 LYS Chi-restraints excluded: chain H residue 85 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 90 optimal weight: 5.9990 chunk 98 optimal weight: 6.9990 chunk 89 optimal weight: 4.9990 chunk 2 optimal weight: 0.7980 chunk 57 optimal weight: 3.9990 chunk 14 optimal weight: 3.9990 chunk 29 optimal weight: 5.9990 chunk 30 optimal weight: 0.8980 chunk 59 optimal weight: 0.9980 chunk 37 optimal weight: 4.9990 chunk 43 optimal weight: 1.9990 overall best weight: 1.7384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 76 GLN C 104 GLN D 44 GLN E 68 GLN E 76 GLN H 44 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4073 r_free = 0.4073 target = 0.175639 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3585 r_free = 0.3585 target = 0.132855 restraints weight = 10810.935| |-----------------------------------------------------------------------------| r_work (start): 0.3542 rms_B_bonded: 0.93 r_work: 0.3345 rms_B_bonded: 2.25 restraints_weight: 0.5000 r_work: 0.3201 rms_B_bonded: 3.59 restraints_weight: 0.2500 r_work (final): 0.3201 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8213 moved from start: 0.3213 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.051 12775 Z= 0.205 Angle : 0.595 8.458 18498 Z= 0.357 Chirality : 0.035 0.138 2109 Planarity : 0.004 0.042 1335 Dihedral : 30.718 177.476 4096 Min Nonbonded Distance : 2.103 Molprobity Statistics. All-atom Clashscore : 6.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.08 % Favored : 98.92 % Rotamer: Outliers : 3.01 % Allowed : 16.46 % Favored : 80.54 % 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: 2.55 (0.29), residues: 743 helix: 2.30 (0.21), residues: 558 sheet: None (None), residues: 0 loop : -0.19 (0.40), residues: 185 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.005 0.001 HIS B 75 PHE 0.014 0.002 PHE A 67 TYR 0.011 0.002 TYR B 51 ARG 0.007 0.000 ARG E 42 Details of bonding type rmsd hydrogen bonds : bond 0.05929 ( 736) hydrogen bonds : angle 3.03594 ( 1861) covalent geometry : bond 0.00455 (12775) covalent geometry : angle 0.59476 (18498) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1486 Ramachandran restraints generated. 743 Oldfield, 0 Emsley, 743 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1486 Ramachandran restraints generated. 743 Oldfield, 0 Emsley, 743 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 165 residues out of total 632 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 146 time to evaluate : 0.815 Fit side-chains revert: symmetry clash REVERT: A 59 GLU cc_start: 0.8517 (pm20) cc_final: 0.8272 (pm20) REVERT: A 131 ARG cc_start: 0.8451 (OUTLIER) cc_final: 0.7536 (mtp180) REVERT: B 79 LYS cc_start: 0.8777 (mtpt) cc_final: 0.8406 (mtmm) REVERT: C 36 LYS cc_start: 0.8517 (mmtm) cc_final: 0.8224 (mmpt) REVERT: C 92 GLU cc_start: 0.8259 (mt-10) cc_final: 0.7980 (mt-10) REVERT: D 82 LYS cc_start: 0.8627 (mmtp) cc_final: 0.8284 (mtmm) REVERT: D 102 GLU cc_start: 0.7686 (mm-30) cc_final: 0.7259 (mm-30) REVERT: F 27 GLN cc_start: 0.8636 (mm110) cc_final: 0.8384 (mm110) REVERT: F 77 LYS cc_start: 0.8495 (OUTLIER) cc_final: 0.8115 (mtpt) REVERT: F 93 GLN cc_start: 0.8332 (mt0) cc_final: 0.7842 (mt0) REVERT: G 15 LYS cc_start: 0.7714 (mtpt) cc_final: 0.6955 (tttt) REVERT: G 75 LYS cc_start: 0.8421 (mmtm) cc_final: 0.8166 (mmtt) REVERT: G 95 LYS cc_start: 0.8697 (OUTLIER) cc_final: 0.8392 (tmtm) REVERT: H 105 LYS cc_start: 0.8166 (mtmm) cc_final: 0.7558 (mmtt) outliers start: 19 outliers final: 11 residues processed: 153 average time/residue: 1.8785 time to fit residues: 302.4624 Evaluate side-chains 158 residues out of total 632 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 144 time to evaluate : 0.803 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 46 VAL Chi-restraints excluded: chain A residue 118 THR Chi-restraints excluded: chain A residue 131 ARG Chi-restraints excluded: chain B residue 47 SER Chi-restraints excluded: chain C residue 64 GLU Chi-restraints excluded: chain C residue 95 LYS Chi-restraints excluded: chain D residue 109 SER Chi-restraints excluded: chain E residue 77 ASP Chi-restraints excluded: chain F residue 77 LYS Chi-restraints excluded: chain F residue 96 THR Chi-restraints excluded: chain G residue 76 THR Chi-restraints excluded: chain G residue 95 LYS Chi-restraints excluded: chain H residue 85 THR Chi-restraints excluded: chain H residue 117 LYS Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 56 optimal weight: 1.9990 chunk 77 optimal weight: 5.9990 chunk 58 optimal weight: 7.9990 chunk 70 optimal weight: 5.9990 chunk 88 optimal weight: 6.9990 chunk 8 optimal weight: 1.9990 chunk 53 optimal weight: 1.9990 chunk 81 optimal weight: 5.9990 chunk 23 optimal weight: 4.9990 chunk 1 optimal weight: 1.9990 chunk 40 optimal weight: 2.9990 overall best weight: 2.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 76 GLN C 104 GLN D 44 GLN E 68 GLN E 76 GLN H 44 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4064 r_free = 0.4064 target = 0.174710 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3573 r_free = 0.3573 target = 0.131877 restraints weight = 10823.708| |-----------------------------------------------------------------------------| r_work (start): 0.3529 rms_B_bonded: 0.93 r_work: 0.3327 rms_B_bonded: 2.27 restraints_weight: 0.5000 r_work: 0.3181 rms_B_bonded: 3.62 restraints_weight: 0.2500 r_work (final): 0.3181 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8232 moved from start: 0.3290 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.058 12775 Z= 0.231 Angle : 0.614 7.874 18498 Z= 0.367 Chirality : 0.037 0.141 2109 Planarity : 0.004 0.043 1335 Dihedral : 30.847 176.344 4096 Min Nonbonded Distance : 2.090 Molprobity Statistics. All-atom Clashscore : 6.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.35 % Favored : 98.65 % Rotamer: Outliers : 3.32 % Allowed : 16.46 % Favored : 80.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.46 (0.29), residues: 743 helix: 2.22 (0.21), residues: 558 sheet: None (None), residues: 0 loop : -0.19 (0.40), residues: 185 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.005 0.001 HIS B 75 PHE 0.014 0.002 PHE A 67 TYR 0.012 0.002 TYR E 54 ARG 0.007 0.001 ARG E 42 Details of bonding type rmsd hydrogen bonds : bond 0.06347 ( 736) hydrogen bonds : angle 3.08389 ( 1861) covalent geometry : bond 0.00517 (12775) covalent geometry : angle 0.61424 (18498) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1486 Ramachandran restraints generated. 743 Oldfield, 0 Emsley, 743 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1486 Ramachandran restraints generated. 743 Oldfield, 0 Emsley, 743 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 167 residues out of total 632 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 146 time to evaluate : 0.846 Fit side-chains REVERT: A 59 GLU cc_start: 0.8514 (pm20) cc_final: 0.8269 (pm20) REVERT: A 131 ARG cc_start: 0.8474 (OUTLIER) cc_final: 0.7514 (mtp180) REVERT: B 52 GLU cc_start: 0.8585 (OUTLIER) cc_final: 0.7686 (mp0) REVERT: B 79 LYS cc_start: 0.8778 (mtpt) cc_final: 0.8430 (mtmm) REVERT: C 36 LYS cc_start: 0.8526 (mmtm) cc_final: 0.8236 (mmpt) REVERT: C 92 GLU cc_start: 0.8270 (mt-10) cc_final: 0.8006 (mt-10) REVERT: D 73 GLU cc_start: 0.8638 (tp30) cc_final: 0.8305 (tp30) REVERT: E 115 LYS cc_start: 0.8678 (OUTLIER) cc_final: 0.8292 (mppt) REVERT: F 27 GLN cc_start: 0.8582 (mm110) cc_final: 0.8328 (mm110) REVERT: F 77 LYS cc_start: 0.8514 (OUTLIER) cc_final: 0.8134 (mtpt) REVERT: F 93 GLN cc_start: 0.8339 (mt0) cc_final: 0.7850 (mt0) REVERT: G 15 LYS cc_start: 0.7723 (mtpt) cc_final: 0.6958 (tttt) REVERT: G 75 LYS cc_start: 0.8465 (mmtm) cc_final: 0.8162 (mmtm) REVERT: G 95 LYS cc_start: 0.8741 (OUTLIER) cc_final: 0.8430 (tmtm) outliers start: 21 outliers final: 10 residues processed: 154 average time/residue: 1.8951 time to fit residues: 307.1071 Evaluate side-chains 158 residues out of total 632 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 143 time to evaluate : 0.816 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 46 VAL Chi-restraints excluded: chain A residue 118 THR Chi-restraints excluded: chain A residue 131 ARG Chi-restraints excluded: chain B residue 47 SER Chi-restraints excluded: chain B residue 52 GLU Chi-restraints excluded: chain C residue 64 GLU Chi-restraints excluded: chain C residue 95 LYS Chi-restraints excluded: chain D residue 109 SER Chi-restraints excluded: chain E residue 115 LYS Chi-restraints excluded: chain F residue 77 LYS Chi-restraints excluded: chain F residue 96 THR Chi-restraints excluded: chain G residue 76 THR Chi-restraints excluded: chain G residue 95 LYS Chi-restraints excluded: chain H residue 85 THR Chi-restraints excluded: chain H residue 117 LYS Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 91 optimal weight: 6.9990 chunk 10 optimal weight: 1.9990 chunk 39 optimal weight: 0.9980 chunk 78 optimal weight: 4.9990 chunk 20 optimal weight: 6.9990 chunk 21 optimal weight: 2.9990 chunk 12 optimal weight: 1.9990 chunk 96 optimal weight: 5.9990 chunk 83 optimal weight: 6.9990 chunk 11 optimal weight: 1.9990 chunk 59 optimal weight: 5.9990 overall best weight: 1.9988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 76 GLN C 104 GLN D 44 GLN E 68 GLN E 76 GLN H 44 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4065 r_free = 0.4065 target = 0.174899 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3575 r_free = 0.3575 target = 0.132158 restraints weight = 10737.034| |-----------------------------------------------------------------------------| r_work (start): 0.3533 rms_B_bonded: 0.93 r_work: 0.3332 rms_B_bonded: 2.27 restraints_weight: 0.5000 r_work: 0.3186 rms_B_bonded: 3.61 restraints_weight: 0.2500 r_work (final): 0.3186 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8229 moved from start: 0.3302 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.056 12775 Z= 0.221 Angle : 0.609 7.454 18498 Z= 0.365 Chirality : 0.036 0.134 2109 Planarity : 0.004 0.043 1335 Dihedral : 30.845 176.557 4096 Min Nonbonded Distance : 2.092 Molprobity Statistics. All-atom Clashscore : 6.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.21 % Favored : 98.79 % Rotamer: Outliers : 3.16 % Allowed : 16.61 % Favored : 80.22 % 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 (0.29), residues: 743 helix: 2.25 (0.21), residues: 558 sheet: None (None), residues: 0 loop : -0.23 (0.40), residues: 185 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.005 0.001 HIS B 75 PHE 0.014 0.002 PHE A 67 TYR 0.011 0.002 TYR E 54 ARG 0.008 0.001 ARG E 42 Details of bonding type rmsd hydrogen bonds : bond 0.06234 ( 736) hydrogen bonds : angle 3.08322 ( 1861) covalent geometry : bond 0.00492 (12775) covalent geometry : angle 0.60941 (18498) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1486 Ramachandran restraints generated. 743 Oldfield, 0 Emsley, 743 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1486 Ramachandran restraints generated. 743 Oldfield, 0 Emsley, 743 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 162 residues out of total 632 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 142 time to evaluate : 0.957 Fit side-chains REVERT: A 59 GLU cc_start: 0.8512 (pm20) cc_final: 0.8267 (pm20) REVERT: A 131 ARG cc_start: 0.8472 (OUTLIER) cc_final: 0.7518 (mtp180) REVERT: B 52 GLU cc_start: 0.8576 (OUTLIER) cc_final: 0.7679 (mp0) REVERT: B 79 LYS cc_start: 0.8770 (mtpt) cc_final: 0.8423 (mtmm) REVERT: C 36 LYS cc_start: 0.8525 (mmtm) cc_final: 0.8233 (mmpt) REVERT: C 92 GLU cc_start: 0.8264 (mt-10) cc_final: 0.8001 (mt-10) REVERT: D 73 GLU cc_start: 0.8629 (tp30) cc_final: 0.8322 (tp30) REVERT: D 82 LYS cc_start: 0.8665 (mmtp) cc_final: 0.8332 (mtmm) REVERT: E 115 LYS cc_start: 0.8669 (OUTLIER) cc_final: 0.8279 (mppt) REVERT: F 27 GLN cc_start: 0.8580 (mm110) cc_final: 0.8329 (mm110) REVERT: F 77 LYS cc_start: 0.8509 (OUTLIER) cc_final: 0.8132 (mtpt) REVERT: F 93 GLN cc_start: 0.8332 (mt0) cc_final: 0.7842 (mt0) REVERT: G 15 LYS cc_start: 0.7724 (mtpt) cc_final: 0.6962 (tttt) REVERT: G 75 LYS cc_start: 0.8458 (mmtm) cc_final: 0.8151 (mmtm) REVERT: G 95 LYS cc_start: 0.8736 (OUTLIER) cc_final: 0.8439 (tmtm) REVERT: H 105 LYS cc_start: 0.8259 (mtmm) cc_final: 0.7650 (mmtt) outliers start: 20 outliers final: 11 residues processed: 149 average time/residue: 1.9403 time to fit residues: 304.4343 Evaluate side-chains 158 residues out of total 632 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 142 time to evaluate : 0.953 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 46 VAL Chi-restraints excluded: chain A residue 118 THR Chi-restraints excluded: chain A residue 131 ARG Chi-restraints excluded: chain B residue 47 SER Chi-restraints excluded: chain B residue 52 GLU Chi-restraints excluded: chain C residue 64 GLU Chi-restraints excluded: chain C residue 95 LYS Chi-restraints excluded: chain D residue 109 SER Chi-restraints excluded: chain E residue 115 LYS Chi-restraints excluded: chain F residue 21 VAL Chi-restraints excluded: chain F residue 77 LYS Chi-restraints excluded: chain F residue 96 THR Chi-restraints excluded: chain G residue 76 THR Chi-restraints excluded: chain G residue 95 LYS Chi-restraints excluded: chain H residue 85 THR Chi-restraints excluded: chain H residue 117 LYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 75 optimal weight: 5.9990 chunk 51 optimal weight: 2.9990 chunk 52 optimal weight: 0.3980 chunk 88 optimal weight: 6.9990 chunk 91 optimal weight: 6.9990 chunk 34 optimal weight: 0.6980 chunk 80 optimal weight: 4.9990 chunk 76 optimal weight: 7.9990 chunk 65 optimal weight: 4.9990 chunk 70 optimal weight: 0.1980 chunk 74 optimal weight: 5.9990 overall best weight: 1.8584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 76 GLN C 104 GLN D 44 GLN E 68 GLN H 44 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4066 r_free = 0.4066 target = 0.175036 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3575 r_free = 0.3575 target = 0.132120 restraints weight = 10671.300| |-----------------------------------------------------------------------------| r_work (start): 0.3534 rms_B_bonded: 0.93 r_work: 0.3336 rms_B_bonded: 2.26 restraints_weight: 0.5000 r_work: 0.3190 rms_B_bonded: 3.60 restraints_weight: 0.2500 r_work (final): 0.3190 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8223 moved from start: 0.3303 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.053 12775 Z= 0.213 Angle : 0.606 7.120 18498 Z= 0.363 Chirality : 0.036 0.131 2109 Planarity : 0.004 0.043 1335 Dihedral : 30.839 176.633 4096 Min Nonbonded Distance : 2.093 Molprobity Statistics. All-atom Clashscore : 6.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.21 % Favored : 98.79 % Rotamer: Outliers : 2.85 % Allowed : 16.77 % Favored : 80.38 % 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 (0.29), residues: 743 helix: 2.26 (0.21), residues: 558 sheet: None (None), residues: 0 loop : -0.23 (0.40), residues: 185 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.005 0.001 HIS B 75 PHE 0.014 0.002 PHE A 67 TYR 0.013 0.002 TYR H 80 ARG 0.008 0.001 ARG E 42 Details of bonding type rmsd hydrogen bonds : bond 0.06144 ( 736) hydrogen bonds : angle 3.07383 ( 1861) covalent geometry : bond 0.00474 (12775) covalent geometry : angle 0.60588 (18498) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1486 Ramachandran restraints generated. 743 Oldfield, 0 Emsley, 743 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1486 Ramachandran restraints generated. 743 Oldfield, 0 Emsley, 743 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 160 residues out of total 632 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 142 time to evaluate : 0.928 Fit side-chains REVERT: A 59 GLU cc_start: 0.8519 (pm20) cc_final: 0.8274 (pm20) REVERT: A 131 ARG cc_start: 0.8467 (OUTLIER) cc_final: 0.7514 (mtp180) REVERT: B 52 GLU cc_start: 0.8570 (OUTLIER) cc_final: 0.7674 (mp0) REVERT: B 79 LYS cc_start: 0.8765 (mtpt) cc_final: 0.8417 (mtmm) REVERT: C 36 LYS cc_start: 0.8517 (mmtm) cc_final: 0.8225 (mmpt) REVERT: C 92 GLU cc_start: 0.8257 (mt-10) cc_final: 0.7993 (mt-10) REVERT: D 73 GLU cc_start: 0.8627 (tp30) cc_final: 0.8316 (tp30) REVERT: D 82 LYS cc_start: 0.8656 (mmtp) cc_final: 0.8324 (mtmm) REVERT: E 115 LYS cc_start: 0.8664 (OUTLIER) cc_final: 0.8270 (mppt) REVERT: F 27 GLN cc_start: 0.8574 (mm110) cc_final: 0.8324 (mm110) REVERT: F 77 LYS cc_start: 0.8504 (OUTLIER) cc_final: 0.8123 (mtpt) REVERT: F 93 GLN cc_start: 0.8331 (mt0) cc_final: 0.7841 (mt0) REVERT: G 15 LYS cc_start: 0.7713 (mtpt) cc_final: 0.6949 (tttt) REVERT: G 75 LYS cc_start: 0.8453 (mmtm) cc_final: 0.8145 (mmtm) REVERT: G 95 LYS cc_start: 0.8733 (OUTLIER) cc_final: 0.8435 (tmtm) REVERT: H 105 LYS cc_start: 0.8238 (mtmm) cc_final: 0.7613 (mmtt) outliers start: 18 outliers final: 10 residues processed: 148 average time/residue: 1.8787 time to fit residues: 292.7838 Evaluate side-chains 157 residues out of total 632 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 142 time to evaluate : 0.831 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 46 VAL Chi-restraints excluded: chain A residue 118 THR Chi-restraints excluded: chain A residue 131 ARG Chi-restraints excluded: chain B residue 47 SER Chi-restraints excluded: chain B residue 52 GLU Chi-restraints excluded: chain C residue 64 GLU Chi-restraints excluded: chain C residue 95 LYS Chi-restraints excluded: chain D residue 109 SER Chi-restraints excluded: chain E residue 115 LYS Chi-restraints excluded: chain F residue 77 LYS Chi-restraints excluded: chain F residue 96 THR Chi-restraints excluded: chain G residue 76 THR Chi-restraints excluded: chain G residue 95 LYS Chi-restraints excluded: chain H residue 85 THR Chi-restraints excluded: chain H residue 117 LYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 74 optimal weight: 6.9990 chunk 54 optimal weight: 4.9990 chunk 21 optimal weight: 2.9990 chunk 38 optimal weight: 0.6980 chunk 59 optimal weight: 5.9990 chunk 18 optimal weight: 1.9990 chunk 48 optimal weight: 0.9980 chunk 72 optimal weight: 10.0000 chunk 33 optimal weight: 1.9990 chunk 96 optimal weight: 5.9990 chunk 5 optimal weight: 0.8980 overall best weight: 1.3184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 76 GLN C 104 GLN D 44 GLN E 68 GLN H 44 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4069 r_free = 0.4069 target = 0.175248 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3584 r_free = 0.3584 target = 0.132742 restraints weight = 10688.092| |-----------------------------------------------------------------------------| r_work (start): 0.3541 rms_B_bonded: 0.91 r_work: 0.3341 rms_B_bonded: 2.26 restraints_weight: 0.5000 r_work: 0.3194 rms_B_bonded: 3.61 restraints_weight: 0.2500 r_work (final): 0.3194 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8221 moved from start: 0.3322 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.046 12775 Z= 0.189 Angle : 0.596 7.560 18498 Z= 0.358 Chirality : 0.034 0.126 2109 Planarity : 0.004 0.042 1335 Dihedral : 30.830 176.756 4096 Min Nonbonded Distance : 2.093 Molprobity Statistics. All-atom Clashscore : 6.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.21 % Favored : 98.79 % Rotamer: Outliers : 2.69 % Allowed : 16.77 % Favored : 80.54 % 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 (0.29), residues: 743 helix: 2.29 (0.21), residues: 558 sheet: None (None), residues: 0 loop : -0.23 (0.40), residues: 185 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.005 0.001 HIS B 75 PHE 0.014 0.002 PHE A 67 TYR 0.012 0.002 TYR H 80 ARG 0.008 0.000 ARG E 42 Details of bonding type rmsd hydrogen bonds : bond 0.05983 ( 736) hydrogen bonds : angle 3.06887 ( 1861) covalent geometry : bond 0.00413 (12775) covalent geometry : angle 0.59631 (18498) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 10385.65 seconds wall clock time: 179 minutes 10.12 seconds (10750.12 seconds total)