Starting phenix.real_space_refine on Sun Dec 29 23:22:03 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8g86_29837/12_2024/8g86_29837.cif Found real_map, /net/cci-nas-00/data/ceres_data/8g86_29837/12_2024/8g86_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_29837/12_2024/8g86_29837.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8g86_29837/12_2024/8g86_29837.map" model { file = "/net/cci-nas-00/data/ceres_data/8g86_29837/12_2024/8g86_29837.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8g86_29837/12_2024/8g86_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-5532/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: 8.04, per 1000 atoms: 0.67 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: 3.08 Conformation dependent library (CDL) restraints added in 987.6 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: 6.85 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: 4.97 Time building geometry restraints manager: 3.48 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: 3.970 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: 0.480 Check model and map are aligned: 0.080 Set scattering table: 0.120 Process input model: 34.490 Find NCS groups from input model: 0.280 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:13.150 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 52.640 ------------------------------------------------------------------------------- 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= 0.178 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 *********************** 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 : 0.950 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: 2.0595 time to fit residues: 353.1196 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 : 0.991 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8131 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= 0.283 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 *********************** 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 : 0.995 Fit side-chains REVERT: A 131 ARG cc_start: 0.8528 (OUTLIER) cc_final: 0.7505 (mtp180) REVERT: B 79 LYS cc_start: 0.8634 (mtpt) cc_final: 0.8289 (mtmm) REVERT: C 36 LYS cc_start: 0.8444 (mmtm) cc_final: 0.8203 (mmpt) REVERT: D 102 GLU cc_start: 0.7564 (OUTLIER) cc_final: 0.7183 (tp30) REVERT: D 113 LYS cc_start: 0.8434 (OUTLIER) cc_final: 0.7912 (tttm) REVERT: E 59 GLU cc_start: 0.8500 (pm20) cc_final: 0.8232 (pm20) REVERT: F 27 GLN cc_start: 0.8564 (mm110) cc_final: 0.8266 (mm110) REVERT: F 77 LYS cc_start: 0.8430 (OUTLIER) cc_final: 0.8035 (mtpt) REVERT: F 93 GLN cc_start: 0.8365 (OUTLIER) cc_final: 0.7894 (mt0) REVERT: G 15 LYS cc_start: 0.7728 (mtpt) cc_final: 0.7061 (tttt) REVERT: G 71 ARG cc_start: 0.7421 (ttp-110) cc_final: 0.6964 (ttm-80) REVERT: G 75 LYS cc_start: 0.8413 (mmtm) cc_final: 0.8149 (mmtt) REVERT: G 95 LYS cc_start: 0.8728 (OUTLIER) cc_final: 0.8410 (tmtm) outliers start: 27 outliers final: 9 residues processed: 165 average time/residue: 2.0948 time to fit residues: 362.9851 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 : 0.917 ------------------------------------------------------------------------------- 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 50 optimal weight: 0.0770 chunk 28 optimal weight: 3.9990 chunk 75 optimal weight: 5.9990 chunk 61 optimal weight: 6.9990 chunk 25 optimal weight: 2.9990 chunk 90 optimal weight: 5.9990 chunk 98 optimal weight: 6.9990 chunk 81 optimal weight: 5.9990 chunk 31 optimal weight: 1.9990 chunk 72 optimal weight: 10.0000 chunk 89 optimal weight: 4.9990 overall best weight: 2.8146 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 76 GLN C 24 GLN C 104 GLN D 44 GLN E 76 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8171 moved from start: 0.2923 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.065 12775 Z= 0.361 Angle : 0.654 8.448 18498 Z= 0.388 Chirality : 0.039 0.166 2109 Planarity : 0.005 0.043 1335 Dihedral : 30.960 176.634 4097 Min Nonbonded Distance : 2.090 Molprobity Statistics. All-atom Clashscore : 6.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.35 % Favored : 98.65 % Rotamer: Outliers : 3.80 % Allowed : 15.98 % 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: 2.31 (0.29), residues: 743 helix: 2.11 (0.21), residues: 558 sheet: None (None), residues: 0 loop : -0.21 (0.39), residues: 185 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.005 0.001 HIS B 75 PHE 0.015 0.002 PHE A 67 TYR 0.014 0.002 TYR B 51 ARG 0.006 0.001 ARG G 77 *********************** 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: 24 poor density : 140 time to evaluate : 0.948 Fit side-chains REVERT: A 131 ARG cc_start: 0.8593 (OUTLIER) cc_final: 0.7619 (mtp180) REVERT: B 52 GLU cc_start: 0.8593 (OUTLIER) cc_final: 0.7664 (mp0) REVERT: B 79 LYS cc_start: 0.8633 (mtpt) cc_final: 0.8302 (mtmm) REVERT: C 36 LYS cc_start: 0.8431 (mmtm) cc_final: 0.8176 (mmpt) REVERT: C 92 GLU cc_start: 0.8213 (mt-10) cc_final: 0.7941 (mt-10) REVERT: D 102 GLU cc_start: 0.7612 (tp30) cc_final: 0.7298 (mm-30) REVERT: D 113 LYS cc_start: 0.8505 (ttmp) cc_final: 0.8026 (tttm) REVERT: E 59 GLU cc_start: 0.8485 (pm20) cc_final: 0.8281 (pm20) REVERT: E 133 GLU cc_start: 0.7454 (OUTLIER) cc_final: 0.7249 (mt-10) REVERT: F 27 GLN cc_start: 0.8595 (mm110) cc_final: 0.8354 (mm110) REVERT: F 77 LYS cc_start: 0.8450 (OUTLIER) cc_final: 0.8032 (mtpt) REVERT: F 93 GLN cc_start: 0.8392 (OUTLIER) cc_final: 0.8185 (mt0) REVERT: G 15 LYS cc_start: 0.7794 (mtpt) cc_final: 0.7198 (tttt) REVERT: G 71 ARG cc_start: 0.7550 (ttp-110) cc_final: 0.7252 (ttm110) REVERT: G 75 LYS cc_start: 0.8438 (mmtm) cc_final: 0.8205 (mmtm) REVERT: G 95 LYS cc_start: 0.8738 (OUTLIER) cc_final: 0.8445 (tmtm) outliers start: 24 outliers final: 10 residues processed: 149 average time/residue: 2.1585 time to fit residues: 337.3223 Evaluate side-chains 154 residues out of total 632 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 138 time to evaluate : 1.131 ------------------------------------------------------------------------------- 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 E residue 133 GLU Chi-restraints excluded: chain F residue 77 LYS Chi-restraints excluded: chain F residue 84 MET 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 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 68 optimal weight: 2.9990 chunk 47 optimal weight: 4.9990 chunk 10 optimal weight: 0.8980 chunk 43 optimal weight: 0.7980 chunk 61 optimal weight: 1.9990 chunk 91 optimal weight: 5.9990 chunk 96 optimal weight: 5.9990 chunk 86 optimal weight: 10.0000 chunk 26 optimal weight: 2.9990 chunk 80 optimal weight: 3.9990 chunk 54 optimal weight: 0.8980 overall best weight: 1.5184 ------------------------------------------------------------------------------- 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 76 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8146 moved from start: 0.3004 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.047 12775 Z= 0.243 Angle : 0.602 6.948 18498 Z= 0.363 Chirality : 0.035 0.137 2109 Planarity : 0.004 0.041 1335 Dihedral : 30.914 176.598 4097 Min Nonbonded Distance : 2.093 Molprobity Statistics. All-atom Clashscore : 6.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.94 % Favored : 99.06 % Rotamer: Outliers : 3.01 % Allowed : 16.93 % 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: 2.47 (0.29), residues: 743 helix: 2.24 (0.21), residues: 558 sheet: None (None), residues: 0 loop : -0.21 (0.39), residues: 185 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.004 0.001 HIS B 75 PHE 0.014 0.002 PHE A 67 TYR 0.012 0.002 TYR B 51 ARG 0.005 0.001 ARG E 72 *********************** 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 168 residues out of total 632 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 149 time to evaluate : 0.976 Fit side-chains REVERT: A 56 LYS cc_start: 0.8297 (OUTLIER) cc_final: 0.8030 (mttp) REVERT: A 131 ARG cc_start: 0.8574 (OUTLIER) cc_final: 0.7631 (mtp180) REVERT: B 52 GLU cc_start: 0.8545 (OUTLIER) cc_final: 0.7633 (mp0) REVERT: B 79 LYS cc_start: 0.8666 (mtpt) cc_final: 0.8325 (mtmm) REVERT: C 36 LYS cc_start: 0.8413 (mmtm) cc_final: 0.8165 (mmpt) REVERT: C 92 GLU cc_start: 0.8190 (mt-10) cc_final: 0.7925 (mt-10) REVERT: D 113 LYS cc_start: 0.8507 (ttmp) cc_final: 0.8002 (tttm) REVERT: F 27 GLN cc_start: 0.8598 (mm110) cc_final: 0.8358 (mm110) REVERT: F 77 LYS cc_start: 0.8420 (OUTLIER) cc_final: 0.8015 (mtpt) REVERT: F 93 GLN cc_start: 0.8359 (OUTLIER) cc_final: 0.8151 (mt0) REVERT: G 15 LYS cc_start: 0.7824 (mtpt) cc_final: 0.7243 (tttt) REVERT: G 75 LYS cc_start: 0.8405 (mmtm) cc_final: 0.8136 (mmtt) REVERT: G 95 LYS cc_start: 0.8739 (OUTLIER) cc_final: 0.8462 (tmtm) outliers start: 19 outliers final: 9 residues processed: 155 average time/residue: 2.1056 time to fit residues: 342.9125 Evaluate side-chains 156 residues out of total 632 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 141 time to evaluate : 0.920 ------------------------------------------------------------------------------- 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 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 77 ASP 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=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 1 optimal weight: 0.9990 chunk 71 optimal weight: 2.9990 chunk 39 optimal weight: 2.9990 chunk 82 optimal weight: 6.9990 chunk 66 optimal weight: 2.9990 chunk 0 optimal weight: 0.7980 chunk 49 optimal weight: 0.7980 chunk 86 optimal weight: 10.0000 chunk 24 optimal weight: 5.9990 chunk 32 optimal weight: 0.7980 chunk 87 optimal weight: 10.0000 overall best weight: 1.2784 ------------------------------------------------------------------------------- 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 76 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8136 moved from start: 0.3040 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= 0.231 Angle : 0.594 7.041 18498 Z= 0.358 Chirality : 0.034 0.137 2109 Planarity : 0.004 0.042 1335 Dihedral : 30.848 177.229 4096 Min Nonbonded Distance : 2.100 Molprobity Statistics. All-atom Clashscore : 6.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.94 % Favored : 99.06 % 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: 2.58 (0.29), residues: 743 helix: 2.33 (0.21), residues: 558 sheet: None (None), residues: 0 loop : -0.22 (0.39), residues: 185 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.004 0.001 HIS B 75 PHE 0.014 0.002 PHE A 67 TYR 0.012 0.002 TYR B 51 ARG 0.010 0.001 ARG E 42 *********************** 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 166 residues out of total 632 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 145 time to evaluate : 1.181 Fit side-chains REVERT: A 131 ARG cc_start: 0.8555 (OUTLIER) cc_final: 0.7649 (mtp180) REVERT: B 52 GLU cc_start: 0.8520 (OUTLIER) cc_final: 0.7613 (mp0) REVERT: B 79 LYS cc_start: 0.8654 (mtpt) cc_final: 0.8303 (mtmm) REVERT: C 36 LYS cc_start: 0.8413 (mmtm) cc_final: 0.8176 (mmpt) REVERT: C 92 GLU cc_start: 0.8190 (mt-10) cc_final: 0.7914 (mt-10) REVERT: D 113 LYS cc_start: 0.8481 (ttmp) cc_final: 0.7959 (tttm) REVERT: E 133 GLU cc_start: 0.7359 (OUTLIER) cc_final: 0.7078 (mt-10) REVERT: F 27 GLN cc_start: 0.8615 (mm110) cc_final: 0.8372 (mm110) REVERT: F 77 LYS cc_start: 0.8421 (OUTLIER) cc_final: 0.8022 (mtpt) REVERT: F 93 GLN cc_start: 0.8340 (OUTLIER) cc_final: 0.8130 (mt0) REVERT: G 15 LYS cc_start: 0.7820 (mtpt) cc_final: 0.7107 (tttt) REVERT: G 75 LYS cc_start: 0.8386 (mmtm) cc_final: 0.8123 (mmtt) REVERT: G 95 LYS cc_start: 0.8723 (OUTLIER) cc_final: 0.8426 (tmtm) REVERT: H 105 LYS cc_start: 0.8187 (mtmm) cc_final: 0.7793 (mmtt) outliers start: 21 outliers final: 12 residues processed: 151 average time/residue: 2.2060 time to fit residues: 349.6024 Evaluate side-chains 161 residues out of total 632 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 143 time to evaluate : 1.076 ------------------------------------------------------------------------------- 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 76 GLN 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 B residue 77 LYS 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 133 GLU 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 Chi-restraints excluded: chain H residue 109 SER Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 19 optimal weight: 2.9990 chunk 56 optimal weight: 2.9990 chunk 23 optimal weight: 2.9990 chunk 96 optimal weight: 5.9990 chunk 80 optimal weight: 4.9990 chunk 44 optimal weight: 1.9990 chunk 8 optimal weight: 1.9990 chunk 32 optimal weight: 0.8980 chunk 50 optimal weight: 0.3980 chunk 93 optimal weight: 4.9990 chunk 10 optimal weight: 0.9990 overall best weight: 1.2586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 76 GLN C 104 GLN E 76 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8115 moved from start: 0.3192 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.047 12775 Z= 0.217 Angle : 0.568 7.282 18498 Z= 0.343 Chirality : 0.033 0.132 2109 Planarity : 0.004 0.042 1335 Dihedral : 30.490 179.099 4096 Min Nonbonded Distance : 2.103 Molprobity Statistics. All-atom Clashscore : 6.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.08 % Favored : 98.92 % Rotamer: Outliers : 2.85 % Allowed : 16.61 % 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: 2.75 (0.29), residues: 743 helix: 2.45 (0.21), residues: 557 sheet: None (None), residues: 0 loop : -0.14 (0.39), residues: 186 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.004 0.001 HIS B 75 PHE 0.013 0.002 PHE A 67 TYR 0.010 0.001 TYR B 51 ARG 0.006 0.000 ARG E 42 *********************** 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 168 residues out of total 632 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 150 time to evaluate : 0.966 Fit side-chains REVERT: A 131 ARG cc_start: 0.8495 (OUTLIER) cc_final: 0.7575 (mtp180) REVERT: B 52 GLU cc_start: 0.8427 (OUTLIER) cc_final: 0.7555 (mp0) REVERT: B 79 LYS cc_start: 0.8652 (mtpt) cc_final: 0.8312 (mtmm) REVERT: C 36 LYS cc_start: 0.8426 (mmtm) cc_final: 0.8187 (mmpt) REVERT: C 92 GLU cc_start: 0.8192 (mt-10) cc_final: 0.7934 (mt-10) REVERT: D 113 LYS cc_start: 0.8468 (OUTLIER) cc_final: 0.7994 (tttm) REVERT: F 77 LYS cc_start: 0.8395 (OUTLIER) cc_final: 0.7999 (mtpt) REVERT: G 15 LYS cc_start: 0.7836 (mtpt) cc_final: 0.7137 (tttt) REVERT: G 75 LYS cc_start: 0.8352 (mmtm) cc_final: 0.8095 (mmtt) REVERT: G 95 LYS cc_start: 0.8709 (OUTLIER) cc_final: 0.8418 (tmtm) outliers start: 18 outliers final: 8 residues processed: 156 average time/residue: 2.0546 time to fit residues: 336.9080 Evaluate side-chains 161 residues out of total 632 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 148 time to evaluate : 1.001 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 46 VAL Chi-restraints excluded: chain A residue 76 GLN 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 D residue 113 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 Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 55 optimal weight: 2.9990 chunk 70 optimal weight: 20.0000 chunk 54 optimal weight: 2.9990 chunk 81 optimal weight: 5.9990 chunk 96 optimal weight: 5.9990 chunk 60 optimal weight: 0.6980 chunk 58 optimal weight: 7.9990 chunk 44 optimal weight: 0.9980 chunk 59 optimal weight: 2.9990 chunk 38 optimal weight: 0.8980 chunk 57 optimal weight: 0.8980 overall best weight: 1.2982 ------------------------------------------------------------------------------- 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 F 27 GLN H 44 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8116 moved from start: 0.3258 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= 0.220 Angle : 0.570 7.417 18498 Z= 0.344 Chirality : 0.033 0.125 2109 Planarity : 0.004 0.042 1335 Dihedral : 30.474 178.654 4096 Min Nonbonded Distance : 2.101 Molprobity Statistics. All-atom Clashscore : 6.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.08 % Favored : 98.92 % Rotamer: Outliers : 3.01 % Allowed : 17.41 % Favored : 79.59 % 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: 2.81 (0.29), residues: 743 helix: 2.47 (0.21), residues: 558 sheet: None (None), residues: 0 loop : -0.06 (0.40), residues: 185 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.004 0.001 HIS B 75 PHE 0.013 0.002 PHE A 67 TYR 0.010 0.002 TYR B 51 ARG 0.007 0.000 ARG E 42 *********************** 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 164 residues out of total 632 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 145 time to evaluate : 0.993 Fit side-chains REVERT: A 131 ARG cc_start: 0.8491 (OUTLIER) cc_final: 0.7568 (mtp180) REVERT: B 52 GLU cc_start: 0.8444 (OUTLIER) cc_final: 0.7570 (mp0) REVERT: B 79 LYS cc_start: 0.8646 (mtpt) cc_final: 0.8312 (mtmm) REVERT: C 36 LYS cc_start: 0.8419 (mmtm) cc_final: 0.8174 (mmpt) REVERT: C 92 GLU cc_start: 0.8189 (mt-10) cc_final: 0.7930 (mt-10) REVERT: D 113 LYS cc_start: 0.8485 (OUTLIER) cc_final: 0.8003 (tttm) REVERT: F 27 GLN cc_start: 0.8571 (mm-40) cc_final: 0.8305 (mm110) REVERT: F 77 LYS cc_start: 0.8400 (OUTLIER) cc_final: 0.8005 (mtpt) REVERT: F 93 GLN cc_start: 0.8180 (OUTLIER) cc_final: 0.7867 (mt0) REVERT: G 15 LYS cc_start: 0.7856 (mtpt) cc_final: 0.7162 (tttt) REVERT: G 75 LYS cc_start: 0.8348 (mmtm) cc_final: 0.8100 (mmtt) outliers start: 19 outliers final: 8 residues processed: 152 average time/residue: 2.0699 time to fit residues: 330.7439 Evaluate side-chains 158 residues out of total 632 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 145 time to evaluate : 0.903 ------------------------------------------------------------------------------- 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 52 GLU Chi-restraints excluded: chain C residue 64 GLU Chi-restraints excluded: chain D residue 109 SER Chi-restraints excluded: chain D residue 113 LYS Chi-restraints excluded: chain F residue 21 VAL 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 H residue 85 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 29 optimal weight: 0.8980 chunk 18 optimal weight: 4.9990 chunk 61 optimal weight: 6.9990 chunk 65 optimal weight: 1.9990 chunk 47 optimal weight: 6.9990 chunk 8 optimal weight: 1.9990 chunk 75 optimal weight: 6.9990 chunk 87 optimal weight: 10.0000 chunk 92 optimal weight: 4.9990 chunk 84 optimal weight: 6.9990 chunk 89 optimal weight: 5.9990 overall best weight: 2.9788 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8171 moved from start: 0.3306 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.063 12775 Z= 0.370 Angle : 0.660 7.904 18498 Z= 0.389 Chirality : 0.039 0.170 2109 Planarity : 0.005 0.043 1335 Dihedral : 31.063 175.870 4096 Min Nonbonded Distance : 2.109 Molprobity Statistics. All-atom Clashscore : 6.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.48 % Favored : 98.52 % Rotamer: Outliers : 3.32 % Allowed : 16.93 % Favored : 79.75 % 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: 2.42 (0.29), residues: 743 helix: 2.18 (0.21), residues: 558 sheet: None (None), residues: 0 loop : -0.17 (0.40), residues: 185 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.004 0.001 HIS B 75 PHE 0.014 0.002 PHE A 67 TYR 0.014 0.002 TYR E 54 ARG 0.008 0.001 ARG E 42 *********************** 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 163 residues out of total 632 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 142 time to evaluate : 0.970 Fit side-chains REVERT: A 131 ARG cc_start: 0.8571 (OUTLIER) cc_final: 0.7594 (mtp180) REVERT: B 52 GLU cc_start: 0.8583 (OUTLIER) cc_final: 0.7695 (mp0) REVERT: B 79 LYS cc_start: 0.8646 (mtpt) cc_final: 0.8332 (mtmm) REVERT: C 36 LYS cc_start: 0.8435 (mmtm) cc_final: 0.8184 (mmpt) REVERT: C 92 GLU cc_start: 0.8221 (mt-10) cc_final: 0.7944 (mt-10) REVERT: D 73 GLU cc_start: 0.8665 (tp30) cc_final: 0.8356 (tp30) REVERT: E 115 LYS cc_start: 0.8603 (OUTLIER) cc_final: 0.8252 (mppt) REVERT: F 27 GLN cc_start: 0.8572 (mm-40) cc_final: 0.8346 (mm110) REVERT: F 77 LYS cc_start: 0.8467 (OUTLIER) cc_final: 0.8056 (mtpt) REVERT: F 93 GLN cc_start: 0.8231 (OUTLIER) cc_final: 0.7954 (mt0) REVERT: G 15 LYS cc_start: 0.7831 (mtpt) cc_final: 0.7169 (tttt) REVERT: G 75 LYS cc_start: 0.8417 (mmtm) cc_final: 0.8154 (mmtm) REVERT: G 95 LYS cc_start: 0.8742 (OUTLIER) cc_final: 0.8462 (tmtm) outliers start: 21 outliers final: 11 residues processed: 152 average time/residue: 2.0512 time to fit residues: 327.6045 Evaluate side-chains 156 residues out of total 632 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 139 time to evaluate : 0.904 ------------------------------------------------------------------------------- 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 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 Chi-restraints excluded: chain H residue 109 SER Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 92 optimal weight: 3.9990 chunk 54 optimal weight: 5.9990 chunk 39 optimal weight: 0.8980 chunk 70 optimal weight: 20.0000 chunk 27 optimal weight: 1.9990 chunk 81 optimal weight: 4.9990 chunk 84 optimal weight: 6.9990 chunk 89 optimal weight: 4.9990 chunk 58 optimal weight: 7.9990 chunk 94 optimal weight: 3.9990 chunk 57 optimal weight: 0.7980 overall best weight: 2.3386 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8164 moved from start: 0.3307 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= 0.317 Angle : 0.637 7.582 18498 Z= 0.379 Chirality : 0.038 0.142 2109 Planarity : 0.005 0.042 1335 Dihedral : 31.044 175.801 4096 Min Nonbonded Distance : 2.105 Molprobity Statistics. All-atom Clashscore : 6.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.08 % Favored : 98.92 % Rotamer: Outliers : 3.48 % Allowed : 16.30 % 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: 2.39 (0.29), residues: 743 helix: 2.16 (0.21), residues: 558 sheet: None (None), residues: 0 loop : -0.19 (0.39), 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 0.013 0.002 TYR E 54 ARG 0.008 0.001 ARG E 42 *********************** 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 164 residues out of total 632 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 142 time to evaluate : 0.881 Fit side-chains REVERT: A 131 ARG cc_start: 0.8567 (OUTLIER) cc_final: 0.7585 (mtp180) REVERT: B 52 GLU cc_start: 0.8567 (OUTLIER) cc_final: 0.7675 (mp0) REVERT: B 79 LYS cc_start: 0.8648 (mtpt) cc_final: 0.8333 (mtmm) REVERT: C 36 LYS cc_start: 0.8429 (mmtm) cc_final: 0.8179 (mmpt) REVERT: C 92 GLU cc_start: 0.8210 (mt-10) cc_final: 0.7940 (mt-10) REVERT: D 73 GLU cc_start: 0.8666 (tp30) cc_final: 0.8381 (tp30) REVERT: D 105 LYS cc_start: 0.8084 (mtmm) cc_final: 0.7868 (mtpt) REVERT: E 115 LYS cc_start: 0.8586 (OUTLIER) cc_final: 0.8231 (mppt) REVERT: F 27 GLN cc_start: 0.8567 (mm-40) cc_final: 0.8343 (mm110) REVERT: F 77 LYS cc_start: 0.8456 (OUTLIER) cc_final: 0.8049 (mtpt) REVERT: F 92 ARG cc_start: 0.8372 (OUTLIER) cc_final: 0.7261 (ttp80) REVERT: F 93 GLN cc_start: 0.8213 (OUTLIER) cc_final: 0.7927 (mt0) REVERT: G 15 LYS cc_start: 0.7831 (mtpt) cc_final: 0.7175 (tttt) REVERT: G 75 LYS cc_start: 0.8407 (mmtm) cc_final: 0.8144 (mmtm) REVERT: G 95 LYS cc_start: 0.8743 (OUTLIER) cc_final: 0.8464 (tmtm) outliers start: 22 outliers final: 11 residues processed: 150 average time/residue: 2.1298 time to fit residues: 335.0701 Evaluate side-chains 158 residues out of total 632 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 140 time to evaluate : 1.034 ------------------------------------------------------------------------------- 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 77 ASP Chi-restraints excluded: chain E residue 115 LYS Chi-restraints excluded: chain F residue 77 LYS Chi-restraints excluded: chain F residue 92 ARG 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 45 optimal weight: 2.9990 chunk 66 optimal weight: 2.9990 chunk 99 optimal weight: 10.0000 chunk 91 optimal weight: 6.9990 chunk 79 optimal weight: 3.9990 chunk 8 optimal weight: 0.5980 chunk 61 optimal weight: 0.7980 chunk 48 optimal weight: 0.7980 chunk 63 optimal weight: 0.9990 chunk 84 optimal weight: 6.9990 chunk 24 optimal weight: 4.9990 overall best weight: 1.2384 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8146 moved from start: 0.3316 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 12775 Z= 0.219 Angle : 0.605 7.540 18498 Z= 0.364 Chirality : 0.034 0.129 2109 Planarity : 0.004 0.040 1335 Dihedral : 31.016 176.077 4096 Min Nonbonded Distance : 2.105 Molprobity Statistics. All-atom Clashscore : 7.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.21 % Favored : 98.79 % 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: 2.54 (0.29), residues: 743 helix: 2.29 (0.21), residues: 558 sheet: None (None), residues: 0 loop : -0.17 (0.39), residues: 185 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.004 0.001 HIS B 75 PHE 0.013 0.002 PHE A 67 TYR 0.013 0.002 TYR H 80 ARG 0.007 0.001 ARG E 42 ********************** 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 165 residues out of total 632 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 144 time to evaluate : 0.954 Fit side-chains REVERT: A 131 ARG cc_start: 0.8532 (OUTLIER) cc_final: 0.7581 (mtp180) REVERT: B 52 GLU cc_start: 0.8535 (OUTLIER) cc_final: 0.7662 (mp0) REVERT: B 79 LYS cc_start: 0.8648 (mtpt) cc_final: 0.8333 (mtmm) REVERT: C 36 LYS cc_start: 0.8413 (mmtm) cc_final: 0.8167 (mmpt) REVERT: C 92 GLU cc_start: 0.8194 (mt-10) cc_final: 0.7929 (mt-10) REVERT: D 105 LYS cc_start: 0.8064 (mtmm) cc_final: 0.7815 (mtpt) REVERT: E 115 LYS cc_start: 0.8579 (OUTLIER) cc_final: 0.8222 (mppt) REVERT: F 27 GLN cc_start: 0.8551 (mm-40) cc_final: 0.8234 (mm110) REVERT: F 77 LYS cc_start: 0.8434 (OUTLIER) cc_final: 0.8024 (mtpt) REVERT: F 92 ARG cc_start: 0.8358 (OUTLIER) cc_final: 0.7266 (ttp80) REVERT: F 93 GLN cc_start: 0.8179 (OUTLIER) cc_final: 0.7894 (mt0) REVERT: G 15 LYS cc_start: 0.7819 (mtpt) cc_final: 0.7120 (tttt) REVERT: G 75 LYS cc_start: 0.8391 (mmtm) cc_final: 0.8127 (mmtm) REVERT: G 95 LYS cc_start: 0.8736 (OUTLIER) cc_final: 0.8462 (tmtm) outliers start: 21 outliers final: 11 residues processed: 150 average time/residue: 2.1056 time to fit residues: 331.6218 Evaluate side-chains 159 residues out of total 632 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 141 time to evaluate : 0.971 ------------------------------------------------------------------------------- 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 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 77 ASP Chi-restraints excluded: chain E residue 115 LYS Chi-restraints excluded: chain F residue 77 LYS Chi-restraints excluded: chain F residue 84 MET Chi-restraints excluded: chain F residue 92 ARG 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 73 optimal weight: 10.0000 chunk 11 optimal weight: 2.9990 chunk 22 optimal weight: 6.9990 chunk 79 optimal weight: 4.9990 chunk 33 optimal weight: 4.9990 chunk 81 optimal weight: 5.9990 chunk 10 optimal weight: 0.6980 chunk 14 optimal weight: 1.9990 chunk 69 optimal weight: 0.7980 chunk 4 optimal weight: 2.9990 chunk 57 optimal weight: 0.8980 overall best weight: 1.4784 ------------------------------------------------------------------------------- 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 = 0.4067 r_free = 0.4067 target = 0.175171 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3582 r_free = 0.3582 target = 0.132653 restraints weight = 10685.681| |-----------------------------------------------------------------------------| r_work (start): 0.3539 rms_B_bonded: 0.92 r_work: 0.3340 rms_B_bonded: 2.25 restraints_weight: 0.5000 r_work: 0.3196 rms_B_bonded: 3.59 restraints_weight: 0.2500 r_work (final): 0.3196 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8218 moved from start: 0.3343 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= 0.252 Angle : 0.610 7.555 18498 Z= 0.365 Chirality : 0.035 0.130 2109 Planarity : 0.004 0.042 1335 Dihedral : 30.965 176.779 4096 Min Nonbonded Distance : 2.105 Molprobity Statistics. All-atom Clashscore : 7.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.21 % Favored : 98.79 % 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: 2.56 (0.29), residues: 743 helix: 2.30 (0.21), residues: 558 sheet: None (None), residues: 0 loop : -0.15 (0.39), 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 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5186.45 seconds wall clock time: 94 minutes 12.96 seconds (5652.96 seconds total)