Starting phenix.real_space_refine on Thu Mar 13 03:35:30 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7y5w_33627/03_2025/7y5w_33627.cif Found real_map, /net/cci-nas-00/data/ceres_data/7y5w_33627/03_2025/7y5w_33627.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.5 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/7y5w_33627/03_2025/7y5w_33627.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7y5w_33627/03_2025/7y5w_33627.map" model { file = "/net/cci-nas-00/data/ceres_data/7y5w_33627/03_2025/7y5w_33627.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7y5w_33627/03_2025/7y5w_33627.cif" } resolution = 3.5 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= 0.017 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 202 5.49 5 S 20 5.16 5 C 4911 2.51 5 N 1652 2.21 5 O 2026 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 4 residue(s): 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5624/modules/chem_data/mon_lib" Total number of atoms: 8811 Number of models: 1 Model: "" Number of chains: 10 Chain: "A" Number of atoms: 619 Number of conformers: 1 Conformer: "" Number of residues, atoms: 76, 619 Classifications: {'peptide': 76} Link IDs: {'PTRANS': 2, 'TRANS': 73} Chain: "B" Number of atoms: 561 Number of conformers: 1 Conformer: "" Number of residues, atoms: 70, 561 Classifications: {'peptide': 70} Link IDs: {'PTRANS': 1, 'TRANS': 68} Chain: "C" Number of atoms: 608 Number of conformers: 1 Conformer: "" Number of residues, atoms: 75, 608 Classifications: {'peptide': 75} Link IDs: {'PTRANS': 2, 'TRANS': 72} Chain: "D" Number of atoms: 576 Number of conformers: 1 Conformer: "" Number of residues, atoms: 72, 576 Classifications: {'peptide': 72} Link IDs: {'PTRANS': 1, 'TRANS': 70} Chain: "E" Number of atoms: 615 Number of conformers: 1 Conformer: "" Number of residues, atoms: 76, 615 Classifications: {'peptide': 76} Link IDs: {'PTRANS': 2, 'TRANS': 73} Chain: "F" Number of atoms: 576 Number of conformers: 1 Conformer: "" Number of residues, atoms: 72, 576 Classifications: {'peptide': 72} Link IDs: {'PTRANS': 1, 'TRANS': 70} Chain: "G" Number of atoms: 591 Number of conformers: 1 Conformer: "" Number of residues, atoms: 73, 591 Classifications: {'peptide': 73} Link IDs: {'PTRANS': 2, 'TRANS': 70} Chain: "H" Number of atoms: 524 Number of conformers: 1 Conformer: "" Number of residues, atoms: 65, 524 Classifications: {'peptide': 65} Link IDs: {'PTRANS': 1, 'TRANS': 63} Chain: "I" Number of atoms: 2054 Number of conformers: 1 Conformer: "" Number of residues, atoms: 101, 2054 Classifications: {'DNA': 101} Link IDs: {'rna3p': 100} Chain: "J" Number of atoms: 2087 Number of conformers: 1 Conformer: "" Number of residues, atoms: 101, 2087 Classifications: {'DNA': 101} Link IDs: {'rna3p': 100} Time building chain proxies: 5.35, per 1000 atoms: 0.61 Number of scatterers: 8811 At special positions: 0 Unit cell: (82, 114, 116, 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 20 16.00 P 202 15.00 O 2026 8.00 N 1652 7.00 C 4911 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: 2.21 Conformation dependent library (CDL) restraints added in 541.1 milliseconds 1126 Ramachandran restraints generated. 563 Oldfield, 0 Emsley, 563 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1100 Finding SS restraints... Secondary structure from input PDB file: 26 helices and 5 sheets defined 79.1% alpha, 1.7% beta 90 base pairs and 167 stacking pairs defined. Time for finding SS restraints: 3.86 Creating SS restraints... Processing helix chain 'A' and resid 63 through 79 Processing helix chain 'A' and resid 85 through 114 Processing helix chain 'A' and resid 120 through 131 removed outlier: 3.505A pdb=" N ILE A 124 " --> pdb=" O MET A 120 " (cutoff:3.500A) 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 removed outlier: 3.653A pdb=" N GLU B 53 " --> pdb=" O LEU B 49 " (cutoff:3.500A) Processing helix chain 'B' and resid 82 through 92 removed outlier: 3.501A pdb=" N ARG B 92 " --> pdb=" O TYR B 88 " (cutoff:3.500A) Processing helix chain 'C' and resid 63 through 79 Processing helix chain 'C' and resid 85 through 114 Processing helix chain 'C' and resid 120 through 131 Processing helix chain 'D' and resid 30 through 41 Processing helix chain 'D' and resid 47 through 76 removed outlier: 4.209A pdb=" N TYR D 51 " --> pdb=" O SER D 47 " (cutoff:3.500A) removed outlier: 4.360A pdb=" N GLU D 52 " --> pdb=" O GLY D 48 " (cutoff:3.500A) Processing helix chain 'D' and resid 82 through 94 Processing helix chain 'E' and resid 63 through 79 Processing helix chain 'E' and resid 85 through 114 Processing helix chain 'E' and resid 120 through 132 Processing helix chain 'F' and resid 25 through 29 Processing helix chain 'F' and resid 30 through 41 Processing helix chain 'F' and resid 49 through 76 removed outlier: 3.503A pdb=" N GLU F 53 " --> pdb=" O LEU F 49 " (cutoff:3.500A) Processing helix chain 'F' and resid 82 through 93 removed outlier: 3.548A pdb=" N VAL F 86 " --> pdb=" O THR F 82 " (cutoff:3.500A) Processing helix chain 'G' and resid 63 through 79 removed outlier: 3.561A pdb=" N PHE G 67 " --> pdb=" O ARG G 63 " (cutoff:3.500A) Processing helix chain 'G' and resid 85 through 114 Processing helix chain 'G' and resid 120 through 132 removed outlier: 3.803A pdb=" N ILE G 124 " --> pdb=" O MET G 120 " (cutoff:3.500A) removed outlier: 3.529A pdb=" N GLY G 132 " --> pdb=" O ARG G 128 " (cutoff:3.500A) Processing helix chain 'H' and resid 30 through 41 Processing helix chain 'H' and resid 49 through 77 Processing helix chain 'H' and resid 82 through 92 Processing sheet with id=AA1, first strand: chain 'A' and resid 118 through 119 Processing sheet with id=AA2, first strand: chain 'C' and resid 83 through 84 removed outlier: 7.247A pdb=" N ARG C 83 " --> pdb=" O VAL D 81 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA2 Processing sheet with id=AA3, first strand: chain 'C' and resid 118 through 119 Processing sheet with id=AA4, first strand: chain 'E' and resid 83 through 84 removed outlier: 7.326A pdb=" N ARG E 83 " --> pdb=" O VAL F 81 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA4 Processing sheet with id=AA5, first strand: chain 'E' and resid 118 through 119 349 hydrogen bonds defined for protein. 1035 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 231 hydrogen bonds 442 hydrogen bond angles 0 basepair planarities 90 basepair parallelities 167 stacking parallelities Total time for adding SS restraints: 2.62 Time building geometry restraints manager: 2.63 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 1879 1.34 - 1.45: 2816 1.45 - 1.57: 4233 1.57 - 1.69: 402 1.69 - 1.81: 32 Bond restraints: 9362 Sorted by residual: bond pdb=" C3' DG I 73 " pdb=" O3' DG I 73 " ideal model delta sigma weight residual 1.422 1.455 -0.033 3.00e-02 1.11e+03 1.19e+00 bond pdb=" C3' DG J 84 " pdb=" O3' DG J 84 " ideal model delta sigma weight residual 1.422 1.453 -0.031 3.00e-02 1.11e+03 1.05e+00 bond pdb=" CG1 ILE G 112 " pdb=" CD1 ILE G 112 " ideal model delta sigma weight residual 1.513 1.473 0.040 3.90e-02 6.57e+02 1.03e+00 bond pdb=" CB GLU G 105 " pdb=" CG GLU G 105 " ideal model delta sigma weight residual 1.520 1.549 -0.029 3.00e-02 1.11e+03 9.35e-01 bond pdb=" C3' DG I 34 " pdb=" O3' DG I 34 " ideal model delta sigma weight residual 1.422 1.449 -0.027 3.00e-02 1.11e+03 8.07e-01 ... (remaining 9357 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.80: 13238 1.80 - 3.61: 233 3.61 - 5.41: 16 5.41 - 7.22: 0 7.22 - 9.02: 1 Bond angle restraints: 13488 Sorted by residual: angle pdb=" CB MET B 84 " pdb=" CG MET B 84 " pdb=" SD MET B 84 " ideal model delta sigma weight residual 112.70 121.72 -9.02 3.00e+00 1.11e-01 9.05e+00 angle pdb=" C3' DG I 121 " pdb=" C2' DG I 121 " pdb=" C1' DG I 121 " ideal model delta sigma weight residual 101.60 98.09 3.51 1.50e+00 4.44e-01 5.48e+00 angle pdb=" CB GLU G 105 " pdb=" CG GLU G 105 " pdb=" CD GLU G 105 " ideal model delta sigma weight residual 112.60 116.46 -3.86 1.70e+00 3.46e-01 5.16e+00 angle pdb=" CB ARG B 40 " pdb=" CG ARG B 40 " pdb=" CD ARG B 40 " ideal model delta sigma weight residual 111.30 116.14 -4.84 2.30e+00 1.89e-01 4.42e+00 angle pdb=" C2' DG I 121 " pdb=" C1' DG I 121 " pdb=" N9 DG I 121 " ideal model delta sigma weight residual 113.50 116.46 -2.96 1.50e+00 4.44e-01 3.90e+00 ... (remaining 13483 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 29.06: 3940 29.06 - 58.13: 1086 58.13 - 87.19: 104 87.19 - 116.25: 1 116.25 - 145.31: 4 Dihedral angle restraints: 5135 sinusoidal: 3448 harmonic: 1687 Sorted by residual: dihedral pdb=" C4' DG I 73 " pdb=" C3' DG I 73 " pdb=" O3' DG I 73 " pdb=" P DC I 74 " ideal model delta sinusoidal sigma weight residual 220.00 74.69 145.31 1 3.50e+01 8.16e-04 1.43e+01 dihedral pdb=" C4' DT J 105 " pdb=" C3' DT J 105 " pdb=" O3' DT J 105 " pdb=" P DG J 106 " ideal model delta sinusoidal sigma weight residual 220.00 89.58 130.42 1 3.50e+01 8.16e-04 1.29e+01 dihedral pdb=" C4' DG I 34 " pdb=" C3' DG I 34 " pdb=" O3' DG I 34 " pdb=" P DT I 35 " ideal model delta sinusoidal sigma weight residual 220.00 91.20 128.80 1 3.50e+01 8.16e-04 1.27e+01 ... (remaining 5132 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.029: 1110 0.029 - 0.059: 327 0.059 - 0.088: 77 0.088 - 0.118: 29 0.118 - 0.147: 6 Chirality restraints: 1549 Sorted by residual: chirality pdb=" CA ILE D 29 " pdb=" N ILE D 29 " pdb=" C ILE D 29 " pdb=" CB ILE D 29 " both_signs ideal model delta sigma weight residual False 2.43 2.58 -0.15 2.00e-01 2.50e+01 5.40e-01 chirality pdb=" CA ILE D 46 " pdb=" N ILE D 46 " pdb=" C ILE D 46 " pdb=" CB ILE D 46 " both_signs ideal model delta sigma weight residual False 2.43 2.56 -0.13 2.00e-01 2.50e+01 4.30e-01 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 ... (remaining 1546 not shown) Planarity restraints: 1004 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C MET G 120 " -0.030 5.00e-02 4.00e+02 4.51e-02 3.26e+00 pdb=" N PRO G 121 " 0.078 5.00e-02 4.00e+02 pdb=" CA PRO G 121 " -0.023 5.00e-02 4.00e+02 pdb=" CD PRO G 121 " -0.025 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C1' DG I 121 " -0.023 2.00e-02 2.50e+03 1.04e-02 3.24e+00 pdb=" N9 DG I 121 " 0.025 2.00e-02 2.50e+03 pdb=" C8 DG I 121 " 0.002 2.00e-02 2.50e+03 pdb=" N7 DG I 121 " -0.001 2.00e-02 2.50e+03 pdb=" C5 DG I 121 " 0.001 2.00e-02 2.50e+03 pdb=" C6 DG I 121 " -0.001 2.00e-02 2.50e+03 pdb=" O6 DG I 121 " -0.006 2.00e-02 2.50e+03 pdb=" N1 DG I 121 " -0.003 2.00e-02 2.50e+03 pdb=" C2 DG I 121 " -0.004 2.00e-02 2.50e+03 pdb=" N2 DG I 121 " 0.005 2.00e-02 2.50e+03 pdb=" N3 DG I 121 " 0.003 2.00e-02 2.50e+03 pdb=" C4 DG I 121 " 0.003 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1' DC I 110 " -0.020 2.00e-02 2.50e+03 9.51e-03 2.04e+00 pdb=" N1 DC I 110 " 0.016 2.00e-02 2.50e+03 pdb=" C2 DC I 110 " 0.001 2.00e-02 2.50e+03 pdb=" O2 DC I 110 " 0.007 2.00e-02 2.50e+03 pdb=" N3 DC I 110 " -0.002 2.00e-02 2.50e+03 pdb=" C4 DC I 110 " -0.003 2.00e-02 2.50e+03 pdb=" N4 DC I 110 " -0.008 2.00e-02 2.50e+03 pdb=" C5 DC I 110 " 0.007 2.00e-02 2.50e+03 pdb=" C6 DC I 110 " 0.004 2.00e-02 2.50e+03 ... (remaining 1001 not shown) Histogram of nonbonded interaction distances: 2.10 - 2.66: 219 2.66 - 3.22: 7704 3.22 - 3.78: 17065 3.78 - 4.34: 20536 4.34 - 4.90: 29648 Nonbonded interactions: 75172 Sorted by model distance: nonbonded pdb=" N2 DG I 34 " pdb=" O2 DC J 114 " model vdw 2.102 2.496 nonbonded pdb=" N2 DG I 33 " pdb=" O2 DC J 115 " model vdw 2.118 2.496 nonbonded pdb=" N2 DG I 85 " pdb=" O2 DC J 63 " model vdw 2.139 2.496 nonbonded pdb=" O2 DC I 82 " pdb=" N2 DG J 66 " model vdw 2.156 2.496 nonbonded pdb=" OG1 THR F 73 " pdb=" OD2 ASP F 85 " model vdw 2.228 3.040 ... (remaining 75167 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 61 through 133) selection = (chain 'C' and resid 61 through 133) selection = (chain 'E' and resid 61 through 133) selection = chain 'G' } ncs_group { reference = (chain 'B' and resid 29 through 93) selection = (chain 'D' and resid 29 through 93) selection = (chain 'F' and resid 29 through 93) 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 group one per residue 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: 0.680 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: 0.000 Extract box with map and model: 0.350 Check model and map are aligned: 0.060 Set scattering table: 0.070 Process input model: 24.400 Find NCS groups from input model: 0.260 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.720 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 28.570 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6989 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 0.040 9362 Z= 0.185 Angle : 0.533 9.023 13488 Z= 0.314 Chirality : 0.032 0.147 1549 Planarity : 0.003 0.045 1004 Dihedral : 27.557 145.314 4035 Min Nonbonded Distance : 2.102 Molprobity Statistics. All-atom Clashscore : 12.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.95 % Favored : 98.05 % Rotamer: Outliers : 0.00 % Allowed : 0.20 % Favored : 99.80 % 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 (0.34), residues: 563 helix: 2.20 (0.23), residues: 458 sheet: None (None), residues: 0 loop : -0.72 (0.50), residues: 105 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.003 0.001 HIS C 113 PHE 0.007 0.001 PHE E 67 TYR 0.008 0.001 TYR B 51 ARG 0.006 0.000 ARG A 129 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1126 Ramachandran restraints generated. 563 Oldfield, 0 Emsley, 563 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1126 Ramachandran restraints generated. 563 Oldfield, 0 Emsley, 563 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 322 residues out of total 494 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 322 time to evaluate : 0.702 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 77 ASP cc_start: 0.6596 (t70) cc_final: 0.6280 (t0) REVERT: E 60 LEU cc_start: 0.7308 (mt) cc_final: 0.6991 (mt) REVERT: F 80 THR cc_start: 0.8225 (m) cc_final: 0.7965 (p) REVERT: G 89 VAL cc_start: 0.8828 (m) cc_final: 0.8532 (m) REVERT: G 90 MET cc_start: 0.7212 (tmm) cc_final: 0.6304 (tmm) REVERT: H 60 VAL cc_start: 0.8165 (t) cc_final: 0.7948 (p) outliers start: 0 outliers final: 0 residues processed: 322 average time/residue: 0.2953 time to fit residues: 118.2115 Evaluate side-chains 224 residues out of total 494 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 224 time to evaluate : 0.718 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 75 random chunks: chunk 63 optimal weight: 6.9990 chunk 56 optimal weight: 5.9990 chunk 31 optimal weight: 0.6980 chunk 19 optimal weight: 0.8980 chunk 38 optimal weight: 0.9990 chunk 30 optimal weight: 2.9990 chunk 58 optimal weight: 5.9990 chunk 22 optimal weight: 2.9990 chunk 35 optimal weight: 0.3980 chunk 43 optimal weight: 5.9990 chunk 68 optimal weight: 5.9990 overall best weight: 1.1984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 76 GLN ** A 108 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 93 GLN C 68 GLN ** C 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 75 HIS E 76 GLN ** E 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3610 r_free = 0.3610 target = 0.059083 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3093 r_free = 0.3093 target = 0.042701 restraints weight = 54682.117| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3139 r_free = 0.3139 target = 0.043987 restraints weight = 26617.126| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 45)----------------| | r_work = 0.3167 r_free = 0.3167 target = 0.044817 restraints weight = 17767.618| |-----------------------------------------------------------------------------| r_work (final): 0.3095 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8362 moved from start: 0.2904 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 9362 Z= 0.240 Angle : 0.667 11.543 13488 Z= 0.373 Chirality : 0.037 0.234 1549 Planarity : 0.005 0.046 1004 Dihedral : 30.658 146.560 2840 Min Nonbonded Distance : 2.071 Molprobity Statistics. All-atom Clashscore : 17.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.78 % Favored : 98.22 % Rotamer: Outliers : 3.64 % Allowed : 26.72 % Favored : 69.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.17 (0.34), residues: 563 helix: 1.91 (0.24), residues: 463 sheet: None (None), residues: 0 loop : -0.74 (0.51), residues: 100 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.005 0.001 HIS C 113 PHE 0.022 0.002 PHE H 61 TYR 0.017 0.002 TYR H 88 ARG 0.008 0.001 ARG E 83 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1126 Ramachandran restraints generated. 563 Oldfield, 0 Emsley, 563 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1126 Ramachandran restraints generated. 563 Oldfield, 0 Emsley, 563 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 279 residues out of total 494 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 261 time to evaluate : 0.649 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 68 GLN cc_start: 0.9688 (mt0) cc_final: 0.9250 (mm-40) REVERT: A 90 MET cc_start: 0.8701 (tmm) cc_final: 0.8426 (tmm) REVERT: A 99 TYR cc_start: 0.9375 (t80) cc_final: 0.9094 (t80) REVERT: A 112 ILE cc_start: 0.9714 (tp) cc_final: 0.9398 (pt) REVERT: A 120 MET cc_start: 0.8621 (mtm) cc_final: 0.8146 (mtm) REVERT: A 134 ARG cc_start: 0.8779 (tpp-160) cc_final: 0.8535 (tpp-160) REVERT: B 44 LYS cc_start: 0.9087 (mmmt) cc_final: 0.8667 (mmmm) REVERT: B 63 GLU cc_start: 0.9324 (mt-10) cc_final: 0.9001 (mm-30) REVERT: B 68 ASP cc_start: 0.8580 (t70) cc_final: 0.8243 (t0) REVERT: B 92 ARG cc_start: 0.8561 (ttp80) cc_final: 0.8300 (ttp80) REVERT: C 73 GLU cc_start: 0.8888 (tm-30) cc_final: 0.8660 (tm-30) REVERT: C 77 ASP cc_start: 0.9000 (t70) cc_final: 0.8752 (t0) REVERT: C 94 GLU cc_start: 0.8745 (tm-30) cc_final: 0.8470 (tm-30) REVERT: C 105 GLU cc_start: 0.9000 (tp30) cc_final: 0.8678 (mm-30) REVERT: C 128 ARG cc_start: 0.9407 (mtp85) cc_final: 0.9091 (mtp85) REVERT: C 129 ARG cc_start: 0.9251 (tpp80) cc_final: 0.9039 (tpp80) REVERT: D 44 LYS cc_start: 0.9318 (ttmm) cc_final: 0.9022 (mtpp) REVERT: E 62 ILE cc_start: 0.8808 (mt) cc_final: 0.8579 (mp) REVERT: E 129 ARG cc_start: 0.8866 (mmm160) cc_final: 0.8338 (mmm160) REVERT: F 31 LYS cc_start: 0.9330 (ttpp) cc_final: 0.8940 (ttmm) REVERT: F 44 LYS cc_start: 0.9501 (OUTLIER) cc_final: 0.9206 (mmmm) REVERT: F 79 LYS cc_start: 0.9072 (mtpp) cc_final: 0.8563 (mtmm) REVERT: F 80 THR cc_start: 0.9367 (m) cc_final: 0.8833 (p) REVERT: F 92 ARG cc_start: 0.8949 (tmt-80) cc_final: 0.8731 (tmt170) REVERT: G 120 MET cc_start: 0.8587 (mmm) cc_final: 0.8369 (mmm) REVERT: G 131 ARG cc_start: 0.8932 (mtp85) cc_final: 0.8596 (mtp85) REVERT: H 43 VAL cc_start: 0.8288 (t) cc_final: 0.7965 (t) REVERT: H 49 LEU cc_start: 0.8192 (mp) cc_final: 0.7889 (mm) REVERT: H 53 GLU cc_start: 0.9420 (mt-10) cc_final: 0.9161 (mt-10) outliers start: 18 outliers final: 12 residues processed: 265 average time/residue: 0.2617 time to fit residues: 87.9739 Evaluate side-chains 251 residues out of total 494 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 238 time to evaluate : 0.744 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 86 SER Chi-restraints excluded: chain B residue 60 VAL Chi-restraints excluded: chain B residue 72 TYR Chi-restraints excluded: chain C residue 68 GLN Chi-restraints excluded: chain E residue 124 ILE Chi-restraints excluded: chain F residue 30 THR Chi-restraints excluded: chain F residue 44 LYS Chi-restraints excluded: chain F residue 66 ILE Chi-restraints excluded: chain F residue 86 VAL Chi-restraints excluded: chain F residue 90 LEU Chi-restraints excluded: chain G residue 94 GLU Chi-restraints excluded: chain H residue 30 THR Chi-restraints excluded: chain H residue 59 LYS Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 75 random chunks: chunk 13 optimal weight: 2.9990 chunk 52 optimal weight: 3.9990 chunk 57 optimal weight: 6.9990 chunk 22 optimal weight: 0.5980 chunk 16 optimal weight: 6.9990 chunk 11 optimal weight: 0.9980 chunk 66 optimal weight: 6.9990 chunk 51 optimal weight: 1.9990 chunk 1 optimal weight: 0.9980 chunk 63 optimal weight: 5.9990 chunk 6 optimal weight: 0.9990 overall best weight: 1.1184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 68 GLN E 93 GLN H 64 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3591 r_free = 0.3591 target = 0.058582 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3081 r_free = 0.3081 target = 0.042364 restraints weight = 54434.582| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 52)----------------| | r_work = 0.3126 r_free = 0.3126 target = 0.043654 restraints weight = 26071.216| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 45)----------------| | r_work = 0.3155 r_free = 0.3155 target = 0.044477 restraints weight = 17109.651| |-----------------------------------------------------------------------------| r_work (final): 0.3090 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8376 moved from start: 0.3367 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 9362 Z= 0.222 Angle : 0.656 10.320 13488 Z= 0.370 Chirality : 0.036 0.171 1549 Planarity : 0.004 0.045 1004 Dihedral : 30.620 148.902 2840 Min Nonbonded Distance : 2.066 Molprobity Statistics. All-atom Clashscore : 16.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.95 % Favored : 98.05 % Rotamer: Outliers : 6.48 % Allowed : 26.72 % Favored : 66.80 % 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: 2.05 (0.34), residues: 563 helix: 1.83 (0.24), residues: 462 sheet: None (None), residues: 0 loop : -0.76 (0.52), residues: 101 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.004 0.001 HIS C 113 PHE 0.017 0.002 PHE H 61 TYR 0.010 0.001 TYR F 88 ARG 0.006 0.001 ARG H 78 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1126 Ramachandran restraints generated. 563 Oldfield, 0 Emsley, 563 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1126 Ramachandran restraints generated. 563 Oldfield, 0 Emsley, 563 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 289 residues out of total 494 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 257 time to evaluate : 0.664 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 74 ILE cc_start: 0.9750 (tt) cc_final: 0.9544 (tt) REVERT: A 90 MET cc_start: 0.8723 (tmm) cc_final: 0.8208 (tmm) REVERT: A 99 TYR cc_start: 0.9361 (t80) cc_final: 0.9045 (t80) REVERT: A 112 ILE cc_start: 0.9699 (tp) cc_final: 0.9404 (pt) REVERT: A 120 MET cc_start: 0.8663 (mtm) cc_final: 0.8309 (mtm) REVERT: A 125 GLN cc_start: 0.9314 (mt0) cc_final: 0.8981 (mm-40) REVERT: B 44 LYS cc_start: 0.9069 (mmmt) cc_final: 0.8831 (mmmt) REVERT: B 63 GLU cc_start: 0.9301 (mt-10) cc_final: 0.8989 (mm-30) REVERT: B 68 ASP cc_start: 0.8625 (t70) cc_final: 0.8223 (t0) REVERT: C 73 GLU cc_start: 0.8971 (tm-30) cc_final: 0.8552 (tm-30) REVERT: C 77 ASP cc_start: 0.9004 (t70) cc_final: 0.8731 (t0) REVERT: C 85 GLN cc_start: 0.9294 (OUTLIER) cc_final: 0.9043 (mt0) REVERT: C 94 GLU cc_start: 0.8722 (tm-30) cc_final: 0.8416 (tm-30) REVERT: C 125 GLN cc_start: 0.9265 (mt0) cc_final: 0.8977 (mp10) REVERT: C 129 ARG cc_start: 0.9225 (tpp80) cc_final: 0.8890 (tpp80) REVERT: D 44 LYS cc_start: 0.9338 (ttmm) cc_final: 0.9067 (mtpp) REVERT: D 74 GLU cc_start: 0.9231 (mm-30) cc_final: 0.8975 (mm-30) REVERT: E 90 MET cc_start: 0.8969 (tpp) cc_final: 0.8756 (mmp) REVERT: E 94 GLU cc_start: 0.8993 (mm-30) cc_final: 0.8782 (mm-30) REVERT: E 115 LYS cc_start: 0.9632 (mmmm) cc_final: 0.9344 (mmmm) REVERT: E 120 MET cc_start: 0.8297 (mmm) cc_final: 0.7921 (mmm) REVERT: E 122 LYS cc_start: 0.9581 (mtmt) cc_final: 0.9365 (ptpt) REVERT: E 129 ARG cc_start: 0.8888 (mmm160) cc_final: 0.8245 (mmm160) REVERT: F 31 LYS cc_start: 0.9344 (ttpp) cc_final: 0.9113 (ttmm) REVERT: F 44 LYS cc_start: 0.9486 (OUTLIER) cc_final: 0.9233 (mmmm) REVERT: F 79 LYS cc_start: 0.9050 (mtpp) cc_final: 0.8544 (mtmm) REVERT: F 80 THR cc_start: 0.9420 (m) cc_final: 0.8788 (p) REVERT: G 78 PHE cc_start: 0.8327 (t80) cc_final: 0.8124 (t80) REVERT: G 90 MET cc_start: 0.9086 (tmm) cc_final: 0.8770 (tpp) REVERT: G 131 ARG cc_start: 0.9030 (mtp85) cc_final: 0.8682 (mtp85) REVERT: H 49 LEU cc_start: 0.8089 (mp) cc_final: 0.7853 (mm) REVERT: H 53 GLU cc_start: 0.9422 (mt-10) cc_final: 0.9163 (mt-10) REVERT: H 67 ARG cc_start: 0.9687 (ptp-110) cc_final: 0.9475 (ptp-110) outliers start: 32 outliers final: 16 residues processed: 266 average time/residue: 0.2848 time to fit residues: 94.9428 Evaluate side-chains 259 residues out of total 494 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 241 time to evaluate : 0.709 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 49 LEU Chi-restraints excluded: chain B residue 60 VAL Chi-restraints excluded: chain B residue 72 TYR Chi-restraints excluded: chain C residue 61 LEU Chi-restraints excluded: chain C residue 80 THR Chi-restraints excluded: chain C residue 85 GLN Chi-restraints excluded: chain C residue 109 LEU Chi-restraints excluded: chain C residue 117 VAL Chi-restraints excluded: chain D residue 62 LEU Chi-restraints excluded: chain E residue 87 SER Chi-restraints excluded: chain E residue 124 ILE Chi-restraints excluded: chain E residue 126 LEU Chi-restraints excluded: chain F residue 30 THR Chi-restraints excluded: chain F residue 44 LYS Chi-restraints excluded: chain F residue 86 VAL Chi-restraints excluded: chain F residue 90 LEU Chi-restraints excluded: chain H residue 30 THR Chi-restraints excluded: chain H residue 46 ILE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 75 random chunks: chunk 74 optimal weight: 8.9990 chunk 37 optimal weight: 6.9990 chunk 27 optimal weight: 5.9990 chunk 64 optimal weight: 10.0000 chunk 7 optimal weight: 2.9990 chunk 43 optimal weight: 7.9990 chunk 13 optimal weight: 3.9990 chunk 0 optimal weight: 5.9990 chunk 36 optimal weight: 3.9990 chunk 40 optimal weight: 4.9990 chunk 4 optimal weight: 0.9990 overall best weight: 3.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 108 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 25 ASN ** F 75 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 68 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3469 r_free = 0.3469 target = 0.054132 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.2925 r_free = 0.2925 target = 0.037427 restraints weight = 56684.492| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 44)----------------| | r_work = 0.2970 r_free = 0.2970 target = 0.038654 restraints weight = 28495.869| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 51)----------------| | r_work = 0.2998 r_free = 0.2998 target = 0.039428 restraints weight = 19197.108| |-----------------------------------------------------------------------------| r_work (final): 0.2933 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8531 moved from start: 0.4185 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.047 9362 Z= 0.378 Angle : 0.724 11.713 13488 Z= 0.411 Chirality : 0.040 0.163 1549 Planarity : 0.005 0.041 1004 Dihedral : 31.041 153.292 2840 Min Nonbonded Distance : 2.040 Molprobity Statistics. All-atom Clashscore : 20.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.78 % Favored : 98.22 % Rotamer: Outliers : 7.49 % Allowed : 28.74 % Favored : 63.77 % 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: 1.85 (0.34), residues: 563 helix: 1.68 (0.23), residues: 466 sheet: None (None), residues: 0 loop : -0.91 (0.51), residues: 97 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.005 0.001 HIS C 113 PHE 0.016 0.002 PHE A 67 TYR 0.015 0.002 TYR H 88 ARG 0.004 0.001 ARG G 128 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1126 Ramachandran restraints generated. 563 Oldfield, 0 Emsley, 563 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1126 Ramachandran restraints generated. 563 Oldfield, 0 Emsley, 563 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 276 residues out of total 494 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 239 time to evaluate : 0.708 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 74 ILE cc_start: 0.9763 (tt) cc_final: 0.9515 (tt) REVERT: A 90 MET cc_start: 0.8743 (tmm) cc_final: 0.8275 (tmm) REVERT: A 119 ILE cc_start: 0.9047 (OUTLIER) cc_final: 0.8765 (pt) REVERT: A 120 MET cc_start: 0.8791 (mtm) cc_final: 0.8441 (mtm) REVERT: A 125 GLN cc_start: 0.9337 (mt0) cc_final: 0.9077 (mm-40) REVERT: A 128 ARG cc_start: 0.9155 (mtp180) cc_final: 0.8457 (mtp-110) REVERT: A 134 ARG cc_start: 0.8784 (tpp-160) cc_final: 0.8006 (tpp-160) REVERT: B 44 LYS cc_start: 0.9189 (mmmt) cc_final: 0.8880 (mmmt) REVERT: B 53 GLU cc_start: 0.9406 (tp30) cc_final: 0.9059 (tp30) REVERT: B 63 GLU cc_start: 0.9308 (mt-10) cc_final: 0.9053 (mm-30) REVERT: B 68 ASP cc_start: 0.8549 (t70) cc_final: 0.8243 (t0) REVERT: C 63 ARG cc_start: 0.8416 (mmp-170) cc_final: 0.8194 (mmp-170) REVERT: C 73 GLU cc_start: 0.9079 (tm-30) cc_final: 0.8591 (tm-30) REVERT: C 77 ASP cc_start: 0.9129 (t70) cc_final: 0.8826 (t0) REVERT: C 85 GLN cc_start: 0.9333 (OUTLIER) cc_final: 0.9091 (mt0) REVERT: C 94 GLU cc_start: 0.8838 (tm-30) cc_final: 0.8511 (tm-30) REVERT: C 97 GLU cc_start: 0.8376 (mt-10) cc_final: 0.7998 (mt-10) REVERT: C 105 GLU cc_start: 0.9168 (tp30) cc_final: 0.8921 (mm-30) REVERT: C 120 MET cc_start: 0.9054 (mmm) cc_final: 0.8813 (mmt) REVERT: C 125 GLN cc_start: 0.9316 (mt0) cc_final: 0.9051 (mp10) REVERT: C 128 ARG cc_start: 0.9466 (mtp85) cc_final: 0.9207 (mtp85) REVERT: D 79 LYS cc_start: 0.8945 (mmmm) cc_final: 0.8718 (mmtt) REVERT: E 63 ARG cc_start: 0.8734 (mmp80) cc_final: 0.8469 (mmp80) REVERT: E 87 SER cc_start: 0.9630 (OUTLIER) cc_final: 0.9307 (t) REVERT: E 120 MET cc_start: 0.8573 (mmm) cc_final: 0.8123 (mmm) REVERT: E 122 LYS cc_start: 0.9567 (mtmt) cc_final: 0.9348 (ptpt) REVERT: E 129 ARG cc_start: 0.8934 (mmm160) cc_final: 0.8306 (mmm160) REVERT: F 44 LYS cc_start: 0.9509 (OUTLIER) cc_final: 0.9152 (mmmm) REVERT: F 53 GLU cc_start: 0.9441 (tp30) cc_final: 0.9124 (tp30) REVERT: F 79 LYS cc_start: 0.9039 (mtpp) cc_final: 0.8496 (mtmm) REVERT: F 80 THR cc_start: 0.9476 (m) cc_final: 0.8998 (p) REVERT: F 84 MET cc_start: 0.9188 (mmp) cc_final: 0.8895 (mmm) REVERT: F 93 GLN cc_start: 0.8740 (tm-30) cc_final: 0.8276 (tm-30) REVERT: G 90 MET cc_start: 0.9052 (tmm) cc_final: 0.8789 (tmm) REVERT: G 125 GLN cc_start: 0.9727 (mm-40) cc_final: 0.9396 (mm-40) REVERT: G 131 ARG cc_start: 0.8937 (mtp85) cc_final: 0.8583 (mtp85) REVERT: H 49 LEU cc_start: 0.8299 (OUTLIER) cc_final: 0.8021 (mm) REVERT: H 50 ILE cc_start: 0.8933 (pt) cc_final: 0.8645 (pt) REVERT: H 53 GLU cc_start: 0.9264 (mt-10) cc_final: 0.8858 (mt-10) outliers start: 37 outliers final: 22 residues processed: 251 average time/residue: 0.2888 time to fit residues: 90.9679 Evaluate side-chains 247 residues out of total 494 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 220 time to evaluate : 0.718 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 65 LEU Chi-restraints excluded: chain A residue 86 SER Chi-restraints excluded: chain A residue 119 ILE Chi-restraints excluded: chain B residue 49 LEU Chi-restraints excluded: chain B residue 60 VAL Chi-restraints excluded: chain B residue 86 VAL Chi-restraints excluded: chain C residue 61 LEU Chi-restraints excluded: chain C residue 65 LEU Chi-restraints excluded: chain C residue 80 THR Chi-restraints excluded: chain C residue 85 GLN Chi-restraints excluded: chain C residue 96 CYS Chi-restraints excluded: chain C residue 109 LEU Chi-restraints excluded: chain C residue 117 VAL Chi-restraints excluded: chain C residue 124 ILE Chi-restraints excluded: chain E residue 65 LEU Chi-restraints excluded: chain E residue 82 LEU Chi-restraints excluded: chain E residue 87 SER Chi-restraints excluded: chain E residue 106 ASP Chi-restraints excluded: chain E residue 124 ILE Chi-restraints excluded: chain E residue 126 LEU Chi-restraints excluded: chain F residue 30 THR Chi-restraints excluded: chain F residue 44 LYS Chi-restraints excluded: chain F residue 86 VAL Chi-restraints excluded: chain F residue 90 LEU Chi-restraints excluded: chain G residue 124 ILE Chi-restraints excluded: chain H residue 46 ILE Chi-restraints excluded: chain H residue 49 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 75 random chunks: chunk 30 optimal weight: 0.4980 chunk 31 optimal weight: 0.9990 chunk 46 optimal weight: 0.9980 chunk 74 optimal weight: 9.9990 chunk 49 optimal weight: 1.9990 chunk 35 optimal weight: 5.9990 chunk 0 optimal weight: 5.9990 chunk 9 optimal weight: 0.6980 chunk 7 optimal weight: 0.7980 chunk 63 optimal weight: 5.9990 chunk 57 optimal weight: 6.9990 overall best weight: 0.7982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 76 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 75 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3535 r_free = 0.3535 target = 0.056803 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 59)----------------| | r_work = 0.3021 r_free = 0.3021 target = 0.040368 restraints weight = 56057.318| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 42)----------------| | r_work = 0.3066 r_free = 0.3066 target = 0.041646 restraints weight = 28169.052| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 53)----------------| | r_work = 0.3095 r_free = 0.3095 target = 0.042470 restraints weight = 18850.086| |-----------------------------------------------------------------------------| r_work (final): 0.3035 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8450 moved from start: 0.4229 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 9362 Z= 0.219 Angle : 0.688 11.007 13488 Z= 0.382 Chirality : 0.036 0.164 1549 Planarity : 0.004 0.043 1004 Dihedral : 30.832 153.413 2840 Min Nonbonded Distance : 2.036 Molprobity Statistics. All-atom Clashscore : 16.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.60 % Favored : 98.40 % Rotamer: Outliers : 5.06 % Allowed : 31.98 % Favored : 62.96 % 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: 1.86 (0.34), residues: 563 helix: 1.69 (0.24), residues: 466 sheet: None (None), residues: 0 loop : -0.91 (0.49), residues: 97 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.004 0.001 HIS C 113 PHE 0.015 0.002 PHE G 67 TYR 0.012 0.001 TYR H 88 ARG 0.006 0.001 ARG D 67 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1126 Ramachandran restraints generated. 563 Oldfield, 0 Emsley, 563 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1126 Ramachandran restraints generated. 563 Oldfield, 0 Emsley, 563 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 270 residues out of total 494 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 245 time to evaluate : 0.656 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 74 ILE cc_start: 0.9760 (tt) cc_final: 0.9516 (tt) REVERT: A 82 LEU cc_start: 0.8613 (OUTLIER) cc_final: 0.7964 (mm) REVERT: A 90 MET cc_start: 0.8726 (tmm) cc_final: 0.8298 (tmm) REVERT: A 99 TYR cc_start: 0.9201 (t80) cc_final: 0.8933 (t80) REVERT: A 112 ILE cc_start: 0.9669 (tp) cc_final: 0.9411 (pt) REVERT: A 120 MET cc_start: 0.8707 (mtm) cc_final: 0.8270 (mtm) REVERT: A 125 GLN cc_start: 0.9339 (mt0) cc_final: 0.9055 (mm-40) REVERT: A 128 ARG cc_start: 0.9067 (mtp180) cc_final: 0.8666 (mtp-110) REVERT: B 44 LYS cc_start: 0.9072 (mmmt) cc_final: 0.8664 (mmmt) REVERT: B 53 GLU cc_start: 0.9376 (tp30) cc_final: 0.9036 (tp30) REVERT: B 63 GLU cc_start: 0.9273 (mt-10) cc_final: 0.9052 (mm-30) REVERT: B 68 ASP cc_start: 0.8547 (t70) cc_final: 0.8216 (t0) REVERT: C 61 LEU cc_start: 0.8300 (OUTLIER) cc_final: 0.7655 (mp) REVERT: C 63 ARG cc_start: 0.8232 (mmp-170) cc_final: 0.7913 (mmp-170) REVERT: C 73 GLU cc_start: 0.9038 (tm-30) cc_final: 0.8645 (tm-30) REVERT: C 85 GLN cc_start: 0.9310 (OUTLIER) cc_final: 0.9068 (mt0) REVERT: C 94 GLU cc_start: 0.8759 (tm-30) cc_final: 0.8410 (tm-30) REVERT: C 105 GLU cc_start: 0.9150 (tp30) cc_final: 0.8679 (mm-30) REVERT: C 107 THR cc_start: 0.9675 (m) cc_final: 0.9317 (t) REVERT: C 125 GLN cc_start: 0.9295 (mt0) cc_final: 0.8994 (mp10) REVERT: C 128 ARG cc_start: 0.9115 (mtp85) cc_final: 0.8851 (mtp85) REVERT: C 129 ARG cc_start: 0.9271 (tpp80) cc_final: 0.8852 (tpt-90) REVERT: D 68 ASP cc_start: 0.9117 (m-30) cc_final: 0.8885 (m-30) REVERT: D 92 ARG cc_start: 0.8683 (tpp80) cc_final: 0.8295 (ttp80) REVERT: E 63 ARG cc_start: 0.8680 (mmp80) cc_final: 0.8415 (mmp80) REVERT: E 120 MET cc_start: 0.8649 (mmm) cc_final: 0.7973 (mmm) REVERT: E 122 LYS cc_start: 0.9545 (mtmt) cc_final: 0.9326 (ptpt) REVERT: E 129 ARG cc_start: 0.8974 (mmm160) cc_final: 0.8726 (mmm160) REVERT: F 31 LYS cc_start: 0.9364 (ttpp) cc_final: 0.9100 (ttmm) REVERT: F 35 ARG cc_start: 0.9389 (ttp80) cc_final: 0.8890 (ttm-80) REVERT: F 44 LYS cc_start: 0.9491 (OUTLIER) cc_final: 0.9239 (mmmm) REVERT: F 74 GLU cc_start: 0.9209 (mm-30) cc_final: 0.8983 (mt-10) REVERT: F 79 LYS cc_start: 0.9053 (mtpp) cc_final: 0.8530 (mtmm) REVERT: F 80 THR cc_start: 0.9409 (m) cc_final: 0.8762 (p) REVERT: F 84 MET cc_start: 0.9098 (mmp) cc_final: 0.8811 (mmm) REVERT: F 92 ARG cc_start: 0.9082 (tmt-80) cc_final: 0.8336 (tmt-80) REVERT: F 93 GLN cc_start: 0.8710 (tm-30) cc_final: 0.8257 (tm-30) REVERT: G 63 ARG cc_start: 0.9224 (tpt170) cc_final: 0.9019 (tpt170) REVERT: G 69 ARG cc_start: 0.7944 (OUTLIER) cc_final: 0.7705 (ppt170) REVERT: G 70 LEU cc_start: 0.9267 (mt) cc_final: 0.9048 (mt) REVERT: G 90 MET cc_start: 0.9070 (tmm) cc_final: 0.8739 (tmm) REVERT: G 123 ASP cc_start: 0.7977 (m-30) cc_final: 0.7207 (t70) REVERT: G 131 ARG cc_start: 0.8949 (mtp85) cc_final: 0.8614 (mtp85) REVERT: H 49 LEU cc_start: 0.8323 (mp) cc_final: 0.8074 (mm) REVERT: H 50 ILE cc_start: 0.8906 (pt) cc_final: 0.8630 (pt) REVERT: H 53 GLU cc_start: 0.9311 (mt-10) cc_final: 0.8997 (mt-10) outliers start: 25 outliers final: 14 residues processed: 255 average time/residue: 0.2835 time to fit residues: 90.7310 Evaluate side-chains 249 residues out of total 494 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 230 time to evaluate : 0.669 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 82 LEU Chi-restraints excluded: chain B residue 49 LEU Chi-restraints excluded: chain B residue 60 VAL Chi-restraints excluded: chain B residue 62 LEU Chi-restraints excluded: chain C residue 61 LEU Chi-restraints excluded: chain C residue 80 THR Chi-restraints excluded: chain C residue 85 GLN Chi-restraints excluded: chain C residue 124 ILE Chi-restraints excluded: chain D residue 62 LEU Chi-restraints excluded: chain E residue 61 LEU Chi-restraints excluded: chain E residue 124 ILE Chi-restraints excluded: chain E residue 126 LEU Chi-restraints excluded: chain F residue 30 THR Chi-restraints excluded: chain F residue 44 LYS Chi-restraints excluded: chain F residue 90 LEU Chi-restraints excluded: chain G residue 61 LEU Chi-restraints excluded: chain G residue 69 ARG Chi-restraints excluded: chain G residue 124 ILE Chi-restraints excluded: chain H residue 30 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 75 random chunks: chunk 57 optimal weight: 7.9990 chunk 64 optimal weight: 10.0000 chunk 30 optimal weight: 3.9990 chunk 7 optimal weight: 0.9980 chunk 28 optimal weight: 4.9990 chunk 51 optimal weight: 6.9990 chunk 38 optimal weight: 0.7980 chunk 36 optimal weight: 0.7980 chunk 73 optimal weight: 6.9990 chunk 8 optimal weight: 0.6980 chunk 23 optimal weight: 2.9990 overall best weight: 1.2582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3526 r_free = 0.3526 target = 0.056616 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3016 r_free = 0.3016 target = 0.040093 restraints weight = 55325.056| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 55)----------------| | r_work = 0.3060 r_free = 0.3060 target = 0.041378 restraints weight = 28168.732| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.3088 r_free = 0.3088 target = 0.042200 restraints weight = 19004.311| |-----------------------------------------------------------------------------| r_work (final): 0.3026 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8472 moved from start: 0.4405 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 9362 Z= 0.237 Angle : 0.685 10.321 13488 Z= 0.384 Chirality : 0.036 0.156 1549 Planarity : 0.004 0.043 1004 Dihedral : 30.805 154.962 2840 Min Nonbonded Distance : 2.036 Molprobity Statistics. All-atom Clashscore : 16.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.95 % Favored : 98.05 % Rotamer: Outliers : 5.87 % Allowed : 32.39 % Favored : 61.74 % 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: 1.85 (0.34), residues: 563 helix: 1.73 (0.23), residues: 462 sheet: None (None), residues: 0 loop : -1.09 (0.48), residues: 101 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.005 0.001 HIS C 113 PHE 0.017 0.002 PHE G 67 TYR 0.015 0.001 TYR H 88 ARG 0.004 0.000 ARG G 128 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1126 Ramachandran restraints generated. 563 Oldfield, 0 Emsley, 563 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1126 Ramachandran restraints generated. 563 Oldfield, 0 Emsley, 563 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 265 residues out of total 494 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 236 time to evaluate : 0.710 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 61 LEU cc_start: 0.9163 (mt) cc_final: 0.8871 (mp) REVERT: A 74 ILE cc_start: 0.9764 (tt) cc_final: 0.9508 (tt) REVERT: A 90 MET cc_start: 0.8703 (tmm) cc_final: 0.8199 (tmm) REVERT: A 97 GLU cc_start: 0.8930 (mm-30) cc_final: 0.8651 (mm-30) REVERT: A 99 TYR cc_start: 0.9208 (t80) cc_final: 0.8952 (t80) REVERT: A 112 ILE cc_start: 0.9668 (tp) cc_final: 0.9419 (pt) REVERT: A 120 MET cc_start: 0.8683 (mtm) cc_final: 0.8222 (mtm) REVERT: A 125 GLN cc_start: 0.9275 (mt0) cc_final: 0.9073 (mt0) REVERT: A 128 ARG cc_start: 0.9182 (mtp180) cc_final: 0.8530 (mtp-110) REVERT: A 134 ARG cc_start: 0.8865 (tpp-160) cc_final: 0.8596 (tpp-160) REVERT: B 44 LYS cc_start: 0.9213 (mmmt) cc_final: 0.8813 (mmmt) REVERT: B 53 GLU cc_start: 0.9342 (tp30) cc_final: 0.9083 (tp30) REVERT: B 63 GLU cc_start: 0.9283 (mt-10) cc_final: 0.9048 (mm-30) REVERT: B 68 ASP cc_start: 0.8595 (t70) cc_final: 0.8229 (t0) REVERT: C 61 LEU cc_start: 0.8198 (OUTLIER) cc_final: 0.7465 (mp) REVERT: C 63 ARG cc_start: 0.8315 (mmp-170) cc_final: 0.8076 (mmp-170) REVERT: C 73 GLU cc_start: 0.9073 (tm-30) cc_final: 0.8680 (tm-30) REVERT: C 85 GLN cc_start: 0.9310 (OUTLIER) cc_final: 0.9077 (mt0) REVERT: C 94 GLU cc_start: 0.8749 (tm-30) cc_final: 0.8386 (tm-30) REVERT: C 105 GLU cc_start: 0.9138 (tp30) cc_final: 0.8794 (mm-30) REVERT: C 107 THR cc_start: 0.9677 (m) cc_final: 0.9274 (t) REVERT: C 120 MET cc_start: 0.8957 (mmm) cc_final: 0.8671 (mmt) REVERT: C 125 GLN cc_start: 0.9269 (mt0) cc_final: 0.8992 (mp10) REVERT: C 128 ARG cc_start: 0.9151 (mtp85) cc_final: 0.8875 (mtp85) REVERT: C 129 ARG cc_start: 0.9231 (tpp80) cc_final: 0.8977 (tpp80) REVERT: D 68 ASP cc_start: 0.9193 (m-30) cc_final: 0.8920 (m-30) REVERT: D 79 LYS cc_start: 0.8957 (mmmm) cc_final: 0.8723 (mmtt) REVERT: D 92 ARG cc_start: 0.8505 (tpp80) cc_final: 0.8198 (ttp80) REVERT: E 63 ARG cc_start: 0.8788 (mmp80) cc_final: 0.8527 (mmp80) REVERT: E 87 SER cc_start: 0.9498 (m) cc_final: 0.9168 (t) REVERT: E 122 LYS cc_start: 0.9559 (mtmt) cc_final: 0.9351 (ptpt) REVERT: E 129 ARG cc_start: 0.8982 (mmm160) cc_final: 0.8437 (mmm160) REVERT: F 31 LYS cc_start: 0.9366 (ttpp) cc_final: 0.9101 (ttmm) REVERT: F 35 ARG cc_start: 0.9397 (ttp80) cc_final: 0.8917 (ttm-80) REVERT: F 44 LYS cc_start: 0.9511 (OUTLIER) cc_final: 0.9270 (mmmt) REVERT: F 74 GLU cc_start: 0.9212 (mm-30) cc_final: 0.8997 (mt-10) REVERT: F 79 LYS cc_start: 0.9070 (mtpp) cc_final: 0.8538 (mtmm) REVERT: F 80 THR cc_start: 0.9439 (m) cc_final: 0.8810 (p) REVERT: F 84 MET cc_start: 0.9047 (mmp) cc_final: 0.8743 (mmm) REVERT: F 92 ARG cc_start: 0.9052 (tmt-80) cc_final: 0.8257 (tmt-80) REVERT: F 93 GLN cc_start: 0.8725 (tm-30) cc_final: 0.8229 (tm-30) REVERT: G 69 ARG cc_start: 0.7751 (OUTLIER) cc_final: 0.7529 (ppt170) REVERT: G 90 MET cc_start: 0.9043 (tmm) cc_final: 0.8791 (tmm) REVERT: G 123 ASP cc_start: 0.7988 (m-30) cc_final: 0.7422 (t70) REVERT: G 131 ARG cc_start: 0.8962 (mtp85) cc_final: 0.8619 (mtp85) REVERT: H 49 LEU cc_start: 0.8289 (OUTLIER) cc_final: 0.8064 (mm) REVERT: H 53 GLU cc_start: 0.9267 (mt-10) cc_final: 0.8929 (mt-10) outliers start: 29 outliers final: 18 residues processed: 246 average time/residue: 0.2950 time to fit residues: 91.0483 Evaluate side-chains 252 residues out of total 494 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 229 time to evaluate : 0.738 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 86 SER Chi-restraints excluded: chain A residue 130 ILE Chi-restraints excluded: chain B residue 49 LEU Chi-restraints excluded: chain B residue 60 VAL Chi-restraints excluded: chain B residue 62 LEU Chi-restraints excluded: chain C residue 61 LEU Chi-restraints excluded: chain C residue 65 LEU Chi-restraints excluded: chain C residue 80 THR Chi-restraints excluded: chain C residue 85 GLN Chi-restraints excluded: chain C residue 117 VAL Chi-restraints excluded: chain C residue 124 ILE Chi-restraints excluded: chain E residue 61 LEU Chi-restraints excluded: chain E residue 65 LEU Chi-restraints excluded: chain E residue 80 THR Chi-restraints excluded: chain E residue 106 ASP Chi-restraints excluded: chain E residue 124 ILE Chi-restraints excluded: chain E residue 126 LEU Chi-restraints excluded: chain F residue 30 THR Chi-restraints excluded: chain F residue 44 LYS Chi-restraints excluded: chain F residue 90 LEU Chi-restraints excluded: chain G residue 69 ARG Chi-restraints excluded: chain G residue 124 ILE Chi-restraints excluded: chain H residue 49 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 75 random chunks: chunk 7 optimal weight: 0.5980 chunk 8 optimal weight: 3.9990 chunk 19 optimal weight: 1.9990 chunk 23 optimal weight: 0.8980 chunk 70 optimal weight: 5.9990 chunk 68 optimal weight: 4.9990 chunk 65 optimal weight: 10.0000 chunk 35 optimal weight: 2.9990 chunk 4 optimal weight: 1.9990 chunk 37 optimal weight: 0.8980 chunk 20 optimal weight: 1.9990 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 108 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3523 r_free = 0.3523 target = 0.056378 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3013 r_free = 0.3013 target = 0.039919 restraints weight = 55274.146| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 45)----------------| | r_work = 0.3057 r_free = 0.3057 target = 0.041207 restraints weight = 27257.854| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 45)----------------| | r_work = 0.3086 r_free = 0.3086 target = 0.042071 restraints weight = 18143.159| |-----------------------------------------------------------------------------| r_work (final): 0.3024 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8468 moved from start: 0.4552 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 9362 Z= 0.245 Angle : 0.715 12.368 13488 Z= 0.391 Chirality : 0.036 0.200 1549 Planarity : 0.004 0.045 1004 Dihedral : 30.787 155.526 2840 Min Nonbonded Distance : 2.032 Molprobity Statistics. All-atom Clashscore : 17.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.13 % Favored : 97.87 % Rotamer: Outliers : 4.86 % Allowed : 34.21 % Favored : 60.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.89 (0.34), residues: 563 helix: 1.74 (0.24), residues: 461 sheet: None (None), residues: 0 loop : -0.94 (0.49), residues: 102 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.004 0.001 HIS C 113 PHE 0.019 0.002 PHE G 67 TYR 0.017 0.001 TYR H 88 ARG 0.006 0.000 ARG H 36 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1126 Ramachandran restraints generated. 563 Oldfield, 0 Emsley, 563 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1126 Ramachandran restraints generated. 563 Oldfield, 0 Emsley, 563 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 263 residues out of total 494 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 239 time to evaluate : 0.667 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 74 ILE cc_start: 0.9773 (tt) cc_final: 0.9475 (tt) REVERT: A 90 MET cc_start: 0.8701 (tmm) cc_final: 0.8152 (tmm) REVERT: A 99 TYR cc_start: 0.9094 (t80) cc_final: 0.8845 (t80) REVERT: A 112 ILE cc_start: 0.9688 (tp) cc_final: 0.9401 (pt) REVERT: A 120 MET cc_start: 0.8703 (mtm) cc_final: 0.8228 (mtm) REVERT: A 128 ARG cc_start: 0.9178 (mtp180) cc_final: 0.8486 (mtp180) REVERT: A 134 ARG cc_start: 0.8830 (tpp-160) cc_final: 0.8354 (tpp-160) REVERT: B 44 LYS cc_start: 0.9210 (mmmt) cc_final: 0.8801 (mmmt) REVERT: B 53 GLU cc_start: 0.9331 (tp30) cc_final: 0.9052 (tp30) REVERT: B 63 GLU cc_start: 0.9278 (mt-10) cc_final: 0.9067 (mm-30) REVERT: B 68 ASP cc_start: 0.8616 (t70) cc_final: 0.8241 (t0) REVERT: C 61 LEU cc_start: 0.8165 (OUTLIER) cc_final: 0.7343 (mp) REVERT: C 63 ARG cc_start: 0.8293 (mmp-170) cc_final: 0.8022 (mmp-170) REVERT: C 73 GLU cc_start: 0.9070 (tm-30) cc_final: 0.8640 (tm-30) REVERT: C 85 GLN cc_start: 0.9303 (OUTLIER) cc_final: 0.9069 (mt0) REVERT: C 94 GLU cc_start: 0.8790 (tm-30) cc_final: 0.8411 (tm-30) REVERT: C 105 GLU cc_start: 0.9123 (tp30) cc_final: 0.8768 (mm-30) REVERT: C 107 THR cc_start: 0.9660 (m) cc_final: 0.9278 (t) REVERT: C 120 MET cc_start: 0.8913 (mmm) cc_final: 0.8641 (mmt) REVERT: C 125 GLN cc_start: 0.9298 (mt0) cc_final: 0.8979 (mp10) REVERT: C 128 ARG cc_start: 0.9128 (mtp85) cc_final: 0.8914 (mtp85) REVERT: C 129 ARG cc_start: 0.9246 (tpp80) cc_final: 0.8962 (ttp80) REVERT: D 79 LYS cc_start: 0.8960 (mmmm) cc_final: 0.8679 (mmtt) REVERT: D 92 ARG cc_start: 0.8515 (tpp80) cc_final: 0.8189 (ttp80) REVERT: E 63 ARG cc_start: 0.8854 (mmp80) cc_final: 0.8576 (mmp80) REVERT: E 87 SER cc_start: 0.9486 (m) cc_final: 0.9160 (t) REVERT: E 120 MET cc_start: 0.8766 (mmm) cc_final: 0.7966 (mmm) REVERT: E 122 LYS cc_start: 0.9562 (mtmt) cc_final: 0.9336 (ptmt) REVERT: E 129 ARG cc_start: 0.9008 (mmm160) cc_final: 0.8457 (mmm160) REVERT: F 31 LYS cc_start: 0.9380 (ttpp) cc_final: 0.9103 (ttmm) REVERT: F 35 ARG cc_start: 0.9392 (ttp80) cc_final: 0.8923 (ttm-80) REVERT: F 44 LYS cc_start: 0.9508 (OUTLIER) cc_final: 0.9275 (mmmt) REVERT: F 49 LEU cc_start: 0.9486 (OUTLIER) cc_final: 0.8896 (tp) REVERT: F 79 LYS cc_start: 0.9061 (mtpp) cc_final: 0.8530 (mtmm) REVERT: F 80 THR cc_start: 0.9424 (m) cc_final: 0.8857 (p) REVERT: F 92 ARG cc_start: 0.9075 (tmt-80) cc_final: 0.8281 (tmt-80) REVERT: F 93 GLN cc_start: 0.8767 (tm-30) cc_final: 0.8243 (tm-30) REVERT: G 67 PHE cc_start: 0.9004 (t80) cc_final: 0.8559 (t80) REVERT: G 69 ARG cc_start: 0.7957 (OUTLIER) cc_final: 0.7675 (ppt170) REVERT: G 90 MET cc_start: 0.9072 (tmm) cc_final: 0.8799 (tmm) REVERT: G 94 GLU cc_start: 0.9124 (OUTLIER) cc_final: 0.8887 (mp0) REVERT: G 123 ASP cc_start: 0.8078 (m-30) cc_final: 0.7466 (t70) REVERT: H 49 LEU cc_start: 0.8246 (OUTLIER) cc_final: 0.8012 (mm) REVERT: H 53 GLU cc_start: 0.9223 (mt-10) cc_final: 0.8921 (mt-10) outliers start: 24 outliers final: 13 residues processed: 248 average time/residue: 0.2864 time to fit residues: 89.4490 Evaluate side-chains 250 residues out of total 494 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 230 time to evaluate : 0.676 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 124 ILE Chi-restraints excluded: chain B residue 49 LEU Chi-restraints excluded: chain B residue 60 VAL Chi-restraints excluded: chain B residue 62 LEU Chi-restraints excluded: chain C residue 61 LEU Chi-restraints excluded: chain C residue 65 LEU Chi-restraints excluded: chain C residue 85 GLN Chi-restraints excluded: chain C residue 117 VAL Chi-restraints excluded: chain C residue 124 ILE Chi-restraints excluded: chain D residue 62 LEU Chi-restraints excluded: chain E residue 65 LEU Chi-restraints excluded: chain E residue 126 LEU Chi-restraints excluded: chain F residue 30 THR Chi-restraints excluded: chain F residue 44 LYS Chi-restraints excluded: chain F residue 49 LEU Chi-restraints excluded: chain F residue 90 LEU Chi-restraints excluded: chain G residue 69 ARG Chi-restraints excluded: chain G residue 94 GLU Chi-restraints excluded: chain G residue 124 ILE Chi-restraints excluded: chain H residue 49 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 75 random chunks: chunk 38 optimal weight: 1.9990 chunk 24 optimal weight: 0.8980 chunk 14 optimal weight: 5.9990 chunk 49 optimal weight: 2.9990 chunk 65 optimal weight: 10.0000 chunk 5 optimal weight: 4.9990 chunk 12 optimal weight: 7.9990 chunk 32 optimal weight: 0.9980 chunk 17 optimal weight: 0.9990 chunk 59 optimal weight: 5.9990 chunk 73 optimal weight: 7.9990 overall best weight: 1.5786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 108 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 25 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 64 ASN G 93 GLN ** G 113 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3519 r_free = 0.3519 target = 0.056045 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3000 r_free = 0.3000 target = 0.039495 restraints weight = 56840.786| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3043 r_free = 0.3043 target = 0.040752 restraints weight = 28667.279| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 57)----------------| | r_work = 0.3070 r_free = 0.3070 target = 0.041573 restraints weight = 19339.381| |-----------------------------------------------------------------------------| r_work (final): 0.3007 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8491 moved from start: 0.4697 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 9362 Z= 0.259 Angle : 0.721 11.501 13488 Z= 0.396 Chirality : 0.037 0.176 1549 Planarity : 0.004 0.043 1004 Dihedral : 30.824 156.209 2840 Min Nonbonded Distance : 2.036 Molprobity Statistics. All-atom Clashscore : 18.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.95 % Favored : 98.05 % Rotamer: Outliers : 4.66 % Allowed : 34.62 % Favored : 60.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.83 (0.34), residues: 563 helix: 1.73 (0.24), residues: 463 sheet: None (None), residues: 0 loop : -1.17 (0.49), residues: 100 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.004 0.001 HIS C 113 PHE 0.013 0.002 PHE G 67 TYR 0.015 0.001 TYR D 72 ARG 0.006 0.000 ARG G 128 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1126 Ramachandran restraints generated. 563 Oldfield, 0 Emsley, 563 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1126 Ramachandran restraints generated. 563 Oldfield, 0 Emsley, 563 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 257 residues out of total 494 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 234 time to evaluate : 0.628 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 74 ILE cc_start: 0.9776 (tt) cc_final: 0.9519 (tt) REVERT: A 90 MET cc_start: 0.8681 (tmm) cc_final: 0.8077 (tmm) REVERT: A 99 TYR cc_start: 0.9184 (t80) cc_final: 0.8938 (t80) REVERT: A 112 ILE cc_start: 0.9694 (tp) cc_final: 0.9397 (pt) REVERT: A 120 MET cc_start: 0.8702 (mtm) cc_final: 0.8279 (mtm) REVERT: A 128 ARG cc_start: 0.9193 (mtp180) cc_final: 0.8494 (mtp-110) REVERT: A 134 ARG cc_start: 0.8805 (tpp-160) cc_final: 0.8333 (tpp-160) REVERT: B 44 LYS cc_start: 0.9204 (mmmt) cc_final: 0.8809 (mmmt) REVERT: B 53 GLU cc_start: 0.9303 (tp30) cc_final: 0.8854 (tp30) REVERT: B 63 GLU cc_start: 0.9271 (mt-10) cc_final: 0.9068 (mm-30) REVERT: B 68 ASP cc_start: 0.8639 (t70) cc_final: 0.8248 (t0) REVERT: C 61 LEU cc_start: 0.8220 (OUTLIER) cc_final: 0.7356 (mp) REVERT: C 63 ARG cc_start: 0.8314 (mmp-170) cc_final: 0.8047 (mmp-170) REVERT: C 73 GLU cc_start: 0.9099 (tm-30) cc_final: 0.8737 (tm-30) REVERT: C 85 GLN cc_start: 0.9300 (OUTLIER) cc_final: 0.9071 (mt0) REVERT: C 94 GLU cc_start: 0.8800 (tm-30) cc_final: 0.8450 (tm-30) REVERT: C 105 GLU cc_start: 0.9108 (tp30) cc_final: 0.8745 (mm-30) REVERT: C 107 THR cc_start: 0.9665 (m) cc_final: 0.9294 (t) REVERT: C 120 MET cc_start: 0.8950 (mmm) cc_final: 0.8508 (mmm) REVERT: C 125 GLN cc_start: 0.9261 (mt0) cc_final: 0.8917 (mp10) REVERT: C 129 ARG cc_start: 0.9207 (tpp80) cc_final: 0.8941 (tpp80) REVERT: D 68 ASP cc_start: 0.9163 (m-30) cc_final: 0.8852 (m-30) REVERT: D 72 TYR cc_start: 0.9052 (m-80) cc_final: 0.8797 (m-80) REVERT: D 92 ARG cc_start: 0.8433 (tpp80) cc_final: 0.8072 (ttp80) REVERT: E 63 ARG cc_start: 0.8920 (mmp80) cc_final: 0.8649 (mmp80) REVERT: E 87 SER cc_start: 0.9498 (OUTLIER) cc_final: 0.9170 (t) REVERT: E 120 MET cc_start: 0.8639 (mmm) cc_final: 0.8258 (mmm) REVERT: E 129 ARG cc_start: 0.9016 (mmm160) cc_final: 0.8551 (mmm160) REVERT: F 23 ARG cc_start: 0.7751 (ptm160) cc_final: 0.7536 (ptm-80) REVERT: F 31 LYS cc_start: 0.9382 (ttpp) cc_final: 0.9111 (ttmm) REVERT: F 35 ARG cc_start: 0.9392 (ttp80) cc_final: 0.8923 (ttm-80) REVERT: F 44 LYS cc_start: 0.9497 (OUTLIER) cc_final: 0.9276 (mmmt) REVERT: F 49 LEU cc_start: 0.9380 (OUTLIER) cc_final: 0.8898 (tp) REVERT: F 53 GLU cc_start: 0.9427 (tp30) cc_final: 0.9120 (tp30) REVERT: F 79 LYS cc_start: 0.9074 (mtpp) cc_final: 0.8543 (mtmm) REVERT: F 80 THR cc_start: 0.9444 (m) cc_final: 0.8888 (p) REVERT: F 92 ARG cc_start: 0.9021 (tmt-80) cc_final: 0.8247 (tmt-80) REVERT: F 93 GLN cc_start: 0.8833 (tm-30) cc_final: 0.8296 (tm-30) REVERT: G 67 PHE cc_start: 0.8985 (t80) cc_final: 0.8571 (t80) REVERT: G 69 ARG cc_start: 0.7990 (OUTLIER) cc_final: 0.7713 (ppt170) REVERT: G 90 MET cc_start: 0.9070 (tmm) cc_final: 0.8790 (tmm) REVERT: G 94 GLU cc_start: 0.9132 (OUTLIER) cc_final: 0.8878 (mp0) REVERT: G 123 ASP cc_start: 0.8039 (m-30) cc_final: 0.7535 (t70) REVERT: G 128 ARG cc_start: 0.8665 (mmm-85) cc_final: 0.8434 (mmm-85) REVERT: H 29 ILE cc_start: 0.8791 (mm) cc_final: 0.8519 (tp) REVERT: H 36 ARG cc_start: 0.9088 (ptt-90) cc_final: 0.8810 (ptt-90) REVERT: H 49 LEU cc_start: 0.8227 (OUTLIER) cc_final: 0.7998 (mm) REVERT: H 53 GLU cc_start: 0.9216 (mt-10) cc_final: 0.8902 (mt-10) outliers start: 23 outliers final: 14 residues processed: 239 average time/residue: 0.2891 time to fit residues: 86.2776 Evaluate side-chains 248 residues out of total 494 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 226 time to evaluate : 0.642 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 49 LEU Chi-restraints excluded: chain B residue 60 VAL Chi-restraints excluded: chain B residue 62 LEU Chi-restraints excluded: chain B residue 81 VAL Chi-restraints excluded: chain C residue 61 LEU Chi-restraints excluded: chain C residue 65 LEU Chi-restraints excluded: chain C residue 85 GLN Chi-restraints excluded: chain C residue 117 VAL Chi-restraints excluded: chain C residue 124 ILE Chi-restraints excluded: chain D residue 50 ILE Chi-restraints excluded: chain D residue 62 LEU Chi-restraints excluded: chain E residue 65 LEU Chi-restraints excluded: chain E residue 87 SER Chi-restraints excluded: chain E residue 126 LEU Chi-restraints excluded: chain F residue 30 THR Chi-restraints excluded: chain F residue 44 LYS Chi-restraints excluded: chain F residue 49 LEU Chi-restraints excluded: chain F residue 90 LEU Chi-restraints excluded: chain G residue 69 ARG Chi-restraints excluded: chain G residue 94 GLU Chi-restraints excluded: chain G residue 124 ILE Chi-restraints excluded: chain H residue 49 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 75 random chunks: chunk 0 optimal weight: 5.9990 chunk 40 optimal weight: 6.9990 chunk 68 optimal weight: 5.9990 chunk 54 optimal weight: 9.9990 chunk 10 optimal weight: 0.9980 chunk 42 optimal weight: 7.9990 chunk 25 optimal weight: 0.9980 chunk 51 optimal weight: 1.9990 chunk 70 optimal weight: 6.9990 chunk 63 optimal weight: 6.9990 chunk 12 optimal weight: 10.0000 overall best weight: 3.1986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 108 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 75 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 25 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 93 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3451 r_free = 0.3451 target = 0.052882 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.2904 r_free = 0.2904 target = 0.036284 restraints weight = 56243.579| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 57)----------------| | r_work = 0.2948 r_free = 0.2948 target = 0.037461 restraints weight = 28124.982| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 41)----------------| | r_work = 0.2977 r_free = 0.2977 target = 0.038236 restraints weight = 18928.587| |-----------------------------------------------------------------------------| r_work (final): 0.2910 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8573 moved from start: 0.5145 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.045 9362 Z= 0.372 Angle : 0.791 12.107 13488 Z= 0.438 Chirality : 0.040 0.182 1549 Planarity : 0.005 0.044 1004 Dihedral : 31.248 158.017 2840 Min Nonbonded Distance : 2.014 Molprobity Statistics. All-atom Clashscore : 21.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.95 % Favored : 98.05 % Rotamer: Outliers : 4.86 % Allowed : 35.63 % Favored : 59.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.71 (0.34), residues: 563 helix: 1.63 (0.23), residues: 462 sheet: None (None), residues: 0 loop : -1.10 (0.53), residues: 101 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.005 0.001 HIS C 113 PHE 0.014 0.002 PHE A 84 TYR 0.014 0.002 TYR H 72 ARG 0.011 0.001 ARG G 63 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1126 Ramachandran restraints generated. 563 Oldfield, 0 Emsley, 563 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1126 Ramachandran restraints generated. 563 Oldfield, 0 Emsley, 563 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 253 residues out of total 494 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 229 time to evaluate : 0.846 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 74 ILE cc_start: 0.9766 (tt) cc_final: 0.9539 (tt) REVERT: A 90 MET cc_start: 0.8755 (tmm) cc_final: 0.8092 (tmm) REVERT: A 112 ILE cc_start: 0.9724 (tp) cc_final: 0.9447 (pt) REVERT: A 120 MET cc_start: 0.8729 (mtm) cc_final: 0.8316 (mtm) REVERT: B 44 LYS cc_start: 0.9257 (mmmt) cc_final: 0.8972 (mmmt) REVERT: B 53 GLU cc_start: 0.9352 (tp30) cc_final: 0.9150 (tp30) REVERT: B 63 GLU cc_start: 0.9284 (mt-10) cc_final: 0.9082 (mm-30) REVERT: B 68 ASP cc_start: 0.8657 (t70) cc_final: 0.8241 (t0) REVERT: C 63 ARG cc_start: 0.8425 (mmp-170) cc_final: 0.8087 (mmp-170) REVERT: C 73 GLU cc_start: 0.9108 (tm-30) cc_final: 0.8706 (tm-30) REVERT: C 85 GLN cc_start: 0.9299 (OUTLIER) cc_final: 0.9061 (mt0) REVERT: C 94 GLU cc_start: 0.8927 (tm-30) cc_final: 0.8526 (tm-30) REVERT: C 105 GLU cc_start: 0.9154 (tp30) cc_final: 0.8805 (mm-30) REVERT: C 107 THR cc_start: 0.9672 (m) cc_final: 0.9369 (t) REVERT: D 31 LYS cc_start: 0.9066 (ttmm) cc_final: 0.8687 (ttmm) REVERT: D 53 GLU cc_start: 0.9263 (tp30) cc_final: 0.9056 (tp30) REVERT: E 63 ARG cc_start: 0.9039 (mmp80) cc_final: 0.8731 (mmp80) REVERT: E 79 LYS cc_start: 0.8579 (tptt) cc_final: 0.8142 (tptp) REVERT: E 82 LEU cc_start: 0.9418 (tp) cc_final: 0.9047 (mm) REVERT: E 87 SER cc_start: 0.9558 (OUTLIER) cc_final: 0.9245 (t) REVERT: E 105 GLU cc_start: 0.9071 (mm-30) cc_final: 0.8753 (mm-30) REVERT: E 120 MET cc_start: 0.8628 (mmm) cc_final: 0.7916 (mmm) REVERT: E 129 ARG cc_start: 0.9042 (mmm160) cc_final: 0.8727 (mmm160) REVERT: F 44 LYS cc_start: 0.9517 (OUTLIER) cc_final: 0.9262 (mmmt) REVERT: F 49 LEU cc_start: 0.9463 (OUTLIER) cc_final: 0.8939 (tp) REVERT: F 53 GLU cc_start: 0.9509 (tp30) cc_final: 0.9286 (tp30) REVERT: F 79 LYS cc_start: 0.9014 (mtpp) cc_final: 0.8578 (mtmm) REVERT: F 80 THR cc_start: 0.9484 (m) cc_final: 0.9053 (p) REVERT: F 93 GLN cc_start: 0.8988 (tm-30) cc_final: 0.8655 (tm-30) REVERT: G 67 PHE cc_start: 0.9022 (t80) cc_final: 0.8600 (t80) REVERT: G 69 ARG cc_start: 0.8013 (OUTLIER) cc_final: 0.7797 (ppt170) REVERT: G 90 MET cc_start: 0.9098 (tmm) cc_final: 0.8824 (tmm) REVERT: G 94 GLU cc_start: 0.9131 (OUTLIER) cc_final: 0.8850 (mp0) REVERT: G 123 ASP cc_start: 0.8083 (m-30) cc_final: 0.7646 (t70) REVERT: G 131 ARG cc_start: 0.8936 (mtp-110) cc_final: 0.8659 (mtp85) REVERT: H 36 ARG cc_start: 0.9100 (ptt-90) cc_final: 0.8809 (ptt-90) REVERT: H 53 GLU cc_start: 0.9189 (mt-10) cc_final: 0.8817 (mt-10) outliers start: 24 outliers final: 16 residues processed: 235 average time/residue: 0.3017 time to fit residues: 90.3548 Evaluate side-chains 245 residues out of total 494 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 223 time to evaluate : 0.680 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 49 LEU Chi-restraints excluded: chain B residue 60 VAL Chi-restraints excluded: chain B residue 81 VAL Chi-restraints excluded: chain C residue 65 LEU Chi-restraints excluded: chain C residue 85 GLN Chi-restraints excluded: chain C residue 117 VAL Chi-restraints excluded: chain C residue 124 ILE Chi-restraints excluded: chain D residue 25 ASN Chi-restraints excluded: chain D residue 29 ILE Chi-restraints excluded: chain D residue 50 ILE Chi-restraints excluded: chain D residue 62 LEU Chi-restraints excluded: chain E residue 61 LEU Chi-restraints excluded: chain E residue 65 LEU Chi-restraints excluded: chain E residue 87 SER Chi-restraints excluded: chain E residue 126 LEU Chi-restraints excluded: chain F residue 30 THR Chi-restraints excluded: chain F residue 44 LYS Chi-restraints excluded: chain F residue 49 LEU Chi-restraints excluded: chain F residue 90 LEU Chi-restraints excluded: chain G residue 69 ARG Chi-restraints excluded: chain G residue 94 GLU Chi-restraints excluded: chain G residue 124 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 75 random chunks: chunk 61 optimal weight: 5.9990 chunk 44 optimal weight: 30.0000 chunk 50 optimal weight: 9.9990 chunk 54 optimal weight: 10.0000 chunk 37 optimal weight: 0.8980 chunk 55 optimal weight: 10.0000 chunk 22 optimal weight: 4.9990 chunk 6 optimal weight: 0.7980 chunk 18 optimal weight: 0.7980 chunk 38 optimal weight: 0.9990 chunk 71 optimal weight: 5.9990 overall best weight: 1.6984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 75 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 25 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 93 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3484 r_free = 0.3484 target = 0.054260 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.2958 r_free = 0.2958 target = 0.037687 restraints weight = 55609.050| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 47)----------------| | r_work = 0.3001 r_free = 0.3001 target = 0.038912 restraints weight = 27623.847| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 40)----------------| | r_work = 0.3030 r_free = 0.3030 target = 0.039722 restraints weight = 18450.123| |-----------------------------------------------------------------------------| r_work (final): 0.2964 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8536 moved from start: 0.5193 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.043 9362 Z= 0.280 Angle : 0.807 17.940 13488 Z= 0.432 Chirality : 0.039 0.243 1549 Planarity : 0.005 0.046 1004 Dihedral : 31.150 157.000 2840 Min Nonbonded Distance : 2.017 Molprobity Statistics. All-atom Clashscore : 19.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.78 % Favored : 98.22 % Rotamer: Outliers : 4.05 % Allowed : 37.65 % Favored : 58.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.69 (0.34), residues: 563 helix: 1.63 (0.24), residues: 461 sheet: None (None), residues: 0 loop : -1.18 (0.52), residues: 102 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.004 0.001 HIS C 113 PHE 0.015 0.002 PHE G 84 TYR 0.013 0.002 TYR A 99 ARG 0.007 0.001 ARG G 69 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1126 Ramachandran restraints generated. 563 Oldfield, 0 Emsley, 563 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1126 Ramachandran restraints generated. 563 Oldfield, 0 Emsley, 563 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 254 residues out of total 494 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 234 time to evaluate : 0.672 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 60 LEU cc_start: 0.8942 (mm) cc_final: 0.8668 (mm) REVERT: A 74 ILE cc_start: 0.9753 (tt) cc_final: 0.9461 (tt) REVERT: A 90 MET cc_start: 0.8724 (tmm) cc_final: 0.7250 (tmm) REVERT: A 112 ILE cc_start: 0.9709 (tp) cc_final: 0.9434 (pt) REVERT: A 120 MET cc_start: 0.8708 (mtm) cc_final: 0.8334 (mtm) REVERT: A 128 ARG cc_start: 0.9166 (mtp180) cc_final: 0.8578 (mtp-110) REVERT: B 44 LYS cc_start: 0.9249 (mmmt) cc_final: 0.8917 (mmmt) REVERT: B 68 ASP cc_start: 0.8662 (t70) cc_final: 0.8238 (t0) REVERT: C 63 ARG cc_start: 0.8325 (mmp-170) cc_final: 0.8034 (mmp-170) REVERT: C 73 GLU cc_start: 0.9111 (tm-30) cc_final: 0.8722 (tm-30) REVERT: C 85 GLN cc_start: 0.9306 (OUTLIER) cc_final: 0.9061 (mt0) REVERT: C 94 GLU cc_start: 0.8853 (tm-30) cc_final: 0.8487 (tm-30) REVERT: C 105 GLU cc_start: 0.9140 (tp30) cc_final: 0.8774 (mm-30) REVERT: C 107 THR cc_start: 0.9671 (m) cc_final: 0.9373 (t) REVERT: C 125 GLN cc_start: 0.9256 (mt0) cc_final: 0.8926 (mp10) REVERT: C 128 ARG cc_start: 0.9137 (mtp85) cc_final: 0.8624 (mtp85) REVERT: C 129 ARG cc_start: 0.9207 (tpp80) cc_final: 0.8901 (tpp80) REVERT: D 53 GLU cc_start: 0.9238 (tp30) cc_final: 0.8969 (tp30) REVERT: D 72 TYR cc_start: 0.9116 (m-80) cc_final: 0.8846 (m-80) REVERT: D 79 LYS cc_start: 0.8860 (mmmt) cc_final: 0.8560 (mmmm) REVERT: E 63 ARG cc_start: 0.8995 (mmp80) cc_final: 0.8705 (mmp80) REVERT: E 79 LYS cc_start: 0.8442 (tptt) cc_final: 0.7989 (tptp) REVERT: E 82 LEU cc_start: 0.9385 (tp) cc_final: 0.9028 (mm) REVERT: E 87 SER cc_start: 0.9507 (m) cc_final: 0.9190 (t) REVERT: E 105 GLU cc_start: 0.9045 (mm-30) cc_final: 0.8726 (mm-30) REVERT: E 120 MET cc_start: 0.8512 (mmm) cc_final: 0.8147 (mmm) REVERT: E 129 ARG cc_start: 0.9046 (mmm160) cc_final: 0.8618 (mmm160) REVERT: F 23 ARG cc_start: 0.7785 (ptm160) cc_final: 0.7313 (ptm160) REVERT: F 35 ARG cc_start: 0.9346 (ttp80) cc_final: 0.8946 (ttm-80) REVERT: F 44 LYS cc_start: 0.9510 (OUTLIER) cc_final: 0.9259 (mmmt) REVERT: F 49 LEU cc_start: 0.9409 (OUTLIER) cc_final: 0.8952 (tp) REVERT: F 79 LYS cc_start: 0.9033 (mtpp) cc_final: 0.8545 (mtmm) REVERT: F 80 THR cc_start: 0.9477 (m) cc_final: 0.9004 (p) REVERT: F 93 GLN cc_start: 0.9034 (tm-30) cc_final: 0.8713 (tm-30) REVERT: G 90 MET cc_start: 0.9143 (tmm) cc_final: 0.8864 (tpp) REVERT: G 120 MET cc_start: 0.9343 (mmm) cc_final: 0.8813 (mtt) REVERT: G 123 ASP cc_start: 0.7964 (m-30) cc_final: 0.7529 (t70) REVERT: G 131 ARG cc_start: 0.8976 (mtp-110) cc_final: 0.8705 (mtp85) REVERT: H 29 ILE cc_start: 0.8869 (mm) cc_final: 0.8398 (tp) REVERT: H 53 GLU cc_start: 0.9156 (mt-10) cc_final: 0.8813 (mt-10) outliers start: 20 outliers final: 14 residues processed: 238 average time/residue: 0.2759 time to fit residues: 82.5514 Evaluate side-chains 244 residues out of total 494 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 227 time to evaluate : 0.626 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 60 VAL Chi-restraints excluded: chain B residue 62 LEU Chi-restraints excluded: chain B residue 81 VAL Chi-restraints excluded: chain C residue 65 LEU Chi-restraints excluded: chain C residue 85 GLN Chi-restraints excluded: chain C residue 117 VAL Chi-restraints excluded: chain C residue 124 ILE Chi-restraints excluded: chain D residue 50 ILE Chi-restraints excluded: chain D residue 62 LEU Chi-restraints excluded: chain E residue 65 LEU Chi-restraints excluded: chain E residue 89 VAL Chi-restraints excluded: chain E residue 126 LEU Chi-restraints excluded: chain F residue 30 THR Chi-restraints excluded: chain F residue 44 LYS Chi-restraints excluded: chain F residue 49 LEU Chi-restraints excluded: chain F residue 90 LEU Chi-restraints excluded: chain G residue 124 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 75 random chunks: chunk 35 optimal weight: 5.9990 chunk 56 optimal weight: 5.9990 chunk 30 optimal weight: 0.7980 chunk 14 optimal weight: 4.9990 chunk 64 optimal weight: 10.0000 chunk 8 optimal weight: 4.9990 chunk 51 optimal weight: 10.0000 chunk 57 optimal weight: 6.9990 chunk 50 optimal weight: 0.9990 chunk 7 optimal weight: 0.9990 chunk 70 optimal weight: 5.9990 overall best weight: 2.5588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 108 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 75 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 25 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3465 r_free = 0.3465 target = 0.053360 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.2928 r_free = 0.2928 target = 0.036801 restraints weight = 57537.772| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 46)----------------| | r_work = 0.2971 r_free = 0.2971 target = 0.037987 restraints weight = 28892.842| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 56)----------------| | r_work = 0.2999 r_free = 0.2999 target = 0.038760 restraints weight = 19448.808| |-----------------------------------------------------------------------------| r_work (final): 0.2930 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8568 moved from start: 0.5370 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.048 9362 Z= 0.332 Angle : 0.825 17.548 13488 Z= 0.446 Chirality : 0.039 0.192 1549 Planarity : 0.005 0.046 1004 Dihedral : 31.221 157.674 2840 Min Nonbonded Distance : 2.016 Molprobity Statistics. All-atom Clashscore : 20.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.49 % Favored : 97.51 % Rotamer: Outliers : 3.85 % Allowed : 38.06 % Favored : 58.10 % 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: 1.46 (0.34), residues: 563 helix: 1.47 (0.23), residues: 461 sheet: None (None), residues: 0 loop : -1.23 (0.53), residues: 102 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.005 0.001 HIS C 113 PHE 0.014 0.002 PHE G 67 TYR 0.023 0.002 TYR A 99 ARG 0.008 0.001 ARG H 36 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3534.29 seconds wall clock time: 61 minutes 36.12 seconds (3696.12 seconds total)