Starting phenix.real_space_refine on Mon Mar 11 17:43:36 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7y5w_33627/03_2024/7y5w_33627.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7y5w_33627/03_2024/7y5w_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/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7y5w_33627/03_2024/7y5w_33627.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7y5w_33627/03_2024/7y5w_33627.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7y5w_33627/03_2024/7y5w_33627.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7y5w_33627/03_2024/7y5w_33627.pdb" } 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 Residue "B GLU 52": "OE1" <-> "OE2" Residue "B GLU 74": "OE1" <-> "OE2" Residue "G GLU 94": "OE1" <-> "OE2" Residue "H GLU 63": "OE1" <-> "OE2" Time to flip residues: 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/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: 5.55, per 1000 atoms: 0.63 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 - 3.50 Amino acid : False - 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: 5.01 Conformation dependent library (CDL) restraints added in 1.1 seconds 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: 4.20 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: 2.88 Time building geometry restraints manager: 5.09 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: 98.09 - 104.97: 817 104.97 - 111.86: 5110 111.86 - 118.74: 2425 118.74 - 125.63: 4469 125.63 - 132.51: 667 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 2.440 ... (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 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: 1.220 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: 3.920 Check model and map are aligned: 0.140 Set scattering table: 0.100 Process input model: 31.630 Find NCS groups from input model: 0.590 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: 0.010 Load rotamer database and sin/cos tables:2.660 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 40.300 ------------------------------------------------------------------------------- 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 fitting. rotamer outliers: 0 poor density : 322 time to evaluate : 0.663 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: 0.2958 time to fit residues: 117.7135 Evaluate side-chains 224 residues out of total 494 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 224 time to evaluate : 0.751 ------------------------------------------------------------------------------- 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: 6.9990 chunk 31 optimal weight: 0.8980 chunk 19 optimal weight: 1.9990 chunk 38 optimal weight: 0.9980 chunk 30 optimal weight: 0.9990 chunk 58 optimal weight: 5.9990 chunk 22 optimal weight: 3.9990 chunk 35 optimal weight: 0.0370 chunk 43 optimal weight: 7.9990 chunk 68 optimal weight: 4.9990 overall best weight: 0.9862 ------------------------------------------------------------------------------- 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 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: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7120 moved from start: 0.2825 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= 0.226 Angle : 0.654 11.522 13488 Z= 0.365 Chirality : 0.037 0.248 1549 Planarity : 0.005 0.046 1004 Dihedral : 30.597 146.479 2840 Min Nonbonded Distance : 2.097 Molprobity Statistics. All-atom Clashscore : 19.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.13 % Favored : 97.87 % Rotamer: Outliers : 3.24 % Allowed : 27.33 % Favored : 69.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.18 (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 0.004 0.001 HIS C 113 PHE 0.021 0.002 PHE G 67 TYR 0.018 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 fitting. rotamer outliers: 16 poor density : 263 time to evaluate : 0.695 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: F 27 GLN cc_start: 0.7966 (mm-40) cc_final: 0.7674 (mm-40) REVERT: F 49 LEU cc_start: 0.7044 (mm) cc_final: 0.6800 (mm) outliers start: 16 outliers final: 9 residues processed: 265 average time/residue: 0.2796 time to fit residues: 93.2134 Evaluate side-chains 241 residues out of total 494 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 232 time to evaluate : 0.724 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 81 ASP Chi-restraints excluded: chain E residue 124 ILE Chi-restraints excluded: chain F residue 30 THR 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 37 optimal weight: 2.9990 chunk 21 optimal weight: 2.9990 chunk 56 optimal weight: 5.9990 chunk 46 optimal weight: 8.9990 chunk 18 optimal weight: 0.9990 chunk 68 optimal weight: 4.9990 chunk 73 optimal weight: 6.9990 chunk 60 optimal weight: 5.9990 chunk 67 optimal weight: 5.9990 chunk 23 optimal weight: 0.7980 chunk 54 optimal weight: 10.0000 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 76 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 93 GLN F 75 HIS ** H 64 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7267 moved from start: 0.3730 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.048 9362 Z= 0.311 Angle : 0.699 10.158 13488 Z= 0.392 Chirality : 0.037 0.176 1549 Planarity : 0.005 0.040 1004 Dihedral : 30.840 150.165 2840 Min Nonbonded Distance : 2.093 Molprobity Statistics. All-atom Clashscore : 21.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.78 % Favored : 98.22 % Rotamer: Outliers : 6.88 % Allowed : 27.94 % Favored : 65.18 % 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: 1.92 (0.34), residues: 563 helix: 1.71 (0.24), residues: 465 sheet: None (None), residues: 0 loop : -0.73 (0.54), residues: 98 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.003 0.001 HIS A 113 PHE 0.020 0.003 PHE H 61 TYR 0.010 0.002 TYR F 88 ARG 0.013 0.001 ARG H 40 *********************** 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 273 residues out of total 494 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 34 poor density : 239 time to evaluate : 0.794 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 74 ILE cc_start: 0.8190 (tt) cc_final: 0.7918 (tt) REVERT: D 79 LYS cc_start: 0.6856 (mmmm) cc_final: 0.6633 (mmtt) REVERT: F 27 GLN cc_start: 0.8024 (mm-40) cc_final: 0.7745 (mm-40) REVERT: F 29 ILE cc_start: 0.8119 (tp) cc_final: 0.7150 (tp) REVERT: G 90 MET cc_start: 0.7046 (tmm) cc_final: 0.6774 (tpp) outliers start: 34 outliers final: 22 residues processed: 248 average time/residue: 0.2912 time to fit residues: 91.4422 Evaluate side-chains 242 residues out of total 494 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 220 time to evaluate : 0.730 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 86 SER 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 74 ILE Chi-restraints excluded: chain C residue 80 THR Chi-restraints excluded: chain C residue 81 ASP 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 D residue 29 ILE Chi-restraints excluded: chain E residue 65 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 86 VAL Chi-restraints excluded: chain F residue 90 LEU Chi-restraints excluded: chain G residue 130 ILE Chi-restraints excluded: chain H residue 30 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 75 random chunks: chunk 67 optimal weight: 5.9990 chunk 51 optimal weight: 5.9990 chunk 35 optimal weight: 4.9990 chunk 7 optimal weight: 2.9990 chunk 32 optimal weight: 4.9990 chunk 45 optimal weight: 6.9990 chunk 68 optimal weight: 4.9990 chunk 72 optimal weight: 5.9990 chunk 64 optimal weight: 10.0000 chunk 19 optimal weight: 0.9990 chunk 60 optimal weight: 3.9990 overall best weight: 3.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7373 moved from start: 0.4550 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.048 9362 Z= 0.387 Angle : 0.748 11.526 13488 Z= 0.425 Chirality : 0.040 0.160 1549 Planarity : 0.005 0.035 1004 Dihedral : 31.202 154.296 2840 Min Nonbonded Distance : 2.084 Molprobity Statistics. All-atom Clashscore : 23.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.31 % Favored : 97.69 % Rotamer: Outliers : 8.10 % Allowed : 29.55 % Favored : 62.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.69 (0.34), residues: 563 helix: 1.61 (0.23), residues: 459 sheet: None (None), residues: 0 loop : -1.00 (0.50), residues: 104 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.006 0.001 HIS F 75 PHE 0.015 0.002 PHE G 67 TYR 0.015 0.002 TYR H 88 ARG 0.006 0.001 ARG H 40 *********************** 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 272 residues out of total 494 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 40 poor density : 232 time to evaluate : 0.713 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: F 27 GLN cc_start: 0.7973 (mm-40) cc_final: 0.7675 (mm-40) REVERT: G 90 MET cc_start: 0.7113 (tmm) cc_final: 0.6485 (tmm) outliers start: 40 outliers final: 30 residues processed: 245 average time/residue: 0.2813 time to fit residues: 86.3948 Evaluate side-chains 238 residues out of total 494 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 208 time to evaluate : 0.672 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 65 LEU Chi-restraints excluded: chain A residue 80 THR Chi-restraints excluded: chain A residue 86 SER 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 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 81 ASP 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 C residue 125 GLN Chi-restraints excluded: chain D residue 25 ASN Chi-restraints excluded: chain D residue 29 ILE Chi-restraints excluded: chain E residue 65 LEU Chi-restraints excluded: chain E residue 82 LEU 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 85 ASP Chi-restraints excluded: chain F residue 86 VAL Chi-restraints excluded: chain F residue 90 LEU Chi-restraints excluded: chain G residue 69 ARG Chi-restraints excluded: chain G residue 130 ILE Chi-restraints excluded: chain H residue 43 VAL Chi-restraints excluded: chain H residue 59 LYS Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 75 random chunks: chunk 41 optimal weight: 0.7980 chunk 1 optimal weight: 0.9990 chunk 53 optimal weight: 5.9990 chunk 29 optimal weight: 0.8980 chunk 61 optimal weight: 5.9990 chunk 50 optimal weight: 20.0000 chunk 0 optimal weight: 3.9990 chunk 37 optimal weight: 6.9990 chunk 65 optimal weight: 10.0000 chunk 18 optimal weight: 0.6980 chunk 24 optimal weight: 0.6980 overall best weight: 0.8182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7222 moved from start: 0.4536 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= 0.233 Angle : 0.708 11.418 13488 Z= 0.395 Chirality : 0.036 0.173 1549 Planarity : 0.004 0.038 1004 Dihedral : 31.043 154.775 2840 Min Nonbonded Distance : 2.073 Molprobity Statistics. All-atom Clashscore : 19.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.13 % Favored : 97.87 % Rotamer: Outliers : 5.26 % Allowed : 34.01 % 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: 1.63 (0.34), residues: 563 helix: 1.51 (0.23), residues: 468 sheet: None (None), residues: 0 loop : -0.92 (0.53), residues: 95 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.004 0.001 HIS C 113 PHE 0.026 0.002 PHE G 78 TYR 0.016 0.001 TYR H 88 ARG 0.013 0.001 ARG H 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 269 residues out of total 494 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 243 time to evaluate : 0.778 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: C 76 GLN cc_start: 0.7750 (pp30) cc_final: 0.7549 (pp30) REVERT: F 27 GLN cc_start: 0.7793 (mm-40) cc_final: 0.7569 (mm-40) REVERT: G 90 MET cc_start: 0.7216 (tmm) cc_final: 0.6583 (tmm) outliers start: 26 outliers final: 14 residues processed: 249 average time/residue: 0.2967 time to fit residues: 92.6498 Evaluate side-chains 233 residues out of total 494 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 219 time to evaluate : 0.769 ------------------------------------------------------------------------------- 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 74 ILE Chi-restraints excluded: chain C residue 125 GLN Chi-restraints excluded: chain D residue 29 ILE Chi-restraints excluded: chain D residue 62 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 G residue 70 LEU Chi-restraints excluded: chain G residue 130 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 65 optimal weight: 10.0000 chunk 14 optimal weight: 4.9990 chunk 42 optimal weight: 2.9990 chunk 17 optimal weight: 0.7980 chunk 72 optimal weight: 6.9990 chunk 60 optimal weight: 5.9990 chunk 33 optimal weight: 4.9990 chunk 6 optimal weight: 0.9990 chunk 24 optimal weight: 0.7980 chunk 38 optimal weight: 0.8980 chunk 69 optimal weight: 4.9990 overall best weight: 1.2984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7240 moved from start: 0.4699 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 9362 Z= 0.249 Angle : 0.712 11.359 13488 Z= 0.396 Chirality : 0.036 0.160 1549 Planarity : 0.005 0.055 1004 Dihedral : 30.973 155.933 2840 Min Nonbonded Distance : 2.090 Molprobity Statistics. All-atom Clashscore : 21.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.13 % Favored : 97.87 % Rotamer: Outliers : 5.26 % Allowed : 37.85 % Favored : 56.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.51 (0.34), residues: 563 helix: 1.47 (0.23), residues: 463 sheet: None (None), residues: 0 loop : -1.09 (0.50), residues: 100 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.004 0.001 HIS C 113 PHE 0.018 0.002 PHE G 67 TYR 0.019 0.001 TYR H 88 ARG 0.008 0.001 ARG D 92 *********************** 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 260 residues out of total 494 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 234 time to evaluate : 0.740 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 61 LEU cc_start: 0.7631 (OUTLIER) cc_final: 0.7378 (mp) REVERT: F 27 GLN cc_start: 0.7759 (mm-40) cc_final: 0.7537 (mm-40) REVERT: F 93 GLN cc_start: 0.6206 (tm-30) cc_final: 0.6005 (tm-30) REVERT: G 90 MET cc_start: 0.7181 (tmm) cc_final: 0.6520 (tmm) REVERT: G 94 GLU cc_start: 0.6983 (OUTLIER) cc_final: 0.6382 (mp0) outliers start: 26 outliers final: 17 residues processed: 239 average time/residue: 0.2798 time to fit residues: 84.0977 Evaluate side-chains 232 residues out of total 494 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 213 time to evaluate : 0.697 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 86 SER 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 125 GLN 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 E residue 65 LEU Chi-restraints excluded: chain E residue 80 THR 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 86 VAL Chi-restraints excluded: chain G residue 94 GLU Chi-restraints excluded: chain H residue 30 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 75 random chunks: chunk 8 optimal weight: 7.9990 chunk 41 optimal weight: 0.7980 chunk 52 optimal weight: 2.9990 chunk 61 optimal weight: 5.9990 chunk 40 optimal weight: 3.9990 chunk 72 optimal weight: 5.9990 chunk 45 optimal weight: 0.9980 chunk 44 optimal weight: 6.9990 chunk 33 optimal weight: 6.9990 chunk 28 optimal weight: 3.9990 chunk 43 optimal weight: 9.9990 overall best weight: 2.5586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F 64 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7318 moved from start: 0.4988 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= 0.320 Angle : 0.747 11.246 13488 Z= 0.416 Chirality : 0.038 0.166 1549 Planarity : 0.005 0.043 1004 Dihedral : 31.072 156.181 2840 Min Nonbonded Distance : 2.077 Molprobity Statistics. All-atom Clashscore : 22.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.95 % Favored : 98.05 % Rotamer: Outliers : 5.87 % Allowed : 38.06 % Favored : 56.07 % 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: 1.37 (0.33), residues: 563 helix: 1.39 (0.23), residues: 459 sheet: None (None), residues: 0 loop : -1.12 (0.47), residues: 104 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.004 0.001 HIS F 75 PHE 0.026 0.002 PHE G 78 TYR 0.019 0.002 TYR H 88 ARG 0.010 0.001 ARG H 40 *********************** 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 248 residues out of total 494 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 219 time to evaluate : 0.798 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: B 84 MET cc_start: 0.6347 (ppp) cc_final: 0.6085 (ppp) REVERT: F 27 GLN cc_start: 0.7822 (mm-40) cc_final: 0.7568 (mm-40) REVERT: F 93 GLN cc_start: 0.6325 (tm-30) cc_final: 0.6101 (tm-30) REVERT: G 90 MET cc_start: 0.7237 (tmm) cc_final: 0.6523 (tmm) REVERT: G 94 GLU cc_start: 0.6933 (OUTLIER) cc_final: 0.6235 (mp0) outliers start: 29 outliers final: 22 residues processed: 227 average time/residue: 0.2887 time to fit residues: 82.2821 Evaluate side-chains 226 residues out of total 494 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 203 time to evaluate : 0.819 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 59 GLU Chi-restraints excluded: chain A residue 86 SER 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 65 LEU Chi-restraints excluded: chain C residue 74 ILE Chi-restraints excluded: chain C residue 81 ASP Chi-restraints excluded: chain C residue 117 VAL Chi-restraints excluded: chain C residue 125 GLN 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 E residue 65 LEU Chi-restraints excluded: chain E residue 80 THR Chi-restraints excluded: chain E residue 89 VAL 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 86 VAL Chi-restraints excluded: chain G residue 94 GLU Chi-restraints excluded: chain H residue 30 THR Chi-restraints excluded: chain H residue 46 ILE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 75 random chunks: chunk 21 optimal weight: 0.4980 chunk 14 optimal weight: 3.9990 chunk 45 optimal weight: 2.9990 chunk 49 optimal weight: 0.9990 chunk 35 optimal weight: 8.9990 chunk 6 optimal weight: 2.9990 chunk 56 optimal weight: 5.9990 chunk 65 optimal weight: 10.0000 chunk 69 optimal weight: 4.9990 chunk 63 optimal weight: 6.9990 chunk 67 optimal weight: 4.9990 overall best weight: 2.2988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** G 85 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 93 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7320 moved from start: 0.5196 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= 0.307 Angle : 0.783 13.024 13488 Z= 0.427 Chirality : 0.038 0.175 1549 Planarity : 0.004 0.035 1004 Dihedral : 31.112 156.299 2840 Min Nonbonded Distance : 2.074 Molprobity Statistics. All-atom Clashscore : 23.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.31 % Favored : 97.69 % Rotamer: Outliers : 5.47 % Allowed : 38.26 % Favored : 56.28 % 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: 1.20 (0.33), residues: 563 helix: 1.28 (0.23), residues: 459 sheet: None (None), residues: 0 loop : -1.22 (0.47), residues: 104 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.004 0.001 HIS C 113 PHE 0.026 0.002 PHE G 67 TYR 0.015 0.002 TYR F 72 ARG 0.015 0.001 ARG H 36 *********************** 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 242 residues out of total 494 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 215 time to evaluate : 0.773 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: B 84 MET cc_start: 0.6262 (ppp) cc_final: 0.6028 (ppp) REVERT: F 50 ILE cc_start: 0.7532 (tp) cc_final: 0.7285 (tp) REVERT: F 93 GLN cc_start: 0.6318 (tm-30) cc_final: 0.6106 (tm-30) REVERT: G 90 MET cc_start: 0.7284 (tmm) cc_final: 0.6569 (tmm) REVERT: G 94 GLU cc_start: 0.7002 (OUTLIER) cc_final: 0.6270 (mp0) REVERT: G 109 LEU cc_start: 0.8546 (mm) cc_final: 0.8107 (mp) REVERT: H 44 LYS cc_start: 0.8122 (mmtm) cc_final: 0.7921 (mmtm) outliers start: 27 outliers final: 22 residues processed: 226 average time/residue: 0.2820 time to fit residues: 79.8129 Evaluate side-chains 226 residues out of total 494 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 203 time to evaluate : 0.774 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 86 SER 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 74 ILE Chi-restraints excluded: chain C residue 80 THR Chi-restraints excluded: chain C residue 117 VAL Chi-restraints excluded: chain C residue 125 GLN 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 E residue 65 LEU Chi-restraints excluded: chain E residue 80 THR Chi-restraints excluded: chain E residue 89 VAL 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 86 VAL Chi-restraints excluded: chain G residue 94 GLU Chi-restraints excluded: chain H residue 30 THR Chi-restraints excluded: chain H residue 46 ILE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 75 random chunks: chunk 69 optimal weight: 5.9990 chunk 40 optimal weight: 3.9990 chunk 29 optimal weight: 5.9990 chunk 52 optimal weight: 8.9990 chunk 20 optimal weight: 0.9980 chunk 60 optimal weight: 4.9990 chunk 63 optimal weight: 6.9990 chunk 67 optimal weight: 4.9990 chunk 44 optimal weight: 3.9990 chunk 71 optimal weight: 5.9990 chunk 43 optimal weight: 0.0040 overall best weight: 2.7998 ------------------------------------------------------------------------------- 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** ** G 85 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 93 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7370 moved from start: 0.5529 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.050 9362 Z= 0.346 Angle : 0.818 16.034 13488 Z= 0.444 Chirality : 0.040 0.190 1549 Planarity : 0.005 0.033 1004 Dihedral : 31.269 156.774 2840 Min Nonbonded Distance : 2.072 Molprobity Statistics. All-atom Clashscore : 24.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.78 % Favored : 98.22 % Rotamer: Outliers : 5.67 % Allowed : 37.85 % Favored : 56.48 % 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: 0.92 (0.33), residues: 563 helix: 1.08 (0.23), residues: 459 sheet: None (None), residues: 0 loop : -1.31 (0.45), residues: 104 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.004 0.001 HIS C 113 PHE 0.030 0.002 PHE G 67 TYR 0.020 0.002 TYR F 72 ARG 0.010 0.001 ARG H 36 *********************** 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 243 residues out of total 494 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 215 time to evaluate : 0.831 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: B 84 MET cc_start: 0.6238 (ppp) cc_final: 0.5999 (ppp) REVERT: C 97 GLU cc_start: 0.6071 (mt-10) cc_final: 0.5853 (mt-10) REVERT: F 27 GLN cc_start: 0.7924 (mm-40) cc_final: 0.7628 (mm-40) REVERT: F 93 GLN cc_start: 0.6502 (tm-30) cc_final: 0.6219 (tm-30) REVERT: G 90 MET cc_start: 0.7345 (tmm) cc_final: 0.7103 (tpp) REVERT: H 36 ARG cc_start: 0.7166 (ptp90) cc_final: 0.6959 (ptp90) outliers start: 28 outliers final: 24 residues processed: 223 average time/residue: 0.2825 time to fit residues: 79.4244 Evaluate side-chains 229 residues out of total 494 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 205 time to evaluate : 0.726 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 86 SER 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 74 ILE Chi-restraints excluded: chain C residue 80 THR Chi-restraints excluded: chain C residue 81 ASP Chi-restraints excluded: chain C residue 117 VAL Chi-restraints excluded: chain C residue 125 GLN 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 E residue 65 LEU Chi-restraints excluded: chain E residue 78 PHE Chi-restraints excluded: chain E residue 80 THR Chi-restraints excluded: chain E residue 89 VAL 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 86 VAL Chi-restraints excluded: chain G residue 124 ILE Chi-restraints excluded: chain H residue 30 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 75 random chunks: chunk 33 optimal weight: 7.9990 chunk 49 optimal weight: 0.9990 chunk 74 optimal weight: 8.9990 chunk 68 optimal weight: 4.9990 chunk 59 optimal weight: 5.9990 chunk 6 optimal weight: 1.9990 chunk 45 optimal weight: 3.9990 chunk 36 optimal weight: 0.0870 chunk 47 optimal weight: 0.9990 chunk 63 optimal weight: 6.9990 chunk 18 optimal weight: 0.6980 overall best weight: 0.9564 ------------------------------------------------------------------------------- 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** ** G 85 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7260 moved from start: 0.5553 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 9362 Z= 0.259 Angle : 0.833 16.537 13488 Z= 0.445 Chirality : 0.039 0.220 1549 Planarity : 0.005 0.032 1004 Dihedral : 31.092 156.736 2840 Min Nonbonded Distance : 2.070 Molprobity Statistics. All-atom Clashscore : 22.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.78 % Favored : 98.22 % Rotamer: Outliers : 3.64 % Allowed : 41.09 % Favored : 55.26 % 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: 0.90 (0.33), residues: 563 helix: 1.05 (0.23), residues: 459 sheet: None (None), residues: 0 loop : -1.18 (0.47), residues: 104 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.005 0.001 HIS C 113 PHE 0.039 0.002 PHE G 67 TYR 0.010 0.001 TYR F 51 ARG 0.012 0.001 ARG G 63 ********************** 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 240 residues out of total 494 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 222 time to evaluate : 0.766 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: B 84 MET cc_start: 0.6129 (ppp) cc_final: 0.5899 (ppp) REVERT: C 97 GLU cc_start: 0.5789 (mt-10) cc_final: 0.5576 (mt-10) REVERT: F 27 GLN cc_start: 0.7866 (mm-40) cc_final: 0.7592 (mm-40) REVERT: F 50 ILE cc_start: 0.7626 (tp) cc_final: 0.7228 (tp) outliers start: 18 outliers final: 14 residues processed: 227 average time/residue: 0.2840 time to fit residues: 81.2210 Evaluate side-chains 229 residues out of total 494 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 215 time to evaluate : 0.705 ------------------------------------------------------------------------------- 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 C residue 61 LEU Chi-restraints excluded: chain C residue 74 ILE Chi-restraints excluded: chain C residue 80 THR Chi-restraints excluded: chain C residue 117 VAL Chi-restraints excluded: chain C residue 125 GLN 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 E residue 89 VAL Chi-restraints excluded: chain E residue 124 ILE Chi-restraints excluded: chain F residue 30 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 75 random chunks: chunk 54 optimal weight: 0.0470 chunk 8 optimal weight: 6.9990 chunk 16 optimal weight: 0.9990 chunk 59 optimal weight: 4.9990 chunk 24 optimal weight: 0.8980 chunk 61 optimal weight: 6.9990 chunk 7 optimal weight: 0.6980 chunk 10 optimal weight: 0.6980 chunk 52 optimal weight: 0.8980 chunk 3 optimal weight: 0.8980 chunk 43 optimal weight: 6.9990 overall best weight: 0.6478 ------------------------------------------------------------------------------- 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** G 93 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3567 r_free = 0.3567 target = 0.056350 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3080 r_free = 0.3080 target = 0.040608 restraints weight = 55790.640| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 48)----------------| | r_work = 0.3124 r_free = 0.3124 target = 0.041892 restraints weight = 27377.788| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 48)----------------| | r_work = 0.3153 r_free = 0.3153 target = 0.042719 restraints weight = 18131.065| |-----------------------------------------------------------------------------| r_work (final): 0.3086 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8449 moved from start: 0.5583 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.055 9362 Z= 0.259 Angle : 0.840 16.378 13488 Z= 0.447 Chirality : 0.039 0.256 1549 Planarity : 0.005 0.033 1004 Dihedral : 30.943 156.532 2840 Min Nonbonded Distance : 2.097 Molprobity Statistics. All-atom Clashscore : 21.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.49 % Favored : 97.51 % Rotamer: Outliers : 2.63 % Allowed : 42.91 % Favored : 54.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.93 (0.34), residues: 563 helix: 1.05 (0.24), residues: 464 sheet: None (None), residues: 0 loop : -1.16 (0.49), residues: 99 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.005 0.001 HIS C 113 PHE 0.043 0.002 PHE G 67 TYR 0.011 0.001 TYR F 72 ARG 0.008 0.001 ARG H 40 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2135.74 seconds wall clock time: 39 minutes 7.25 seconds (2347.25 seconds total)