Starting phenix.real_space_refine on Sat Dec 28 13:29:14 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7y5w_33627/12_2024/7y5w_33627.cif Found real_map, /net/cci-nas-00/data/ceres_data/7y5w_33627/12_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/cci-nas-00/data/ceres_data/7y5w_33627/12_2024/7y5w_33627.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7y5w_33627/12_2024/7y5w_33627.map" model { file = "/net/cci-nas-00/data/ceres_data/7y5w_33627/12_2024/7y5w_33627.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7y5w_33627/12_2024/7y5w_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-5532/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 - 3.00 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: 2.45 Conformation dependent library (CDL) restraints added in 628.6 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: 4.45 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: 3.21 Time building geometry restraints manager: 2.84 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: 0.990 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.380 Check model and map are aligned: 0.060 Set scattering table: 0.090 Process input model: 25.460 Find NCS groups from input model: 0.260 Set up NCS constraints: 0.040 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:3.040 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 30.330 ------------------------------------------------------------------------------- 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 : 0.724 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: 0.3120 time to fit residues: 124.2762 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 : 0.703 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7135 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 : 0.676 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 99 TYR cc_start: 0.7409 (t80) cc_final: 0.7176 (t80) REVERT: C 76 GLN cc_start: 0.7496 (pp30) cc_final: 0.7251 (pp30) REVERT: F 27 GLN cc_start: 0.7973 (mm-40) cc_final: 0.7671 (mm-40) REVERT: H 63 GLU cc_start: 0.7600 (tm-30) cc_final: 0.6734 (tm-30) outliers start: 18 outliers final: 12 residues processed: 265 average time/residue: 0.2801 time to fit residues: 93.9307 Evaluate side-chains 243 residues out of total 494 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 231 time to evaluate : 0.813 ------------------------------------------------------------------------------- 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 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: 1.9990 chunk 21 optimal weight: 0.9990 chunk 56 optimal weight: 5.9990 chunk 46 optimal weight: 8.9990 chunk 18 optimal weight: 0.7980 chunk 68 optimal weight: 4.9990 chunk 73 optimal weight: 7.9990 chunk 60 optimal weight: 5.9990 chunk 67 optimal weight: 4.9990 chunk 23 optimal weight: 0.8980 chunk 54 optimal weight: 5.9990 overall best weight: 1.9386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 68 GLN ** C 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 93 GLN F 75 HIS H 64 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7212 moved from start: 0.3547 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.044 9362 Z= 0.267 Angle : 0.678 10.513 13488 Z= 0.383 Chirality : 0.037 0.182 1549 Planarity : 0.005 0.038 1004 Dihedral : 30.764 149.605 2840 Min Nonbonded Distance : 2.060 Molprobity Statistics. All-atom Clashscore : 18.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.95 % Favored : 98.05 % Rotamer: Outliers : 7.09 % Allowed : 26.52 % Favored : 66.40 % 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: 1.81 (0.24), residues: 463 sheet: None (None), residues: 0 loop : -0.73 (0.52), residues: 100 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.004 0.001 HIS C 113 PHE 0.016 0.002 PHE H 61 TYR 0.009 0.001 TYR F 88 ARG 0.005 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 283 residues out of total 494 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 248 time to evaluate : 0.711 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: C 97 GLU cc_start: 0.5562 (mt-10) cc_final: 0.5349 (mt-10) REVERT: F 27 GLN cc_start: 0.8070 (mm-40) cc_final: 0.7793 (mm-40) REVERT: F 29 ILE cc_start: 0.8116 (tp) cc_final: 0.7747 (tp) REVERT: G 90 MET cc_start: 0.6980 (tmm) cc_final: 0.6765 (tpp) outliers start: 35 outliers final: 19 residues processed: 258 average time/residue: 0.2912 time to fit residues: 94.4532 Evaluate side-chains 244 residues out of total 494 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 225 time to evaluate : 0.693 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 65 LEU 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 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 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 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 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: 4.9990 chunk 51 optimal weight: 8.9990 chunk 35 optimal weight: 0.7980 chunk 7 optimal weight: 1.9990 chunk 32 optimal weight: 0.8980 chunk 45 optimal weight: 1.9990 chunk 68 optimal weight: 4.9990 chunk 72 optimal weight: 4.9990 chunk 64 optimal weight: 10.0000 chunk 19 optimal weight: 1.9990 chunk 60 optimal weight: 4.9990 overall best weight: 1.5386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F 25 ASN G 68 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7205 moved from start: 0.3947 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 9362 Z= 0.252 Angle : 0.698 11.355 13488 Z= 0.390 Chirality : 0.037 0.171 1549 Planarity : 0.004 0.038 1004 Dihedral : 30.789 152.074 2840 Min Nonbonded Distance : 2.053 Molprobity Statistics. All-atom Clashscore : 17.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.78 % Favored : 98.22 % Rotamer: Outliers : 6.88 % Allowed : 27.53 % Favored : 65.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.76 (0.34), residues: 563 helix: 1.58 (0.24), residues: 466 sheet: None (None), residues: 0 loop : -0.71 (0.53), residues: 97 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.005 0.001 HIS C 113 PHE 0.016 0.002 PHE G 67 TYR 0.016 0.001 TYR H 88 ARG 0.009 0.001 ARG E 83 *********************** 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 278 residues out of total 494 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 244 time to evaluate : 0.690 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 70 LEU cc_start: 0.7310 (tt) cc_final: 0.7100 (tt) REVERT: C 76 GLN cc_start: 0.7738 (pp30) cc_final: 0.7412 (pp30) REVERT: C 97 GLU cc_start: 0.5685 (mt-10) cc_final: 0.5410 (mt-10) REVERT: F 23 ARG cc_start: 0.5895 (ptm-80) cc_final: 0.5618 (ptm160) REVERT: F 27 GLN cc_start: 0.7960 (mm-40) cc_final: 0.7679 (mm-40) REVERT: G 64 LYS cc_start: 0.7251 (tptt) cc_final: 0.6553 (tptp) REVERT: G 90 MET cc_start: 0.7035 (tmm) cc_final: 0.6482 (tmm) outliers start: 34 outliers final: 20 residues processed: 252 average time/residue: 0.2962 time to fit residues: 93.5970 Evaluate side-chains 245 residues out of total 494 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 225 time to evaluate : 0.673 ------------------------------------------------------------------------------- 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 72 TYR 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 117 VAL 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 82 LEU Chi-restraints excluded: chain E residue 87 SER Chi-restraints excluded: chain E residue 106 ASP 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 F residue 92 ARG Chi-restraints excluded: chain H residue 78 ARG 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: 0.9980 chunk 53 optimal weight: 4.9990 chunk 29 optimal weight: 0.8980 chunk 61 optimal weight: 5.9990 chunk 50 optimal weight: 3.9990 chunk 0 optimal weight: 3.9990 chunk 37 optimal weight: 0.7980 chunk 65 optimal weight: 10.0000 chunk 18 optimal weight: 0.5980 chunk 24 optimal weight: 0.8980 overall best weight: 0.7980 ------------------------------------------------------------------------------- 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: 0.7149 moved from start: 0.4240 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 : 0.704 10.578 13488 Z= 0.388 Chirality : 0.036 0.171 1549 Planarity : 0.006 0.108 1004 Dihedral : 30.737 153.284 2840 Min Nonbonded Distance : 2.055 Molprobity Statistics. All-atom Clashscore : 16.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.95 % Favored : 98.05 % Rotamer: Outliers : 5.67 % Allowed : 31.38 % 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: 1.72 (0.34), residues: 563 helix: 1.57 (0.24), residues: 462 sheet: None (None), residues: 0 loop : -0.74 (0.52), residues: 101 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.005 0.001 HIS C 113 PHE 0.031 0.002 PHE G 78 TYR 0.017 0.002 TYR H 88 ARG 0.011 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 263 residues out of total 494 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 235 time to evaluate : 0.751 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 58 LEU cc_start: 0.7681 (tp) cc_final: 0.7323 (tp) REVERT: C 76 GLN cc_start: 0.7700 (pp30) cc_final: 0.7317 (pp30) REVERT: F 27 GLN cc_start: 0.7897 (mm-40) cc_final: 0.7654 (mm-40) REVERT: F 50 ILE cc_start: 0.7436 (mm) cc_final: 0.7076 (tp) REVERT: F 68 ASP cc_start: 0.5622 (m-30) cc_final: 0.4963 (m-30) REVERT: G 90 MET cc_start: 0.7137 (tmm) cc_final: 0.6300 (tmm) outliers start: 28 outliers final: 17 residues processed: 244 average time/residue: 0.2936 time to fit residues: 89.7056 Evaluate side-chains 235 residues out of total 494 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 218 time to evaluate : 0.665 ------------------------------------------------------------------------------- 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 65 LEU Chi-restraints excluded: chain C residue 117 VAL 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 65 LEU Chi-restraints excluded: chain E residue 82 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 G residue 61 LEU 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: 5.9990 chunk 42 optimal weight: 0.7980 chunk 17 optimal weight: 2.9990 chunk 72 optimal weight: 5.9990 chunk 60 optimal weight: 5.9990 chunk 33 optimal weight: 2.9990 chunk 6 optimal weight: 3.9990 chunk 24 optimal weight: 0.6980 chunk 38 optimal weight: 3.9990 chunk 69 optimal weight: 4.9990 overall best weight: 2.2986 ------------------------------------------------------------------------------- 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: 0.7263 moved from start: 0.4615 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= 0.308 Angle : 0.746 13.106 13488 Z= 0.412 Chirality : 0.037 0.166 1549 Planarity : 0.005 0.056 1004 Dihedral : 30.959 155.197 2840 Min Nonbonded Distance : 2.035 Molprobity Statistics. All-atom Clashscore : 18.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.78 % Favored : 98.22 % Rotamer: Outliers : 5.87 % Allowed : 33.00 % Favored : 61.13 % 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: 1.53 (0.24), residues: 462 sheet: None (None), residues: 0 loop : -0.89 (0.50), residues: 101 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.006 0.002 HIS C 113 PHE 0.027 0.002 PHE G 78 TYR 0.019 0.002 TYR H 88 ARG 0.011 0.001 ARG F 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 255 residues out of total 494 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 226 time to evaluate : 0.684 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: C 61 LEU cc_start: 0.7602 (OUTLIER) cc_final: 0.7334 (mp) REVERT: F 27 GLN cc_start: 0.7851 (mm-40) cc_final: 0.7593 (mm-40) REVERT: F 50 ILE cc_start: 0.7461 (mm) cc_final: 0.7177 (tp) REVERT: G 90 MET cc_start: 0.7172 (tmm) cc_final: 0.6523 (tmm) REVERT: G 94 GLU cc_start: 0.7054 (OUTLIER) cc_final: 0.6172 (mp0) outliers start: 29 outliers final: 19 residues processed: 235 average time/residue: 0.2715 time to fit residues: 80.5972 Evaluate side-chains 231 residues out of total 494 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 210 time to evaluate : 0.681 ------------------------------------------------------------------------------- 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 72 TYR Chi-restraints excluded: chain C residue 61 LEU Chi-restraints excluded: chain C residue 65 LEU Chi-restraints excluded: chain C residue 109 LEU Chi-restraints excluded: chain C residue 117 VAL Chi-restraints excluded: chain C residue 125 GLN Chi-restraints excluded: chain D residue 29 ILE Chi-restraints excluded: chain D residue 50 ILE Chi-restraints excluded: chain E residue 61 LEU 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 126 LEU Chi-restraints excluded: chain F residue 30 THR Chi-restraints excluded: chain G residue 61 LEU Chi-restraints excluded: chain G residue 94 GLU Chi-restraints excluded: chain G residue 130 ILE 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: 0.9980 chunk 41 optimal weight: 0.8980 chunk 52 optimal weight: 10.0000 chunk 61 optimal weight: 5.9990 chunk 40 optimal weight: 0.9990 chunk 72 optimal weight: 5.9990 chunk 45 optimal weight: 0.7980 chunk 44 optimal weight: 8.9990 chunk 33 optimal weight: 4.9990 chunk 28 optimal weight: 3.9990 chunk 43 optimal weight: 6.9990 overall best weight: 1.5384 ------------------------------------------------------------------------------- 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: 0.7230 moved from start: 0.4775 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.039 9362 Z= 0.268 Angle : 0.768 10.299 13488 Z= 0.418 Chirality : 0.038 0.306 1549 Planarity : 0.005 0.089 1004 Dihedral : 30.907 155.375 2840 Min Nonbonded Distance : 2.027 Molprobity Statistics. All-atom Clashscore : 17.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.95 % Favored : 98.05 % Rotamer: Outliers : 4.66 % Allowed : 34.01 % Favored : 61.34 % 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: 1.56 (0.34), residues: 563 helix: 1.47 (0.24), residues: 464 sheet: None (None), residues: 0 loop : -0.86 (0.50), residues: 99 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.005 0.001 HIS C 113 PHE 0.016 0.002 PHE G 78 TYR 0.018 0.002 TYR H 88 ARG 0.012 0.001 ARG H 67 *********************** 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 249 residues out of total 494 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 226 time to evaluate : 0.741 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: F 27 GLN cc_start: 0.7831 (mm-40) cc_final: 0.7590 (mm-40) REVERT: F 50 ILE cc_start: 0.7492 (mm) cc_final: 0.7179 (tp) REVERT: G 90 MET cc_start: 0.7200 (tmm) cc_final: 0.6602 (tmm) REVERT: G 94 GLU cc_start: 0.6952 (OUTLIER) cc_final: 0.6191 (mp0) outliers start: 23 outliers final: 19 residues processed: 234 average time/residue: 0.2987 time to fit residues: 87.6051 Evaluate side-chains 230 residues out of total 494 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 210 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 65 LEU Chi-restraints excluded: chain C residue 80 THR Chi-restraints excluded: chain C residue 109 LEU Chi-restraints excluded: chain C residue 117 VAL Chi-restraints excluded: chain C residue 125 GLN 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 65 LEU Chi-restraints excluded: chain E residue 82 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 94 GLU Chi-restraints excluded: chain G residue 124 ILE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 75 random chunks: chunk 21 optimal weight: 0.9990 chunk 14 optimal weight: 3.9990 chunk 45 optimal weight: 10.0000 chunk 49 optimal weight: 3.9990 chunk 35 optimal weight: 0.5980 chunk 6 optimal weight: 1.9990 chunk 56 optimal weight: 6.9990 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: 2.3188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** F 25 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 64 ASN G 93 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7284 moved from start: 0.5002 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.047 9362 Z= 0.315 Angle : 0.790 11.787 13488 Z= 0.433 Chirality : 0.039 0.229 1549 Planarity : 0.005 0.055 1004 Dihedral : 30.996 155.930 2840 Min Nonbonded Distance : 2.017 Molprobity Statistics. All-atom Clashscore : 19.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.13 % Favored : 97.87 % Rotamer: Outliers : 5.47 % Allowed : 36.23 % 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: 1.48 (0.34), residues: 563 helix: 1.46 (0.24), residues: 463 sheet: None (None), residues: 0 loop : -1.14 (0.50), residues: 100 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.006 0.001 HIS C 113 PHE 0.020 0.002 PHE A 84 TYR 0.021 0.002 TYR A 99 ARG 0.010 0.001 ARG F 92 *********************** 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 251 residues out of total 494 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 224 time to evaluate : 0.834 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: F 27 GLN cc_start: 0.7854 (mm-40) cc_final: 0.7614 (mm-40) REVERT: F 50 ILE cc_start: 0.7609 (mm) cc_final: 0.7251 (tp) REVERT: G 90 MET cc_start: 0.7318 (tmm) cc_final: 0.6774 (tmm) REVERT: G 94 GLU cc_start: 0.6974 (OUTLIER) cc_final: 0.6159 (mp0) REVERT: G 109 LEU cc_start: 0.8362 (mm) cc_final: 0.8017 (mp) outliers start: 27 outliers final: 22 residues processed: 232 average time/residue: 0.2848 time to fit residues: 83.3373 Evaluate side-chains 230 residues out of total 494 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 207 time to evaluate : 0.840 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 86 SER Chi-restraints excluded: chain B residue 37 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 65 LEU Chi-restraints excluded: chain C residue 80 THR Chi-restraints excluded: chain C residue 109 LEU Chi-restraints excluded: chain C residue 117 VAL Chi-restraints excluded: chain C residue 125 GLN Chi-restraints excluded: chain D residue 29 ILE Chi-restraints excluded: chain D residue 50 ILE Chi-restraints excluded: chain D residue 86 VAL Chi-restraints excluded: chain E residue 61 LEU Chi-restraints excluded: chain E residue 65 LEU Chi-restraints excluded: chain E residue 82 LEU 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 G residue 94 GLU Chi-restraints excluded: chain G residue 124 ILE Chi-restraints excluded: chain H residue 82 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 75 random chunks: chunk 69 optimal weight: 4.9990 chunk 40 optimal weight: 2.9990 chunk 29 optimal weight: 4.9990 chunk 52 optimal weight: 7.9990 chunk 20 optimal weight: 0.3980 chunk 60 optimal weight: 4.9990 chunk 63 optimal weight: 6.9990 chunk 67 optimal weight: 4.9990 chunk 44 optimal weight: 5.9990 chunk 71 optimal weight: 5.9990 chunk 43 optimal weight: 6.9990 overall best weight: 3.6788 ------------------------------------------------------------------------------- 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 G 108 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7392 moved from start: 0.5465 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.062 9362 Z= 0.419 Angle : 0.868 12.615 13488 Z= 0.475 Chirality : 0.043 0.369 1549 Planarity : 0.006 0.058 1004 Dihedral : 31.385 157.173 2840 Min Nonbonded Distance : 2.010 Molprobity Statistics. All-atom Clashscore : 22.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.66 % Favored : 97.34 % Rotamer: Outliers : 5.67 % Allowed : 37.65 % Favored : 56.68 % 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: 1.15 (0.34), residues: 563 helix: 1.26 (0.24), residues: 459 sheet: None (None), residues: 0 loop : -1.31 (0.49), residues: 104 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.005 0.001 HIS C 113 PHE 0.012 0.002 PHE A 84 TYR 0.018 0.003 TYR D 51 ARG 0.010 0.001 ARG G 131 *********************** 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 238 residues out of total 494 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 210 time to evaluate : 0.723 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: B 84 MET cc_start: 0.6124 (ppp) cc_final: 0.5891 (ppp) REVERT: C 128 ARG cc_start: 0.7223 (mtp85) cc_final: 0.6862 (mtp85) REVERT: F 50 ILE cc_start: 0.7691 (mm) cc_final: 0.7340 (tp) outliers start: 28 outliers final: 23 residues processed: 218 average time/residue: 0.2936 time to fit residues: 80.2545 Evaluate side-chains 224 residues out of total 494 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 201 time to evaluate : 0.721 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 86 SER Chi-restraints excluded: chain B residue 37 LEU 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 65 LEU Chi-restraints excluded: chain C residue 109 LEU 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 49 LEU Chi-restraints excluded: chain D residue 50 ILE Chi-restraints excluded: chain E residue 61 LEU Chi-restraints excluded: chain E residue 65 LEU Chi-restraints excluded: chain E residue 82 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 61 LEU Chi-restraints excluded: chain G residue 70 LEU Chi-restraints excluded: chain G residue 119 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 75 random chunks: chunk 33 optimal weight: 3.9990 chunk 49 optimal weight: 5.9990 chunk 74 optimal weight: 8.9990 chunk 68 optimal weight: 4.9990 chunk 59 optimal weight: 4.9990 chunk 6 optimal weight: 0.7980 chunk 45 optimal weight: 3.9990 chunk 36 optimal weight: 2.9990 chunk 47 optimal weight: 5.9990 chunk 63 optimal weight: 5.9990 chunk 18 optimal weight: 0.7980 overall best weight: 2.5186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 125 GLN ** F 25 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 93 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7346 moved from start: 0.5573 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.046 9362 Z= 0.337 Angle : 0.868 13.704 13488 Z= 0.469 Chirality : 0.041 0.384 1549 Planarity : 0.005 0.044 1004 Dihedral : 31.377 156.679 2840 Min Nonbonded Distance : 2.007 Molprobity Statistics. All-atom Clashscore : 20.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.66 % Favored : 97.34 % Rotamer: Outliers : 4.86 % Allowed : 38.46 % Favored : 56.68 % 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: 1.07 (0.34), residues: 563 helix: 1.19 (0.24), residues: 457 sheet: None (None), residues: 0 loop : -1.21 (0.51), residues: 106 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.006 0.001 HIS C 113 PHE 0.035 0.002 PHE G 67 TYR 0.015 0.002 TYR A 99 ARG 0.009 0.001 ARG G 128 ********************** 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 235 residues out of total 494 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 211 time to evaluate : 0.721 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: F 27 GLN cc_start: 0.7950 (mm-40) cc_final: 0.7503 (mm-40) REVERT: F 50 ILE cc_start: 0.7632 (mm) cc_final: 0.7285 (tp) outliers start: 24 outliers final: 22 residues processed: 218 average time/residue: 0.2934 time to fit residues: 80.6330 Evaluate side-chains 227 residues out of total 494 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 205 time to evaluate : 0.733 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 86 SER Chi-restraints excluded: chain B residue 37 LEU Chi-restraints excluded: chain B residue 60 VAL Chi-restraints excluded: chain B residue 62 LEU Chi-restraints excluded: chain B residue 86 VAL Chi-restraints excluded: chain C residue 65 LEU Chi-restraints excluded: chain C residue 80 THR Chi-restraints excluded: chain C residue 109 LEU Chi-restraints excluded: chain C residue 117 VAL Chi-restraints excluded: chain C residue 125 GLN Chi-restraints excluded: chain D residue 29 ILE Chi-restraints excluded: chain D residue 50 ILE Chi-restraints excluded: chain E residue 61 LEU Chi-restraints excluded: chain E residue 65 LEU Chi-restraints excluded: chain E residue 82 LEU 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 G residue 70 LEU Chi-restraints excluded: chain G residue 119 ILE Chi-restraints excluded: chain G residue 130 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 75 random chunks: chunk 54 optimal weight: 0.9990 chunk 8 optimal weight: 8.9990 chunk 16 optimal weight: 3.9990 chunk 59 optimal weight: 4.9990 chunk 24 optimal weight: 0.9990 chunk 61 optimal weight: 5.9990 chunk 7 optimal weight: 0.9990 chunk 10 optimal weight: 0.5980 chunk 52 optimal weight: 5.9990 chunk 3 optimal weight: 1.9990 chunk 43 optimal weight: 1.9990 overall best weight: 1.1188 ------------------------------------------------------------------------------- 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** ** 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 = 0.3507 r_free = 0.3507 target = 0.055099 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 60)----------------| | r_work = 0.2999 r_free = 0.2999 target = 0.038810 restraints weight = 55652.527| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 62)----------------| | r_work = 0.3043 r_free = 0.3043 target = 0.040043 restraints weight = 27825.247| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3072 r_free = 0.3072 target = 0.040807 restraints weight = 18651.234| |-----------------------------------------------------------------------------| r_work (final): 0.3009 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8502 moved from start: 0.5595 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.054 9362 Z= 0.271 Angle : 0.875 13.852 13488 Z= 0.468 Chirality : 0.041 0.383 1549 Planarity : 0.005 0.050 1004 Dihedral : 31.148 157.041 2840 Min Nonbonded Distance : 2.023 Molprobity Statistics. All-atom Clashscore : 18.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.31 % Favored : 97.69 % Rotamer: Outliers : 4.05 % Allowed : 39.27 % Favored : 56.68 % 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: 1.04 (0.34), residues: 563 helix: 1.14 (0.24), residues: 453 sheet: None (None), residues: 0 loop : -1.00 (0.51), residues: 110 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.006 0.001 HIS C 113 PHE 0.032 0.002 PHE G 67 TYR 0.013 0.002 TYR D 51 ARG 0.015 0.001 ARG H 40 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2087.06 seconds wall clock time: 38 minutes 42.40 seconds (2322.40 seconds total)