Starting phenix.real_space_refine on Thu Nov 14 07:48:58 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8sza_40905/11_2024/8sza_40905.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8sza_40905/11_2024/8sza_40905.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.75 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8sza_40905/11_2024/8sza_40905.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8sza_40905/11_2024/8sza_40905.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8sza_40905/11_2024/8sza_40905.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8sza_40905/11_2024/8sza_40905.cif" } resolution = 2.75 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= 0.001 sd= 0.025 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: 4 Type Number sf(0) Gaussians S 12 5.16 5 C 3258 2.51 5 N 726 2.21 5 O 804 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 14 residue(s): 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5513/modules/chem_data/mon_lib" Total number of atoms: 4800 Number of models: 1 Model: "" Number of chains: 11 Chain: "A" Number of atoms: 772 Number of conformers: 1 Conformer: "" Number of residues, atoms: 101, 772 Classifications: {'peptide': 101} Link IDs: {'PTRANS': 3, 'TRANS': 97} Chain: "B" Number of atoms: 772 Number of conformers: 1 Conformer: "" Number of residues, atoms: 101, 772 Classifications: {'peptide': 101} Link IDs: {'PTRANS': 3, 'TRANS': 97} Chain: "C" Number of atoms: 772 Number of conformers: 1 Conformer: "" Number of residues, atoms: 101, 772 Classifications: {'peptide': 101} Link IDs: {'PTRANS': 3, 'TRANS': 97} Chain: "D" Number of atoms: 772 Number of conformers: 1 Conformer: "" Number of residues, atoms: 101, 772 Classifications: {'peptide': 101} Link IDs: {'PTRANS': 3, 'TRANS': 97} Chain: "E" Number of atoms: 772 Number of conformers: 1 Conformer: "" Number of residues, atoms: 101, 772 Classifications: {'peptide': 101} Link IDs: {'PTRANS': 3, 'TRANS': 97} Chain: "F" Number of atoms: 772 Number of conformers: 1 Conformer: "" Number of residues, atoms: 101, 772 Classifications: {'peptide': 101} Link IDs: {'PTRANS': 3, 'TRANS': 97} Chain: "B" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 28 Unusual residues: {'CLR': 1} Classifications: {'undetermined': 1} Chain: "C" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 28 Unusual residues: {'CLR': 1} Classifications: {'undetermined': 1} Chain: "D" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 28 Unusual residues: {'CLR': 1} Classifications: {'undetermined': 1} Chain: "E" Number of atoms: 56 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 56 Unusual residues: {'CLR': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "F" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 28 Unusual residues: {'CLR': 1} Classifications: {'undetermined': 1} Time building chain proxies: 4.32, per 1000 atoms: 0.90 Number of scatterers: 4800 At special positions: 0 Unit cell: (56.76, 70.62, 94.38, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 12 16.00 O 804 8.00 N 726 7.00 C 3258 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: 1.27 Conformation dependent library (CDL) restraints added in 537.3 milliseconds 1188 Ramachandran restraints generated. 594 Oldfield, 0 Emsley, 594 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1164 Finding SS restraints... Secondary structure from input PDB file: 26 helices and 0 sheets defined 88.1% alpha, 0.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.35 Creating SS restraints... Processing helix chain 'A' and resid 40 through 50 Processing helix chain 'A' and resid 54 through 71 removed outlier: 3.517A pdb=" N GLY A 71 " --> pdb=" O VAL A 67 " (cutoff:3.500A) Processing helix chain 'A' and resid 76 through 103 removed outlier: 4.120A pdb=" N LYS A 103 " --> pdb=" O ILE A 99 " (cutoff:3.500A) Processing helix chain 'A' and resid 103 through 108 removed outlier: 4.005A pdb=" N ASN A 108 " --> pdb=" O TYR A 104 " (cutoff:3.500A) Processing helix chain 'A' and resid 111 through 139 Processing helix chain 'B' and resid 40 through 50 Processing helix chain 'B' and resid 54 through 71 removed outlier: 3.572A pdb=" N GLY B 71 " --> pdb=" O VAL B 67 " (cutoff:3.500A) Processing helix chain 'B' and resid 76 through 107 removed outlier: 4.175A pdb=" N LYS B 103 " --> pdb=" O ILE B 99 " (cutoff:3.500A) removed outlier: 4.213A pdb=" N TYR B 104 " --> pdb=" O PHE B 100 " (cutoff:3.500A) removed outlier: 3.674A pdb=" N ASP B 105 " --> pdb=" O LEU B 101 " (cutoff:3.500A) removed outlier: 3.943A pdb=" N LEU B 106 " --> pdb=" O VAL B 102 " (cutoff:3.500A) Processing helix chain 'B' and resid 111 through 139 Processing helix chain 'C' and resid 40 through 50 removed outlier: 3.506A pdb=" N SER C 50 " --> pdb=" O SER C 46 " (cutoff:3.500A) Processing helix chain 'C' and resid 54 through 71 Processing helix chain 'C' and resid 76 through 102 Processing helix chain 'C' and resid 111 through 139 Processing helix chain 'D' and resid 40 through 50 Processing helix chain 'D' and resid 54 through 71 removed outlier: 3.744A pdb=" N MET D 58 " --> pdb=" O ILE D 54 " (cutoff:3.500A) removed outlier: 3.569A pdb=" N GLY D 71 " --> pdb=" O VAL D 67 " (cutoff:3.500A) Processing helix chain 'D' and resid 76 through 107 removed outlier: 3.512A pdb=" N VAL D 102 " --> pdb=" O LEU D 98 " (cutoff:3.500A) removed outlier: 4.328A pdb=" N LYS D 103 " --> pdb=" O ILE D 99 " (cutoff:3.500A) removed outlier: 4.366A pdb=" N TYR D 104 " --> pdb=" O PHE D 100 " (cutoff:3.500A) removed outlier: 3.753A pdb=" N LEU D 106 " --> pdb=" O VAL D 102 " (cutoff:3.500A) Processing helix chain 'D' and resid 111 through 139 removed outlier: 3.643A pdb=" N PHE D 135 " --> pdb=" O VAL D 131 " (cutoff:3.500A) Processing helix chain 'E' and resid 40 through 50 Processing helix chain 'E' and resid 54 through 71 removed outlier: 3.660A pdb=" N GLY E 71 " --> pdb=" O VAL E 67 " (cutoff:3.500A) Processing helix chain 'E' and resid 76 through 103 removed outlier: 4.151A pdb=" N LYS E 103 " --> pdb=" O ILE E 99 " (cutoff:3.500A) Processing helix chain 'E' and resid 103 through 108 removed outlier: 3.667A pdb=" N ASN E 108 " --> pdb=" O TYR E 104 " (cutoff:3.500A) Processing helix chain 'E' and resid 111 through 139 Processing helix chain 'F' and resid 40 through 50 Processing helix chain 'F' and resid 54 through 71 removed outlier: 3.500A pdb=" N GLY F 71 " --> pdb=" O VAL F 67 " (cutoff:3.500A) Processing helix chain 'F' and resid 76 through 102 Processing helix chain 'F' and resid 111 through 139 410 hydrogen bonds defined for protein. 1230 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 1.27 Time building geometry restraints manager: 1.44 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.35: 1416 1.35 - 1.46: 1057 1.46 - 1.58: 2405 1.58 - 1.70: 0 1.70 - 1.82: 24 Bond restraints: 4902 Sorted by residual: bond pdb=" CB GLU A 69 " pdb=" CG GLU A 69 " ideal model delta sigma weight residual 1.520 1.563 -0.043 3.00e-02 1.11e+03 2.06e+00 bond pdb=" CA PHE C 74 " pdb=" CB PHE C 74 " ideal model delta sigma weight residual 1.528 1.507 0.021 1.58e-02 4.01e+03 1.70e+00 bond pdb=" CD2 HIS F 112 " pdb=" NE2 HIS F 112 " ideal model delta sigma weight residual 1.374 1.360 0.014 1.10e-02 8.26e+03 1.61e+00 bond pdb=" CA HIS F 112 " pdb=" CB HIS F 112 " ideal model delta sigma weight residual 1.528 1.510 0.019 1.59e-02 3.96e+03 1.39e+00 bond pdb=" CG HIS F 112 " pdb=" ND1 HIS F 112 " ideal model delta sigma weight residual 1.378 1.390 -0.012 1.10e-02 8.26e+03 1.28e+00 ... (remaining 4897 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.15: 6596 2.15 - 4.31: 81 4.31 - 6.46: 25 6.46 - 8.61: 3 8.61 - 10.77: 3 Bond angle restraints: 6708 Sorted by residual: angle pdb=" CB MET A 51 " pdb=" CG MET A 51 " pdb=" SD MET A 51 " ideal model delta sigma weight residual 112.70 123.47 -10.77 3.00e+00 1.11e-01 1.29e+01 angle pdb=" CA MET A 58 " pdb=" CB MET A 58 " pdb=" CG MET A 58 " ideal model delta sigma weight residual 114.10 120.87 -6.77 2.00e+00 2.50e-01 1.14e+01 angle pdb=" CA GLU A 69 " pdb=" CB GLU A 69 " pdb=" CG GLU A 69 " ideal model delta sigma weight residual 114.10 120.83 -6.73 2.00e+00 2.50e-01 1.13e+01 angle pdb=" C TYR D 77 " pdb=" N VAL D 78 " pdb=" CA VAL D 78 " ideal model delta sigma weight residual 120.33 122.84 -2.51 8.00e-01 1.56e+00 9.83e+00 angle pdb=" CB GLU A 69 " pdb=" CG GLU A 69 " pdb=" CD GLU A 69 " ideal model delta sigma weight residual 112.60 117.81 -5.21 1.70e+00 3.46e-01 9.41e+00 ... (remaining 6703 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.55: 2792 16.55 - 33.09: 284 33.09 - 49.64: 88 49.64 - 66.19: 27 66.19 - 82.73: 1 Dihedral angle restraints: 3192 sinusoidal: 1410 harmonic: 1782 Sorted by residual: dihedral pdb=" CG LYS B 65 " pdb=" CD LYS B 65 " pdb=" CE LYS B 65 " pdb=" NZ LYS B 65 " ideal model delta sinusoidal sigma weight residual -60.00 -2.88 -57.12 3 1.50e+01 4.44e-03 9.43e+00 dihedral pdb=" CG LYS B 103 " pdb=" CD LYS B 103 " pdb=" CE LYS B 103 " pdb=" NZ LYS B 103 " ideal model delta sinusoidal sigma weight residual 180.00 122.94 57.06 3 1.50e+01 4.44e-03 9.43e+00 dihedral pdb=" N MET E 51 " pdb=" CA MET E 51 " pdb=" CB MET E 51 " pdb=" CG MET E 51 " ideal model delta sinusoidal sigma weight residual -180.00 -123.30 -56.70 3 1.50e+01 4.44e-03 9.41e+00 ... (remaining 3189 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.021: 454 0.021 - 0.042: 244 0.042 - 0.063: 109 0.063 - 0.084: 45 0.084 - 0.104: 18 Chirality restraints: 870 Sorted by residual: chirality pdb=" CB VAL A 67 " pdb=" CA VAL A 67 " pdb=" CG1 VAL A 67 " pdb=" CG2 VAL A 67 " both_signs ideal model delta sigma weight residual False -2.63 -2.52 -0.10 2.00e-01 2.50e+01 2.73e-01 chirality pdb=" CA PRO F 79 " pdb=" N PRO F 79 " pdb=" C PRO F 79 " pdb=" CB PRO F 79 " both_signs ideal model delta sigma weight residual False 2.72 2.62 0.10 2.00e-01 2.50e+01 2.48e-01 chirality pdb=" CA PRO C 79 " pdb=" N PRO C 79 " pdb=" C PRO C 79 " pdb=" CB PRO C 79 " both_signs ideal model delta sigma weight residual False 2.72 2.62 0.10 2.00e-01 2.50e+01 2.42e-01 ... (remaining 867 not shown) Planarity restraints: 780 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB PHE A 127 " -0.013 2.00e-02 2.50e+03 1.72e-02 5.18e+00 pdb=" CG PHE A 127 " 0.039 2.00e-02 2.50e+03 pdb=" CD1 PHE A 127 " -0.011 2.00e-02 2.50e+03 pdb=" CD2 PHE A 127 " -0.015 2.00e-02 2.50e+03 pdb=" CE1 PHE A 127 " -0.002 2.00e-02 2.50e+03 pdb=" CE2 PHE A 127 " 0.002 2.00e-02 2.50e+03 pdb=" CZ PHE A 127 " -0.000 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CG GLU A 69 " -0.010 2.00e-02 2.50e+03 2.12e-02 4.50e+00 pdb=" CD GLU A 69 " 0.037 2.00e-02 2.50e+03 pdb=" OE1 GLU A 69 " -0.013 2.00e-02 2.50e+03 pdb=" OE2 GLU A 69 " -0.013 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB ASP F 53 " -0.006 2.00e-02 2.50e+03 1.29e-02 1.66e+00 pdb=" CG ASP F 53 " 0.022 2.00e-02 2.50e+03 pdb=" OD1 ASP F 53 " -0.008 2.00e-02 2.50e+03 pdb=" OD2 ASP F 53 " -0.008 2.00e-02 2.50e+03 ... (remaining 777 not shown) Histogram of nonbonded interaction distances: 2.19 - 2.73: 184 2.73 - 3.27: 5207 3.27 - 3.81: 7791 3.81 - 4.36: 8925 4.36 - 4.90: 15072 Nonbonded interactions: 37179 Sorted by model distance: nonbonded pdb=" O MET D 58 " pdb=" OG SER D 62 " model vdw 2.185 3.040 nonbonded pdb=" OH TYR F 104 " pdb=" O1 CLR F 201 " model vdw 2.196 3.040 nonbonded pdb=" O MET E 58 " pdb=" OG SER E 62 " model vdw 2.225 3.040 nonbonded pdb=" OD1 ASN D 120 " pdb=" NZ LYS E 103 " model vdw 2.351 3.120 nonbonded pdb=" O MET F 58 " pdb=" OG SER F 62 " model vdw 2.414 3.040 ... (remaining 37174 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' selection = (chain 'B' and resid 39 through 139) selection = (chain 'C' and resid 39 through 139) selection = (chain 'D' and resid 39 through 139) selection = (chain 'E' and resid 39 through 139) selection = (chain 'F' and resid 39 through 139) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 3.360 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: 0.200 Check model and map are aligned: 0.030 Set scattering table: 0.050 Process input model: 16.160 Find NCS groups from input model: 0.240 Set up NCS constraints: 0.020 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:13.030 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 33.100 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7660 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 0.043 4902 Z= 0.203 Angle : 0.652 10.766 6708 Z= 0.325 Chirality : 0.033 0.104 870 Planarity : 0.002 0.022 780 Dihedral : 15.140 82.732 2028 Min Nonbonded Distance : 2.185 Molprobity Statistics. All-atom Clashscore : 8.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.34 % Favored : 99.66 % Rotamer: Outliers : 0.98 % Allowed : 20.98 % Favored : 78.04 % 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: 2.12 (0.35), residues: 594 helix: 1.96 (0.23), residues: 492 sheet: None (None), residues: 0 loop : -1.39 (0.67), residues: 102 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.001 0.000 HIS B 112 PHE 0.039 0.001 PHE A 127 TYR 0.009 0.001 TYR B 77 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1188 Ramachandran restraints generated. 594 Oldfield, 0 Emsley, 594 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1188 Ramachandran restraints generated. 594 Oldfield, 0 Emsley, 594 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 92 residues out of total 510 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 87 time to evaluate : 0.492 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: D 44 LYS cc_start: 0.6964 (mmtt) cc_final: 0.5977 (tmtt) outliers start: 5 outliers final: 5 residues processed: 90 average time/residue: 0.7875 time to fit residues: 75.2795 Evaluate side-chains 89 residues out of total 510 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 84 time to evaluate : 0.533 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 136 ILE Chi-restraints excluded: chain C residue 102 VAL Chi-restraints excluded: chain C residue 128 ILE Chi-restraints excluded: chain F residue 52 LEU Chi-restraints excluded: chain F residue 54 ILE Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 60 random chunks: chunk 50 optimal weight: 0.5980 chunk 45 optimal weight: 0.6980 chunk 25 optimal weight: 1.9990 chunk 15 optimal weight: 0.6980 chunk 30 optimal weight: 10.0000 chunk 24 optimal weight: 0.8980 chunk 47 optimal weight: 0.4980 chunk 18 optimal weight: 0.8980 chunk 28 optimal weight: 0.5980 chunk 35 optimal weight: 0.6980 chunk 54 optimal weight: 0.3980 overall best weight: 0.5580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 63 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 120 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 133 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 63 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7649 moved from start: 0.1492 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 4902 Z= 0.189 Angle : 0.550 6.863 6708 Z= 0.278 Chirality : 0.036 0.136 870 Planarity : 0.003 0.017 780 Dihedral : 9.507 50.538 1017 Min Nonbonded Distance : 2.630 Molprobity Statistics. All-atom Clashscore : 8.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.34 % Favored : 99.66 % Rotamer: Outliers : 1.57 % Allowed : 19.80 % Favored : 78.63 % 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: 3.17 (0.35), residues: 594 helix: 2.62 (0.23), residues: 504 sheet: None (None), residues: 0 loop : -1.13 (0.76), residues: 90 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.001 0.000 HIS B 112 PHE 0.019 0.001 PHE F 127 TYR 0.011 0.001 TYR D 41 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1188 Ramachandran restraints generated. 594 Oldfield, 0 Emsley, 594 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1188 Ramachandran restraints generated. 594 Oldfield, 0 Emsley, 594 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 106 residues out of total 510 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 98 time to evaluate : 0.525 Fit side-chains REVERT: A 58 MET cc_start: 0.8023 (mpt) cc_final: 0.7729 (mpt) REVERT: A 104 TYR cc_start: 0.8025 (OUTLIER) cc_final: 0.6322 (t80) REVERT: B 58 MET cc_start: 0.7291 (mtp) cc_final: 0.7030 (mtm) REVERT: D 44 LYS cc_start: 0.7064 (mmtt) cc_final: 0.6088 (tmtt) outliers start: 8 outliers final: 4 residues processed: 101 average time/residue: 0.6849 time to fit residues: 73.8877 Evaluate side-chains 93 residues out of total 510 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 88 time to evaluate : 0.520 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 97 LEU Chi-restraints excluded: chain A residue 104 TYR Chi-restraints excluded: chain B residue 88 LEU Chi-restraints excluded: chain B residue 115 LEU Chi-restraints excluded: chain D residue 102 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 60 random chunks: chunk 30 optimal weight: 10.0000 chunk 16 optimal weight: 3.9990 chunk 45 optimal weight: 0.7980 chunk 37 optimal weight: 1.9990 chunk 15 optimal weight: 0.6980 chunk 54 optimal weight: 1.9990 chunk 58 optimal weight: 3.9990 chunk 48 optimal weight: 2.9990 chunk 18 optimal weight: 1.9990 chunk 43 optimal weight: 4.9990 chunk 53 optimal weight: 4.9990 overall best weight: 1.4986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 63 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 120 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 63 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 60 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 63 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7721 moved from start: 0.1989 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 4902 Z= 0.278 Angle : 0.595 6.982 6708 Z= 0.293 Chirality : 0.039 0.125 870 Planarity : 0.003 0.013 780 Dihedral : 9.618 52.228 1008 Min Nonbonded Distance : 2.618 Molprobity Statistics. All-atom Clashscore : 8.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.17 % Favored : 99.83 % Rotamer: Outliers : 2.75 % Allowed : 21.18 % Favored : 76.08 % 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: 2.86 (0.35), residues: 594 helix: 2.38 (0.22), residues: 498 sheet: None (None), residues: 0 loop : -0.80 (0.73), residues: 96 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.001 0.000 HIS F 112 PHE 0.017 0.002 PHE C 127 TYR 0.012 0.001 TYR B 77 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1188 Ramachandran restraints generated. 594 Oldfield, 0 Emsley, 594 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1188 Ramachandran restraints generated. 594 Oldfield, 0 Emsley, 594 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 107 residues out of total 510 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 93 time to evaluate : 0.561 Fit side-chains revert: symmetry clash REVERT: A 54 ILE cc_start: 0.7995 (mp) cc_final: 0.7291 (mp) REVERT: A 58 MET cc_start: 0.7959 (mpt) cc_final: 0.7357 (mpt) REVERT: A 104 TYR cc_start: 0.8024 (OUTLIER) cc_final: 0.6382 (t80) REVERT: B 58 MET cc_start: 0.7424 (mtp) cc_final: 0.7147 (mtm) REVERT: D 44 LYS cc_start: 0.7082 (mmtt) cc_final: 0.5886 (tmtt) REVERT: D 101 LEU cc_start: 0.7858 (OUTLIER) cc_final: 0.7526 (tt) REVERT: F 62 SER cc_start: 0.8306 (m) cc_final: 0.8084 (p) outliers start: 14 outliers final: 7 residues processed: 100 average time/residue: 0.7333 time to fit residues: 77.9324 Evaluate side-chains 95 residues out of total 510 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 86 time to evaluate : 0.514 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 97 LEU Chi-restraints excluded: chain A residue 104 TYR Chi-restraints excluded: chain B residue 88 LEU Chi-restraints excluded: chain B residue 102 VAL Chi-restraints excluded: chain B residue 115 LEU Chi-restraints excluded: chain D residue 99 ILE Chi-restraints excluded: chain D residue 101 LEU Chi-restraints excluded: chain D residue 102 VAL Chi-restraints excluded: chain E residue 73 SER Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 60 random chunks: chunk 41 optimal weight: 3.9990 chunk 28 optimal weight: 0.8980 chunk 6 optimal weight: 4.9990 chunk 26 optimal weight: 0.2980 chunk 36 optimal weight: 2.9990 chunk 54 optimal weight: 0.7980 chunk 57 optimal weight: 3.9990 chunk 51 optimal weight: 0.6980 chunk 15 optimal weight: 0.8980 chunk 48 optimal weight: 0.6980 chunk 32 optimal weight: 2.9990 overall best weight: 0.6780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 63 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 120 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 119 ASN ** B 133 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 63 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 60 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 63 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7676 moved from start: 0.2176 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 4902 Z= 0.182 Angle : 0.535 7.212 6708 Z= 0.264 Chirality : 0.036 0.132 870 Planarity : 0.002 0.015 780 Dihedral : 9.311 50.592 1008 Min Nonbonded Distance : 2.611 Molprobity Statistics. All-atom Clashscore : 9.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.84 % Favored : 99.16 % Rotamer: Outliers : 2.55 % Allowed : 22.16 % Favored : 75.29 % 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: 3.31 (0.36), residues: 594 helix: 2.68 (0.23), residues: 504 sheet: None (None), residues: 0 loop : -0.84 (0.79), residues: 90 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.001 0.000 HIS F 112 PHE 0.026 0.002 PHE F 127 TYR 0.007 0.001 TYR B 77 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1188 Ramachandran restraints generated. 594 Oldfield, 0 Emsley, 594 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1188 Ramachandran restraints generated. 594 Oldfield, 0 Emsley, 594 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 109 residues out of total 510 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 96 time to evaluate : 0.599 Fit side-chains revert: symmetry clash REVERT: A 54 ILE cc_start: 0.8015 (mp) cc_final: 0.7241 (mp) REVERT: A 58 MET cc_start: 0.7809 (mpt) cc_final: 0.7328 (mpt) REVERT: A 104 TYR cc_start: 0.7991 (OUTLIER) cc_final: 0.6373 (t80) REVERT: B 58 MET cc_start: 0.7474 (mtp) cc_final: 0.7160 (mtm) REVERT: D 44 LYS cc_start: 0.7070 (mmtt) cc_final: 0.5877 (tmtt) REVERT: D 88 LEU cc_start: 0.8378 (OUTLIER) cc_final: 0.7691 (mt) REVERT: D 101 LEU cc_start: 0.7863 (OUTLIER) cc_final: 0.7526 (tt) REVERT: E 88 LEU cc_start: 0.8322 (OUTLIER) cc_final: 0.8010 (tm) outliers start: 13 outliers final: 4 residues processed: 103 average time/residue: 0.7271 time to fit residues: 80.3283 Evaluate side-chains 97 residues out of total 510 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 89 time to evaluate : 0.680 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 51 MET Chi-restraints excluded: chain A residue 97 LEU Chi-restraints excluded: chain A residue 104 TYR Chi-restraints excluded: chain B residue 88 LEU Chi-restraints excluded: chain D residue 88 LEU Chi-restraints excluded: chain D residue 101 LEU Chi-restraints excluded: chain D residue 102 VAL Chi-restraints excluded: chain E residue 88 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 60 random chunks: chunk 0 optimal weight: 6.9990 chunk 43 optimal weight: 5.9990 chunk 23 optimal weight: 6.9990 chunk 49 optimal weight: 1.9990 chunk 40 optimal weight: 0.9980 chunk 29 optimal weight: 0.6980 chunk 52 optimal weight: 0.9990 chunk 14 optimal weight: 0.5980 chunk 19 optimal weight: 0.7980 chunk 11 optimal weight: 0.9980 chunk 34 optimal weight: 0.7980 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 63 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 120 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 63 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 120 ASN E 60 ASN E 63 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7684 moved from start: 0.2338 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 4902 Z= 0.190 Angle : 0.537 7.089 6708 Z= 0.265 Chirality : 0.036 0.138 870 Planarity : 0.002 0.014 780 Dihedral : 9.242 50.127 1008 Min Nonbonded Distance : 2.615 Molprobity Statistics. All-atom Clashscore : 8.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.17 % Favored : 99.83 % Rotamer: Outliers : 2.35 % Allowed : 21.96 % Favored : 75.69 % 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: 3.32 (0.36), residues: 594 helix: 2.67 (0.23), residues: 504 sheet: None (None), residues: 0 loop : -0.74 (0.81), residues: 90 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.001 0.000 HIS F 112 PHE 0.019 0.002 PHE D 74 TYR 0.007 0.001 TYR A 77 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1188 Ramachandran restraints generated. 594 Oldfield, 0 Emsley, 594 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1188 Ramachandran restraints generated. 594 Oldfield, 0 Emsley, 594 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 108 residues out of total 510 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 96 time to evaluate : 0.522 Fit side-chains revert: symmetry clash REVERT: A 54 ILE cc_start: 0.8018 (mp) cc_final: 0.7195 (mp) REVERT: A 58 MET cc_start: 0.7840 (OUTLIER) cc_final: 0.7370 (mpt) REVERT: A 104 TYR cc_start: 0.7983 (OUTLIER) cc_final: 0.6373 (t80) REVERT: B 58 MET cc_start: 0.7466 (mtp) cc_final: 0.7242 (mtp) REVERT: D 44 LYS cc_start: 0.7072 (mmtt) cc_final: 0.5836 (tmtt) REVERT: D 88 LEU cc_start: 0.8406 (OUTLIER) cc_final: 0.7716 (mt) REVERT: D 101 LEU cc_start: 0.7876 (OUTLIER) cc_final: 0.7626 (tt) REVERT: E 88 LEU cc_start: 0.8319 (OUTLIER) cc_final: 0.8024 (tm) outliers start: 12 outliers final: 4 residues processed: 101 average time/residue: 0.7654 time to fit residues: 82.0086 Evaluate side-chains 96 residues out of total 510 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 87 time to evaluate : 0.629 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 51 MET Chi-restraints excluded: chain A residue 58 MET Chi-restraints excluded: chain A residue 97 LEU Chi-restraints excluded: chain A residue 104 TYR Chi-restraints excluded: chain B residue 88 LEU Chi-restraints excluded: chain D residue 88 LEU Chi-restraints excluded: chain D residue 101 LEU Chi-restraints excluded: chain D residue 102 VAL Chi-restraints excluded: chain E residue 88 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 60 random chunks: chunk 14 optimal weight: 1.9990 chunk 58 optimal weight: 2.9990 chunk 48 optimal weight: 2.9990 chunk 26 optimal weight: 3.9990 chunk 4 optimal weight: 0.9990 chunk 19 optimal weight: 2.9990 chunk 30 optimal weight: 10.0000 chunk 55 optimal weight: 0.6980 chunk 6 optimal weight: 0.0020 chunk 33 optimal weight: 2.9990 chunk 42 optimal weight: 5.9990 overall best weight: 1.3394 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 63 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 120 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 63 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7719 moved from start: 0.2487 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 4902 Z= 0.253 Angle : 0.598 9.284 6708 Z= 0.291 Chirality : 0.038 0.155 870 Planarity : 0.002 0.015 780 Dihedral : 9.412 50.658 1008 Min Nonbonded Distance : 2.594 Molprobity Statistics. All-atom Clashscore : 9.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.34 % Favored : 99.66 % Rotamer: Outliers : 2.16 % Allowed : 23.73 % Favored : 74.12 % 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: 3.09 (0.36), residues: 594 helix: 2.49 (0.23), residues: 504 sheet: None (None), residues: 0 loop : -0.69 (0.82), residues: 90 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.001 0.000 HIS B 112 PHE 0.031 0.002 PHE A 127 TYR 0.007 0.001 TYR E 104 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1188 Ramachandran restraints generated. 594 Oldfield, 0 Emsley, 594 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1188 Ramachandran restraints generated. 594 Oldfield, 0 Emsley, 594 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 106 residues out of total 510 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 95 time to evaluate : 0.508 Fit side-chains REVERT: A 54 ILE cc_start: 0.8059 (mp) cc_final: 0.7273 (mp) REVERT: A 58 MET cc_start: 0.7827 (OUTLIER) cc_final: 0.7382 (mpt) REVERT: B 58 MET cc_start: 0.7493 (mtp) cc_final: 0.7254 (mtp) REVERT: C 70 GLN cc_start: 0.8454 (tp-100) cc_final: 0.8163 (tp-100) REVERT: D 44 LYS cc_start: 0.7164 (mmtt) cc_final: 0.5815 (tmtt) REVERT: D 101 LEU cc_start: 0.7937 (OUTLIER) cc_final: 0.7597 (tt) outliers start: 11 outliers final: 4 residues processed: 99 average time/residue: 0.7551 time to fit residues: 79.4138 Evaluate side-chains 93 residues out of total 510 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 87 time to evaluate : 0.559 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 58 MET Chi-restraints excluded: chain A residue 97 LEU Chi-restraints excluded: chain B residue 88 LEU Chi-restraints excluded: chain B residue 102 VAL Chi-restraints excluded: chain D residue 101 LEU Chi-restraints excluded: chain D residue 102 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 60 random chunks: chunk 32 optimal weight: 2.9990 chunk 48 optimal weight: 2.9990 chunk 57 optimal weight: 0.9990 chunk 36 optimal weight: 0.3980 chunk 35 optimal weight: 2.9990 chunk 26 optimal weight: 3.9990 chunk 23 optimal weight: 4.9990 chunk 34 optimal weight: 0.9990 chunk 17 optimal weight: 0.1980 chunk 11 optimal weight: 3.9990 chunk 39 optimal weight: 0.8980 overall best weight: 0.6984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 63 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 63 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7684 moved from start: 0.2597 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 4902 Z= 0.184 Angle : 0.571 8.748 6708 Z= 0.280 Chirality : 0.037 0.183 870 Planarity : 0.002 0.018 780 Dihedral : 9.232 49.387 1008 Min Nonbonded Distance : 2.602 Molprobity Statistics. All-atom Clashscore : 8.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.51 % Favored : 99.49 % Rotamer: Outliers : 1.76 % Allowed : 25.88 % Favored : 72.35 % 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: 3.38 (0.36), residues: 594 helix: 2.70 (0.23), residues: 504 sheet: None (None), residues: 0 loop : -0.64 (0.82), residues: 90 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.001 0.000 HIS E 40 PHE 0.025 0.002 PHE C 127 TYR 0.005 0.001 TYR A 77 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1188 Ramachandran restraints generated. 594 Oldfield, 0 Emsley, 594 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1188 Ramachandran restraints generated. 594 Oldfield, 0 Emsley, 594 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 101 residues out of total 510 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 92 time to evaluate : 0.514 Fit side-chains revert: symmetry clash REVERT: A 54 ILE cc_start: 0.8066 (mp) cc_final: 0.7395 (mp) REVERT: A 58 MET cc_start: 0.7769 (OUTLIER) cc_final: 0.7444 (mpt) REVERT: A 104 TYR cc_start: 0.7946 (OUTLIER) cc_final: 0.6274 (t80) REVERT: A 127 PHE cc_start: 0.8073 (t80) cc_final: 0.7868 (t80) REVERT: B 58 MET cc_start: 0.7490 (mtp) cc_final: 0.7242 (mtp) REVERT: C 70 GLN cc_start: 0.8482 (tp-100) cc_final: 0.8178 (tp-100) REVERT: D 44 LYS cc_start: 0.7126 (mmtt) cc_final: 0.5799 (tmtt) REVERT: D 88 LEU cc_start: 0.8389 (OUTLIER) cc_final: 0.7706 (mt) REVERT: D 101 LEU cc_start: 0.7925 (OUTLIER) cc_final: 0.7501 (tt) outliers start: 9 outliers final: 3 residues processed: 94 average time/residue: 0.7091 time to fit residues: 70.9937 Evaluate side-chains 96 residues out of total 510 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 89 time to evaluate : 0.531 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 58 MET Chi-restraints excluded: chain A residue 97 LEU Chi-restraints excluded: chain A residue 104 TYR Chi-restraints excluded: chain B residue 88 LEU Chi-restraints excluded: chain D residue 88 LEU Chi-restraints excluded: chain D residue 101 LEU Chi-restraints excluded: chain D residue 102 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 60 random chunks: chunk 28 optimal weight: 3.9990 chunk 5 optimal weight: 4.9990 chunk 45 optimal weight: 2.9990 chunk 52 optimal weight: 0.6980 chunk 55 optimal weight: 0.7980 chunk 50 optimal weight: 2.9990 chunk 53 optimal weight: 5.9990 chunk 32 optimal weight: 2.9990 chunk 23 optimal weight: 0.9990 chunk 42 optimal weight: 5.9990 chunk 16 optimal weight: 0.9990 overall best weight: 1.2986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 63 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 120 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 63 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7721 moved from start: 0.2636 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 4902 Z= 0.254 Angle : 0.622 8.980 6708 Z= 0.304 Chirality : 0.039 0.173 870 Planarity : 0.002 0.018 780 Dihedral : 9.388 50.518 1008 Min Nonbonded Distance : 2.593 Molprobity Statistics. All-atom Clashscore : 9.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.17 % Favored : 99.83 % Rotamer: Outliers : 1.96 % Allowed : 26.27 % Favored : 71.76 % 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: 3.09 (0.35), residues: 594 helix: 2.50 (0.23), residues: 498 sheet: None (None), residues: 0 loop : -0.50 (0.75), residues: 96 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.001 0.000 HIS B 112 PHE 0.028 0.002 PHE F 127 TYR 0.008 0.001 TYR B 77 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1188 Ramachandran restraints generated. 594 Oldfield, 0 Emsley, 594 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1188 Ramachandran restraints generated. 594 Oldfield, 0 Emsley, 594 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 97 residues out of total 510 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 87 time to evaluate : 0.557 Fit side-chains revert: symmetry clash REVERT: A 54 ILE cc_start: 0.8056 (mp) cc_final: 0.7354 (mp) REVERT: A 58 MET cc_start: 0.7792 (OUTLIER) cc_final: 0.7389 (mpt) REVERT: A 104 TYR cc_start: 0.7950 (OUTLIER) cc_final: 0.6402 (t80) REVERT: B 58 MET cc_start: 0.7491 (mtp) cc_final: 0.7234 (mtp) REVERT: C 70 GLN cc_start: 0.8461 (tp-100) cc_final: 0.8142 (tp-100) REVERT: D 53 ASP cc_start: 0.7740 (p0) cc_final: 0.7318 (t0) REVERT: D 88 LEU cc_start: 0.8437 (OUTLIER) cc_final: 0.7736 (mt) REVERT: D 101 LEU cc_start: 0.7907 (OUTLIER) cc_final: 0.7491 (tt) outliers start: 10 outliers final: 4 residues processed: 92 average time/residue: 0.7326 time to fit residues: 72.1190 Evaluate side-chains 93 residues out of total 510 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 85 time to evaluate : 0.528 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 58 MET Chi-restraints excluded: chain A residue 97 LEU Chi-restraints excluded: chain A residue 104 TYR Chi-restraints excluded: chain B residue 88 LEU Chi-restraints excluded: chain B residue 115 LEU Chi-restraints excluded: chain D residue 88 LEU Chi-restraints excluded: chain D residue 101 LEU Chi-restraints excluded: chain D residue 102 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 60 random chunks: chunk 48 optimal weight: 2.9990 chunk 50 optimal weight: 3.9990 chunk 53 optimal weight: 4.9990 chunk 35 optimal weight: 3.9990 chunk 56 optimal weight: 0.5980 chunk 34 optimal weight: 0.8980 chunk 27 optimal weight: 0.0030 chunk 39 optimal weight: 0.9990 chunk 59 optimal weight: 0.9980 chunk 55 optimal weight: 0.9980 chunk 47 optimal weight: 3.9990 overall best weight: 0.6990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 63 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 120 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 63 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 133 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7691 moved from start: 0.2699 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 4902 Z= 0.190 Angle : 0.590 9.864 6708 Z= 0.290 Chirality : 0.037 0.190 870 Planarity : 0.002 0.019 780 Dihedral : 9.218 49.376 1008 Min Nonbonded Distance : 2.590 Molprobity Statistics. All-atom Clashscore : 9.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.67 % Favored : 99.33 % Rotamer: Outliers : 1.96 % Allowed : 26.86 % Favored : 71.18 % 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: 3.30 (0.35), residues: 594 helix: 2.66 (0.23), residues: 498 sheet: None (None), residues: 0 loop : -0.52 (0.75), residues: 96 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.001 0.000 HIS B 112 PHE 0.029 0.002 PHE A 127 TYR 0.008 0.001 TYR B 77 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1188 Ramachandran restraints generated. 594 Oldfield, 0 Emsley, 594 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1188 Ramachandran restraints generated. 594 Oldfield, 0 Emsley, 594 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 104 residues out of total 510 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 94 time to evaluate : 0.549 Fit side-chains revert: symmetry clash REVERT: A 104 TYR cc_start: 0.7956 (OUTLIER) cc_final: 0.6411 (t80) REVERT: B 58 MET cc_start: 0.7500 (mtp) cc_final: 0.7250 (mtp) REVERT: C 70 GLN cc_start: 0.8458 (tp-100) cc_final: 0.8143 (tp-100) REVERT: D 88 LEU cc_start: 0.8414 (OUTLIER) cc_final: 0.7724 (mt) REVERT: D 101 LEU cc_start: 0.7890 (OUTLIER) cc_final: 0.7475 (tt) outliers start: 10 outliers final: 4 residues processed: 97 average time/residue: 0.8469 time to fit residues: 86.9458 Evaluate side-chains 93 residues out of total 510 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 86 time to evaluate : 0.573 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 97 LEU Chi-restraints excluded: chain A residue 104 TYR Chi-restraints excluded: chain B residue 88 LEU Chi-restraints excluded: chain B residue 115 LEU Chi-restraints excluded: chain D residue 88 LEU Chi-restraints excluded: chain D residue 101 LEU Chi-restraints excluded: chain D residue 102 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 60 random chunks: chunk 4 optimal weight: 0.7980 chunk 36 optimal weight: 4.9990 chunk 29 optimal weight: 1.9990 chunk 37 optimal weight: 1.9990 chunk 50 optimal weight: 0.8980 chunk 14 optimal weight: 0.6980 chunk 43 optimal weight: 1.9990 chunk 7 optimal weight: 0.8980 chunk 13 optimal weight: 1.9990 chunk 47 optimal weight: 4.9990 chunk 19 optimal weight: 1.9990 overall best weight: 1.0582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 63 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 120 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 63 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7705 moved from start: 0.2749 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 4902 Z= 0.229 Angle : 0.621 9.390 6708 Z= 0.309 Chirality : 0.038 0.196 870 Planarity : 0.003 0.021 780 Dihedral : 9.268 49.552 1008 Min Nonbonded Distance : 2.585 Molprobity Statistics. All-atom Clashscore : 9.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.51 % Favored : 99.49 % Rotamer: Outliers : 1.76 % Allowed : 27.06 % Favored : 71.18 % 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: 3.14 (0.35), residues: 594 helix: 2.53 (0.23), residues: 498 sheet: None (None), residues: 0 loop : -0.48 (0.75), residues: 96 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.001 0.000 HIS B 112 PHE 0.035 0.002 PHE A 127 TYR 0.009 0.001 TYR B 77 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1188 Ramachandran restraints generated. 594 Oldfield, 0 Emsley, 594 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1188 Ramachandran restraints generated. 594 Oldfield, 0 Emsley, 594 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 95 residues out of total 510 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 86 time to evaluate : 0.541 Fit side-chains revert: symmetry clash REVERT: A 54 ILE cc_start: 0.7793 (mp) cc_final: 0.7249 (mp) REVERT: A 104 TYR cc_start: 0.7966 (OUTLIER) cc_final: 0.6423 (t80) REVERT: B 58 MET cc_start: 0.7497 (mtp) cc_final: 0.7239 (mtp) REVERT: C 70 GLN cc_start: 0.8474 (tp-100) cc_final: 0.8083 (tp-100) REVERT: D 53 ASP cc_start: 0.7759 (p0) cc_final: 0.7289 (t0) REVERT: D 101 LEU cc_start: 0.7902 (OUTLIER) cc_final: 0.7492 (tt) outliers start: 9 outliers final: 3 residues processed: 89 average time/residue: 0.7186 time to fit residues: 68.4026 Evaluate side-chains 89 residues out of total 510 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 84 time to evaluate : 0.992 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 97 LEU Chi-restraints excluded: chain A residue 104 TYR Chi-restraints excluded: chain B residue 88 LEU Chi-restraints excluded: chain B residue 115 LEU Chi-restraints excluded: chain D residue 101 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 60 random chunks: chunk 48 optimal weight: 2.9990 chunk 6 optimal weight: 0.0030 chunk 8 optimal weight: 2.9990 chunk 41 optimal weight: 5.9990 chunk 2 optimal weight: 0.7980 chunk 34 optimal weight: 0.7980 chunk 54 optimal weight: 0.8980 chunk 32 optimal weight: 0.9980 chunk 40 optimal weight: 0.9990 chunk 1 optimal weight: 6.9990 chunk 38 optimal weight: 0.6980 overall best weight: 0.6390 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 63 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 120 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 63 GLN ** 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 = 0.4533 r_free = 0.4533 target = 0.185824 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.4206 r_free = 0.4206 target = 0.155388 restraints weight = 6465.953| |-----------------------------------------------------------------------------| r_work (start): 0.4215 rms_B_bonded: 2.44 r_work: 0.4108 rms_B_bonded: 3.55 restraints_weight: 0.5000 r_work (final): 0.4108 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7612 moved from start: 0.2750 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 4902 Z= 0.195 Angle : 0.640 12.125 6708 Z= 0.313 Chirality : 0.038 0.198 870 Planarity : 0.002 0.020 780 Dihedral : 9.161 48.668 1008 Min Nonbonded Distance : 2.586 Molprobity Statistics. All-atom Clashscore : 9.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.84 % Favored : 99.16 % Rotamer: Outliers : 1.37 % Allowed : 27.25 % Favored : 71.37 % 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: 3.24 (0.35), residues: 594 helix: 2.61 (0.23), residues: 498 sheet: None (None), residues: 0 loop : -0.50 (0.75), residues: 96 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.001 0.000 HIS B 112 PHE 0.016 0.002 PHE D 74 TYR 0.008 0.001 TYR B 77 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1989.53 seconds wall clock time: 37 minutes 2.22 seconds (2222.22 seconds total)