Starting phenix.real_space_refine on Mon Jun 24 17:33:58 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8r9x_19015/06_2024/8r9x_19015.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8r9x_19015/06_2024/8r9x_19015.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.1 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8r9x_19015/06_2024/8r9x_19015.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8r9x_19015/06_2024/8r9x_19015.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8r9x_19015/06_2024/8r9x_19015.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8r9x_19015/06_2024/8r9x_19015.pdb" } resolution = 3.1 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= 0.015 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 18 5.16 5 C 2381 2.51 5 N 612 2.21 5 O 771 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped None Time to flip residues: 0.01s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5370/modules/chem_data/mon_lib" Total number of atoms: 3782 Number of models: 1 Model: "" Number of chains: 8 Chain: "A" Number of atoms: 1844 Number of conformers: 1 Conformer: "" Number of residues, atoms: 235, 1844 Classifications: {'peptide': 235} Link IDs: {'PTRANS': 9, 'TRANS': 225} Chain: "H" Number of atoms: 929 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 121, 920 Classifications: {'peptide': 121} Link IDs: {'PTRANS': 3, 'TRANS': 117} Conformer: "B" Number of residues, atoms: 121, 920 Classifications: {'peptide': 121} Link IDs: {'PTRANS': 3, 'TRANS': 117} bond proxies already assigned to first conformer: 930 Chain: "L" Number of atoms: 812 Number of conformers: 1 Conformer: "" Number of residues, atoms: 105, 812 Classifications: {'peptide': 105} Link IDs: {'PTRANS': 5, 'TRANS': 99} Chain: "B" Number of atoms: 38 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 38 Unusual residues: {'FUC': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "C" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "D" Number of atoms: 61 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 61 Unusual residues: {'BMA': 1, 'MAN': 2, 'NAG': 2} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 15 Unresolved non-hydrogen chiralities: 5 Chain: "E" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "A" Number of atoms: 42 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 42 Unusual residues: {'NAG': 3} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Time building chain proxies: 3.73, per 1000 atoms: 0.99 Number of scatterers: 3782 At special positions: 0 Unit cell: (97.09, 68.474, 70.518, 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 18 16.00 O 771 8.00 N 612 7.00 C 2381 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=5, symmetry=0 Simple disulfide: pdb=" SG CYS A 93 " - pdb=" SG CYS A 116 " distance=2.03 Simple disulfide: pdb=" SG CYS A 157 " - pdb=" SG CYS A 181 " distance=2.03 Simple disulfide: pdb=" SG CYS A 260 " - pdb=" SG CYS A 270 " distance=2.03 Simple disulfide: pdb=" SG CYS H 22 " - pdb=" SG CYS H 96 " distance=2.03 Simple disulfide: pdb=" SG CYS L 23 " - pdb=" SG CYS L 88 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Links applied ALPHA1-3 " BMA D 3 " - " MAN D 4 " ALPHA1-6 " BMA D 3 " - " MAN D 5 " BETA1-4 " NAG B 1 " - " NAG B 2 " " NAG C 1 " - " NAG C 2 " " NAG D 1 " - " NAG D 2 " " NAG D 2 " - " BMA D 3 " " NAG E 1 " - " NAG E 2 " BETA1-6 " NAG B 1 " - " FUC B 3 " ~> Even though FUC is an alpha isomer, a beta linkage is required... NAG-ASN " NAG A1101 " - " ASN A 162 " " NAG A1102 " - " ASN A 169 " " NAG A1103 " - " ASN A 251 " " NAG B 1 " - " ASN A 99 " " NAG C 1 " - " ASN A 184 " " NAG D 1 " - " ASN A 241 " " NAG E 1 " - " ASN A 74 " Time building additional restraints: 2.03 Conformation dependent library (CDL) restraints added in 818.5 milliseconds 912 Ramachandran restraints generated. 456 Oldfield, 0 Emsley, 456 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 854 Finding SS restraints... Secondary structure from input PDB file: 6 helices and 9 sheets defined 8.9% alpha, 36.7% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.48 Creating SS restraints... Processing helix chain 'A' and resid 65 through 69 removed outlier: 3.790A pdb=" N LEU A 68 " --> pdb=" O ASN A 65 " (cutoff:3.500A) Processing helix chain 'A' and resid 117 through 124 removed outlier: 3.650A pdb=" N MET A 120 " --> pdb=" O GLY A 117 " (cutoff:3.500A) removed outlier: 3.944A pdb=" N VAL A 121 " --> pdb=" O GLY A 118 " (cutoff:3.500A) removed outlier: 3.686A pdb=" N LYS A 122 " --> pdb=" O ALA A 119 " (cutoff:3.500A) Processing helix chain 'A' and resid 162 through 169 Processing helix chain 'A' and resid 263 through 272 Processing helix chain 'H' and resid 28 through 32 Processing helix chain 'H' and resid 87 through 91 removed outlier: 3.711A pdb=" N THR H 91 " --> pdb=" O ALA H 88 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 80 through 88 removed outlier: 3.600A pdb=" N GLY A 81 " --> pdb=" O LEU A 249 " (cutoff:3.500A) removed outlier: 3.544A pdb=" N GLN A 256 " --> pdb=" O THR A 248 " (cutoff:3.500A) removed outlier: 6.468A pdb=" N THR A 250 " --> pdb=" O ILE A 254 " (cutoff:3.500A) removed outlier: 5.234A pdb=" N ILE A 254 " --> pdb=" O THR A 250 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 95 through 96 removed outlier: 4.618A pdb=" N GLN A 205 " --> pdb=" O TYR A 201 " (cutoff:3.500A) removed outlier: 7.085A pdb=" N PHE A 206 " --> pdb=" O LEU A 213 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 101 through 105 removed outlier: 7.251A pdb=" N ILE A 141 " --> pdb=" O CYS A 157 " (cutoff:3.500A) removed outlier: 5.627A pdb=" N CYS A 157 " --> pdb=" O ILE A 141 " (cutoff:3.500A) removed outlier: 6.791A pdb=" N CYS A 181 " --> pdb=" O LEU A 188 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'H' and resid 3 through 7 Processing sheet with id=AA5, first strand: chain 'H' and resid 11 through 12 removed outlier: 6.918A pdb=" N MET H 34 " --> pdb=" O ILE H 50 " (cutoff:3.500A) removed outlier: 4.691A pdb=" N ILE H 50 " --> pdb=" O MET H 34 " (cutoff:3.500A) removed outlier: 6.696A pdb=" N TRP H 36 " --> pdb=" O VAL H 48 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'H' and resid 11 through 12 removed outlier: 3.663A pdb=" N TYR H 111 " --> pdb=" O LYS H 98 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'L' and resid 4 through 5 Processing sheet with id=AA8, first strand: chain 'L' and resid 10 through 12 removed outlier: 6.346A pdb=" N LEU L 11 " --> pdb=" O GLU L 104 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA8 Processing sheet with id=AA9, first strand: chain 'L' and resid 53 through 54 removed outlier: 5.767A pdb=" N LEU L 46 " --> pdb=" O GLN L 37 " (cutoff:3.500A) removed outlier: 6.632A pdb=" N GLN L 37 " --> pdb=" O LEU L 46 " (cutoff:3.500A) 127 hydrogen bonds defined for protein. 318 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: 0.97 Time building geometry restraints manager: 1.86 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: 1174 1.34 - 1.46: 912 1.46 - 1.57: 1756 1.57 - 1.69: 0 1.69 - 1.81: 24 Bond restraints: 3866 Sorted by residual: bond pdb=" C1 NAG C 1 " pdb=" O5 NAG C 1 " ideal model delta sigma weight residual 1.406 1.438 -0.032 2.00e-02 2.50e+03 2.59e+00 bond pdb=" CA SER A 43 " pdb=" CB SER A 43 " ideal model delta sigma weight residual 1.530 1.498 0.032 2.00e-02 2.50e+03 2.53e+00 bond pdb=" C1 NAG A1102 " pdb=" O5 NAG A1102 " ideal model delta sigma weight residual 1.406 1.436 -0.030 2.00e-02 2.50e+03 2.30e+00 bond pdb=" C1 NAG B 2 " pdb=" O5 NAG B 2 " ideal model delta sigma weight residual 1.406 1.436 -0.030 2.00e-02 2.50e+03 2.25e+00 bond pdb=" N SER A 43 " pdb=" CA SER A 43 " ideal model delta sigma weight residual 1.458 1.485 -0.027 1.90e-02 2.77e+03 1.97e+00 ... (remaining 3861 not shown) Histogram of bond angle deviations from ideal: 100.17 - 106.93: 108 106.93 - 113.69: 2207 113.69 - 120.44: 1341 120.44 - 127.20: 1578 127.20 - 133.96: 35 Bond angle restraints: 5269 Sorted by residual: angle pdb=" N LEU A 58 " pdb=" CA LEU A 58 " pdb=" C LEU A 58 " ideal model delta sigma weight residual 109.81 115.70 -5.89 2.21e+00 2.05e-01 7.09e+00 angle pdb=" CA LEU A 106 " pdb=" CB LEU A 106 " pdb=" CG LEU A 106 " ideal model delta sigma weight residual 116.30 124.45 -8.15 3.50e+00 8.16e-02 5.42e+00 angle pdb=" C1 BMA D 3 " pdb=" O5 BMA D 3 " pdb=" C5 BMA D 3 " ideal model delta sigma weight residual 118.82 112.31 6.51 3.00e+00 1.11e-01 4.71e+00 angle pdb=" C3 BMA D 3 " pdb=" C2 BMA D 3 " pdb=" O2 BMA D 3 " ideal model delta sigma weight residual 112.95 106.48 6.47 3.00e+00 1.11e-01 4.65e+00 angle pdb=" C3 MAN D 4 " pdb=" C2 MAN D 4 " pdb=" O2 MAN D 4 " ideal model delta sigma weight residual 111.77 105.37 6.40 3.00e+00 1.11e-01 4.56e+00 ... (remaining 5264 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 21.65: 2226 21.65 - 43.30: 196 43.30 - 64.94: 23 64.94 - 86.59: 11 86.59 - 108.24: 5 Dihedral angle restraints: 2461 sinusoidal: 1118 harmonic: 1343 Sorted by residual: dihedral pdb=" CA LEU A 58 " pdb=" C LEU A 58 " pdb=" N PRO A 59 " pdb=" CA PRO A 59 " ideal model delta harmonic sigma weight residual 180.00 150.41 29.59 0 5.00e+00 4.00e-02 3.50e+01 dihedral pdb=" CA PHE A 182 " pdb=" C PHE A 182 " pdb=" N THR A 183 " pdb=" CA THR A 183 " ideal model delta harmonic sigma weight residual 180.00 159.24 20.76 0 5.00e+00 4.00e-02 1.72e+01 dihedral pdb=" O4 BMA D 3 " pdb=" C4 BMA D 3 " pdb=" C5 BMA D 3 " pdb=" O5 BMA D 3 " ideal model delta sinusoidal sigma weight residual -71.29 -179.53 108.24 1 3.00e+01 1.11e-03 1.40e+01 ... (remaining 2458 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.044: 494 0.044 - 0.089: 104 0.089 - 0.133: 46 0.133 - 0.177: 2 0.177 - 0.221: 1 Chirality restraints: 647 Sorted by residual: chirality pdb=" C5 BMA D 3 " pdb=" C4 BMA D 3 " pdb=" C6 BMA D 3 " pdb=" O5 BMA D 3 " both_signs ideal model delta sigma weight residual False -2.27 -2.50 0.22 2.00e-01 2.50e+01 1.23e+00 chirality pdb=" C1 NAG D 1 " pdb=" ND2 ASN A 241 " pdb=" C2 NAG D 1 " pdb=" O5 NAG D 1 " both_signs ideal model delta sigma weight residual False -2.40 -2.23 -0.17 2.00e-01 2.50e+01 6.99e-01 chirality pdb=" C3 FUC B 3 " pdb=" C2 FUC B 3 " pdb=" C4 FUC B 3 " pdb=" O3 FUC B 3 " both_signs ideal model delta sigma weight residual False -2.45 -2.59 0.13 2.00e-01 2.50e+01 4.47e-01 ... (remaining 644 not shown) Planarity restraints: 655 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C LEU A 58 " -0.033 5.00e-02 4.00e+02 5.03e-02 4.05e+00 pdb=" N PRO A 59 " 0.087 5.00e-02 4.00e+02 pdb=" CA PRO A 59 " -0.025 5.00e-02 4.00e+02 pdb=" CD PRO A 59 " -0.028 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA VAL L 3 " 0.005 2.00e-02 2.50e+03 1.01e-02 1.03e+00 pdb=" C VAL L 3 " -0.018 2.00e-02 2.50e+03 pdb=" O VAL L 3 " 0.007 2.00e-02 2.50e+03 pdb=" N MET L 4 " 0.006 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C ALA L 43 " -0.015 5.00e-02 4.00e+02 2.28e-02 8.34e-01 pdb=" N PRO L 44 " 0.039 5.00e-02 4.00e+02 pdb=" CA PRO L 44 " -0.012 5.00e-02 4.00e+02 pdb=" CD PRO L 44 " -0.013 5.00e-02 4.00e+02 ... (remaining 652 not shown) Histogram of nonbonded interaction distances: 2.28 - 2.80: 1005 2.80 - 3.33: 3150 3.33 - 3.85: 6103 3.85 - 4.38: 7321 4.38 - 4.90: 13218 Nonbonded interactions: 30797 Sorted by model distance: nonbonded pdb=" NH1 ARG A 48 " pdb=" OD2 ASP A 134 " model vdw 2.277 2.520 nonbonded pdb=" O THR L 20 " pdb=" OG1 THR L 20 " model vdw 2.292 2.440 nonbonded pdb=" NH1 ARG L 61 " pdb=" OE1 GLN L 79 " model vdw 2.307 2.520 nonbonded pdb=" O ASP L 82 " pdb=" OH TYR L 86 " model vdw 2.362 2.440 nonbonded pdb=" O ASN A 251 " pdb=" OG1 THR A 252 " model vdw 2.379 2.440 ... (remaining 30792 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = chain 'C' selection = chain 'E' } 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=0.38 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: 2.070 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.000 Extract box with map and model: 9.830 Check model and map are aligned: 0.050 Set scattering table: 0.060 Process input model: 16.450 Find NCS groups from input model: 0.110 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:2.550 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 31.140 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8629 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 : 0.004 0.032 3866 Z= 0.253 Angle : 0.650 8.147 5269 Z= 0.298 Chirality : 0.044 0.221 647 Planarity : 0.003 0.050 648 Dihedral : 16.479 108.236 1592 Min Nonbonded Distance : 2.277 Molprobity Statistics. All-atom Clashscore : 5.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.40 % Favored : 95.60 % Rotamer: Outliers : 0.00 % Allowed : 20.95 % Favored : 79.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.47 (0.41), residues: 456 helix: -0.35 (1.07), residues: 25 sheet: -0.02 (0.41), residues: 176 loop : -0.44 (0.41), residues: 255 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP H 112 HIS 0.003 0.001 HIS A 168 PHE 0.011 0.001 PHE A 237 TYR 0.009 0.001 TYR A 222 ARG 0.002 0.000 ARG H 19 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 912 Ramachandran restraints generated. 456 Oldfield, 0 Emsley, 456 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 912 Ramachandran restraints generated. 456 Oldfield, 0 Emsley, 456 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 85 residues out of total 399 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 85 time to evaluate : 0.426 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 85 average time/residue: 0.2422 time to fit residues: 23.8920 Evaluate side-chains 74 residues out of total 399 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 74 time to evaluate : 0.438 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 45 random chunks: chunk 37 optimal weight: 4.9990 chunk 34 optimal weight: 0.9990 chunk 18 optimal weight: 2.9990 chunk 11 optimal weight: 0.9990 chunk 23 optimal weight: 2.9990 chunk 35 optimal weight: 3.9990 chunk 13 optimal weight: 0.7980 chunk 21 optimal weight: 1.9990 chunk 26 optimal weight: 0.7980 chunk 40 optimal weight: 0.5980 chunk 22 optimal weight: 0.8980 overall best weight: 0.8182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 271 GLN ** H 114 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8648 moved from start: 0.1371 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 3866 Z= 0.222 Angle : 0.610 7.702 5269 Z= 0.309 Chirality : 0.043 0.174 647 Planarity : 0.004 0.049 648 Dihedral : 10.197 83.065 815 Min Nonbonded Distance : 2.256 Molprobity Statistics. All-atom Clashscore : 6.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.96 % Favored : 96.04 % Rotamer: Outliers : 3.24 % Allowed : 20.70 % Favored : 76.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.24 (0.40), residues: 456 helix: 0.39 (1.18), residues: 25 sheet: 0.17 (0.40), residues: 169 loop : -0.37 (0.40), residues: 262 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP H 112 HIS 0.003 0.001 HIS A 236 PHE 0.013 0.001 PHE A 206 TYR 0.014 0.001 TYR A 222 ARG 0.006 0.001 ARG L 42 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 912 Ramachandran restraints generated. 456 Oldfield, 0 Emsley, 456 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 912 Ramachandran restraints generated. 456 Oldfield, 0 Emsley, 456 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 87 residues out of total 399 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 74 time to evaluate : 0.456 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: L 42 ARG cc_start: 0.7457 (mmm-85) cc_final: 0.7238 (mmm160) outliers start: 13 outliers final: 6 residues processed: 83 average time/residue: 0.2224 time to fit residues: 21.6770 Evaluate side-chains 77 residues out of total 399 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 71 time to evaluate : 0.422 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 171 THR Chi-restraints excluded: chain A residue 175 LEU Chi-restraints excluded: chain A residue 219 THR Chi-restraints excluded: chain A residue 265 VAL Chi-restraints excluded: chain H residue 117 LEU Chi-restraints excluded: chain L residue 2 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 45 random chunks: chunk 12 optimal weight: 3.9990 chunk 34 optimal weight: 3.9990 chunk 27 optimal weight: 0.8980 chunk 11 optimal weight: 1.9990 chunk 40 optimal weight: 6.9990 chunk 44 optimal weight: 0.5980 chunk 36 optimal weight: 6.9990 chunk 13 optimal weight: 1.9990 chunk 32 optimal weight: 0.9990 chunk 30 optimal weight: 1.9990 chunk 21 optimal weight: 1.9990 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 112 GLN H 114 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8682 moved from start: 0.1686 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.032 3866 Z= 0.311 Angle : 0.602 7.773 5269 Z= 0.305 Chirality : 0.043 0.199 647 Planarity : 0.004 0.051 648 Dihedral : 9.758 80.814 815 Min Nonbonded Distance : 2.269 Molprobity Statistics. All-atom Clashscore : 6.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.62 % Favored : 95.38 % Rotamer: Outliers : 2.99 % Allowed : 21.20 % Favored : 75.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.34 (0.40), residues: 456 helix: 0.45 (1.20), residues: 25 sheet: 0.23 (0.41), residues: 158 loop : -0.53 (0.39), residues: 273 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP H 112 HIS 0.002 0.001 HIS A 236 PHE 0.011 0.001 PHE A 206 TYR 0.016 0.001 TYR A 222 ARG 0.006 0.001 ARG L 18 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 912 Ramachandran restraints generated. 456 Oldfield, 0 Emsley, 456 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 912 Ramachandran restraints generated. 456 Oldfield, 0 Emsley, 456 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 84 residues out of total 399 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 72 time to evaluate : 0.465 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: H 87 ARG cc_start: 0.8161 (OUTLIER) cc_final: 0.7754 (ptp-170) REVERT: L 11 LEU cc_start: 0.8832 (OUTLIER) cc_final: 0.8602 (tt) outliers start: 12 outliers final: 6 residues processed: 82 average time/residue: 0.2271 time to fit residues: 21.8567 Evaluate side-chains 77 residues out of total 399 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 69 time to evaluate : 0.447 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 135 LEU Chi-restraints excluded: chain A residue 171 THR Chi-restraints excluded: chain A residue 175 LEU Chi-restraints excluded: chain A residue 190 ILE Chi-restraints excluded: chain A residue 219 THR Chi-restraints excluded: chain H residue 87 ARG Chi-restraints excluded: chain L residue 11 LEU Chi-restraints excluded: chain L residue 20 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 45 random chunks: chunk 4 optimal weight: 0.9980 chunk 19 optimal weight: 0.8980 chunk 27 optimal weight: 0.0570 chunk 41 optimal weight: 4.9990 chunk 43 optimal weight: 0.8980 chunk 21 optimal weight: 0.9980 chunk 38 optimal weight: 0.7980 chunk 11 optimal weight: 0.9990 chunk 36 optimal weight: 6.9990 chunk 24 optimal weight: 6.9990 chunk 0 optimal weight: 3.9990 overall best weight: 0.7298 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: L 79 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8659 moved from start: 0.1895 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.025 3866 Z= 0.198 Angle : 0.590 7.788 5269 Z= 0.296 Chirality : 0.042 0.220 647 Planarity : 0.004 0.048 648 Dihedral : 8.957 75.098 815 Min Nonbonded Distance : 2.275 Molprobity Statistics. All-atom Clashscore : 6.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.96 % Favored : 96.04 % Rotamer: Outliers : 2.24 % Allowed : 21.95 % Favored : 75.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.27 (0.40), residues: 456 helix: 0.66 (1.23), residues: 25 sheet: 0.33 (0.42), residues: 158 loop : -0.53 (0.38), residues: 273 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP H 112 HIS 0.002 0.001 HIS A 236 PHE 0.011 0.001 PHE A 237 TYR 0.013 0.001 TYR A 222 ARG 0.006 0.001 ARG L 18 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 912 Ramachandran restraints generated. 456 Oldfield, 0 Emsley, 456 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 912 Ramachandran restraints generated. 456 Oldfield, 0 Emsley, 456 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 79 residues out of total 399 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 70 time to evaluate : 0.430 Fit side-chains revert: symmetry clash REVERT: H 87 ARG cc_start: 0.8179 (OUTLIER) cc_final: 0.7931 (ptp-170) REVERT: L 11 LEU cc_start: 0.8824 (OUTLIER) cc_final: 0.8586 (tt) outliers start: 9 outliers final: 7 residues processed: 76 average time/residue: 0.2304 time to fit residues: 20.4498 Evaluate side-chains 78 residues out of total 399 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 69 time to evaluate : 0.442 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 121 VAL Chi-restraints excluded: chain A residue 135 LEU Chi-restraints excluded: chain A residue 175 LEU Chi-restraints excluded: chain A residue 190 ILE Chi-restraints excluded: chain A residue 219 THR Chi-restraints excluded: chain A residue 265 VAL Chi-restraints excluded: chain H residue 87 ARG Chi-restraints excluded: chain L residue 2 LEU Chi-restraints excluded: chain L residue 11 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 45 random chunks: chunk 32 optimal weight: 1.9990 chunk 17 optimal weight: 0.0030 chunk 37 optimal weight: 0.8980 chunk 30 optimal weight: 5.9990 chunk 0 optimal weight: 2.9990 chunk 22 optimal weight: 0.5980 chunk 39 optimal weight: 0.5980 chunk 10 optimal weight: 1.9990 chunk 14 optimal weight: 0.5980 chunk 8 optimal weight: 3.9990 chunk 25 optimal weight: 0.6980 overall best weight: 0.4990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 112 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8644 moved from start: 0.2063 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.020 3866 Z= 0.158 Angle : 0.573 8.008 5269 Z= 0.287 Chirality : 0.042 0.231 647 Planarity : 0.003 0.046 648 Dihedral : 8.391 71.024 815 Min Nonbonded Distance : 2.253 Molprobity Statistics. All-atom Clashscore : 6.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.96 % Favored : 96.04 % Rotamer: Outliers : 2.99 % Allowed : 22.44 % Favored : 74.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.16 (0.40), residues: 456 helix: 0.68 (1.21), residues: 25 sheet: 0.41 (0.42), residues: 158 loop : -0.46 (0.38), residues: 273 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP H 112 HIS 0.002 0.001 HIS A 236 PHE 0.011 0.001 PHE A 237 TYR 0.014 0.001 TYR H 59 ARG 0.005 0.001 ARG H 3 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 912 Ramachandran restraints generated. 456 Oldfield, 0 Emsley, 456 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 912 Ramachandran restraints generated. 456 Oldfield, 0 Emsley, 456 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 87 residues out of total 399 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 75 time to evaluate : 0.466 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: L 11 LEU cc_start: 0.8860 (OUTLIER) cc_final: 0.8616 (tt) outliers start: 12 outliers final: 9 residues processed: 82 average time/residue: 0.2363 time to fit residues: 22.6211 Evaluate side-chains 82 residues out of total 399 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 72 time to evaluate : 0.404 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 135 LEU Chi-restraints excluded: chain A residue 171 THR Chi-restraints excluded: chain A residue 175 LEU Chi-restraints excluded: chain A residue 190 ILE Chi-restraints excluded: chain A residue 219 THR Chi-restraints excluded: chain A residue 265 VAL Chi-restraints excluded: chain H residue 52 THR Chi-restraints excluded: chain L residue 2 LEU Chi-restraints excluded: chain L residue 11 LEU Chi-restraints excluded: chain L residue 20 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 45 random chunks: chunk 10 optimal weight: 0.9990 chunk 43 optimal weight: 5.9990 chunk 36 optimal weight: 8.9990 chunk 20 optimal weight: 2.9990 chunk 3 optimal weight: 2.9990 chunk 14 optimal weight: 0.0060 chunk 22 optimal weight: 0.9980 chunk 41 optimal weight: 5.9990 chunk 4 optimal weight: 1.9990 chunk 24 optimal weight: 7.9990 chunk 31 optimal weight: 0.5980 overall best weight: 0.9200 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 100 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8668 moved from start: 0.2158 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.025 3866 Z= 0.233 Angle : 0.593 7.681 5269 Z= 0.296 Chirality : 0.042 0.237 647 Planarity : 0.004 0.045 648 Dihedral : 8.170 69.231 815 Min Nonbonded Distance : 2.294 Molprobity Statistics. All-atom Clashscore : 6.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.40 % Favored : 95.60 % Rotamer: Outliers : 3.24 % Allowed : 20.70 % Favored : 76.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.18 (0.40), residues: 456 helix: 0.53 (1.19), residues: 25 sheet: 0.40 (0.42), residues: 158 loop : -0.46 (0.39), residues: 273 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.003 0.001 TRP H 112 HIS 0.002 0.001 HIS A 236 PHE 0.010 0.001 PHE A 237 TYR 0.014 0.001 TYR A 222 ARG 0.008 0.001 ARG L 18 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 912 Ramachandran restraints generated. 456 Oldfield, 0 Emsley, 456 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 912 Ramachandran restraints generated. 456 Oldfield, 0 Emsley, 456 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 84 residues out of total 399 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 71 time to evaluate : 0.438 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 134 ASP cc_start: 0.7614 (t0) cc_final: 0.7408 (t70) outliers start: 13 outliers final: 12 residues processed: 82 average time/residue: 0.2236 time to fit residues: 21.4779 Evaluate side-chains 79 residues out of total 399 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 67 time to evaluate : 0.424 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 116 CYS Chi-restraints excluded: chain A residue 121 VAL Chi-restraints excluded: chain A residue 135 LEU Chi-restraints excluded: chain A residue 171 THR Chi-restraints excluded: chain A residue 175 LEU Chi-restraints excluded: chain A residue 190 ILE Chi-restraints excluded: chain A residue 219 THR Chi-restraints excluded: chain A residue 265 VAL Chi-restraints excluded: chain H residue 52 THR Chi-restraints excluded: chain L residue 2 LEU Chi-restraints excluded: chain L residue 20 THR Chi-restraints excluded: chain L residue 82 ASP Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 45 random chunks: chunk 24 optimal weight: 5.9990 chunk 36 optimal weight: 0.6980 chunk 43 optimal weight: 0.9980 chunk 27 optimal weight: 0.8980 chunk 26 optimal weight: 2.9990 chunk 20 optimal weight: 2.9990 chunk 17 optimal weight: 2.9990 chunk 25 optimal weight: 1.9990 chunk 13 optimal weight: 0.7980 chunk 8 optimal weight: 2.9990 chunk 29 optimal weight: 0.9980 overall best weight: 0.8780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** H 114 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 79 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8665 moved from start: 0.2242 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.025 3866 Z= 0.222 Angle : 0.585 7.915 5269 Z= 0.293 Chirality : 0.042 0.238 647 Planarity : 0.004 0.046 648 Dihedral : 7.994 67.417 815 Min Nonbonded Distance : 2.292 Molprobity Statistics. All-atom Clashscore : 6.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.40 % Favored : 95.60 % Rotamer: Outliers : 3.49 % Allowed : 20.95 % Favored : 75.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.18 (0.40), residues: 456 helix: 0.58 (1.20), residues: 25 sheet: 0.43 (0.43), residues: 158 loop : -0.50 (0.39), residues: 273 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.003 0.001 TRP H 112 HIS 0.001 0.001 HIS A 236 PHE 0.010 0.001 PHE A 237 TYR 0.016 0.001 TYR H 59 ARG 0.008 0.001 ARG L 61 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 912 Ramachandran restraints generated. 456 Oldfield, 0 Emsley, 456 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 912 Ramachandran restraints generated. 456 Oldfield, 0 Emsley, 456 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 80 residues out of total 399 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 66 time to evaluate : 0.442 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 134 ASP cc_start: 0.7602 (t0) cc_final: 0.7391 (t70) REVERT: L 11 LEU cc_start: 0.8864 (OUTLIER) cc_final: 0.8628 (tt) outliers start: 14 outliers final: 10 residues processed: 77 average time/residue: 0.2403 time to fit residues: 21.7191 Evaluate side-chains 77 residues out of total 399 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 66 time to evaluate : 0.427 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 116 CYS Chi-restraints excluded: chain A residue 135 LEU Chi-restraints excluded: chain A residue 171 THR Chi-restraints excluded: chain A residue 175 LEU Chi-restraints excluded: chain A residue 190 ILE Chi-restraints excluded: chain A residue 219 THR Chi-restraints excluded: chain A residue 265 VAL Chi-restraints excluded: chain H residue 52 THR Chi-restraints excluded: chain L residue 2 LEU Chi-restraints excluded: chain L residue 11 LEU Chi-restraints excluded: chain L residue 20 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 45 random chunks: chunk 21 optimal weight: 1.9990 chunk 4 optimal weight: 0.6980 chunk 34 optimal weight: 1.9990 chunk 39 optimal weight: 0.9990 chunk 41 optimal weight: 1.9990 chunk 37 optimal weight: 0.6980 chunk 40 optimal weight: 0.0070 chunk 24 optimal weight: 7.9990 chunk 17 optimal weight: 2.9990 chunk 31 optimal weight: 1.9990 chunk 12 optimal weight: 1.9990 overall best weight: 0.8802 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 114 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8668 moved from start: 0.2336 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.024 3866 Z= 0.223 Angle : 0.592 7.691 5269 Z= 0.297 Chirality : 0.042 0.239 647 Planarity : 0.004 0.049 648 Dihedral : 7.812 65.778 815 Min Nonbonded Distance : 2.277 Molprobity Statistics. All-atom Clashscore : 7.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.18 % Favored : 95.82 % Rotamer: Outliers : 2.99 % Allowed : 21.70 % Favored : 75.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.14 (0.40), residues: 456 helix: 0.56 (1.19), residues: 25 sheet: 0.47 (0.43), residues: 158 loop : -0.47 (0.39), residues: 273 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.003 0.001 TRP H 112 HIS 0.002 0.000 HIS A 236 PHE 0.010 0.001 PHE A 237 TYR 0.015 0.001 TYR H 59 ARG 0.008 0.001 ARG L 18 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 912 Ramachandran restraints generated. 456 Oldfield, 0 Emsley, 456 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 912 Ramachandran restraints generated. 456 Oldfield, 0 Emsley, 456 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 80 residues out of total 399 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 68 time to evaluate : 0.407 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 134 ASP cc_start: 0.7616 (t0) cc_final: 0.7416 (t70) REVERT: L 11 LEU cc_start: 0.8883 (OUTLIER) cc_final: 0.8621 (tt) outliers start: 12 outliers final: 11 residues processed: 78 average time/residue: 0.2269 time to fit residues: 20.6120 Evaluate side-chains 79 residues out of total 399 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 67 time to evaluate : 0.418 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 116 CYS Chi-restraints excluded: chain A residue 121 VAL Chi-restraints excluded: chain A residue 135 LEU Chi-restraints excluded: chain A residue 170 SER Chi-restraints excluded: chain A residue 171 THR Chi-restraints excluded: chain A residue 175 LEU Chi-restraints excluded: chain A residue 190 ILE Chi-restraints excluded: chain A residue 219 THR Chi-restraints excluded: chain H residue 52 THR Chi-restraints excluded: chain L residue 2 LEU Chi-restraints excluded: chain L residue 11 LEU Chi-restraints excluded: chain L residue 20 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 45 random chunks: chunk 36 optimal weight: 3.9990 chunk 38 optimal weight: 3.9990 chunk 40 optimal weight: 3.9990 chunk 26 optimal weight: 0.9980 chunk 42 optimal weight: 0.1980 chunk 20 optimal weight: 1.9990 chunk 29 optimal weight: 2.9990 chunk 44 optimal weight: 0.9990 chunk 41 optimal weight: 0.9980 chunk 35 optimal weight: 2.9990 chunk 3 optimal weight: 4.9990 overall best weight: 1.0384 ------------------------------------------------------------------------------- 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: 0.8678 moved from start: 0.2347 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.028 3866 Z= 0.257 Angle : 0.602 7.907 5269 Z= 0.303 Chirality : 0.043 0.238 647 Planarity : 0.004 0.050 648 Dihedral : 7.768 64.620 815 Min Nonbonded Distance : 2.279 Molprobity Statistics. All-atom Clashscore : 6.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.18 % Favored : 95.82 % Rotamer: Outliers : 2.99 % Allowed : 21.70 % Favored : 75.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.09 (0.41), residues: 456 helix: 0.58 (1.19), residues: 25 sheet: 0.50 (0.42), residues: 163 loop : -0.45 (0.40), residues: 268 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.003 0.001 TRP L 35 HIS 0.001 0.001 HIS A 236 PHE 0.011 0.001 PHE A 237 TYR 0.014 0.001 TYR A 222 ARG 0.008 0.001 ARG L 18 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 912 Ramachandran restraints generated. 456 Oldfield, 0 Emsley, 456 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 912 Ramachandran restraints generated. 456 Oldfield, 0 Emsley, 456 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 80 residues out of total 399 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 68 time to evaluate : 0.413 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 134 ASP cc_start: 0.7645 (t0) cc_final: 0.7430 (t70) REVERT: L 11 LEU cc_start: 0.8862 (OUTLIER) cc_final: 0.8607 (tt) outliers start: 12 outliers final: 11 residues processed: 78 average time/residue: 0.2350 time to fit residues: 21.3615 Evaluate side-chains 78 residues out of total 399 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 66 time to evaluate : 0.430 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 116 CYS Chi-restraints excluded: chain A residue 121 VAL Chi-restraints excluded: chain A residue 135 LEU Chi-restraints excluded: chain A residue 170 SER Chi-restraints excluded: chain A residue 171 THR Chi-restraints excluded: chain A residue 175 LEU Chi-restraints excluded: chain A residue 190 ILE Chi-restraints excluded: chain A residue 219 THR Chi-restraints excluded: chain H residue 52 THR Chi-restraints excluded: chain L residue 2 LEU Chi-restraints excluded: chain L residue 11 LEU Chi-restraints excluded: chain L residue 20 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 45 random chunks: chunk 27 optimal weight: 0.0020 chunk 21 optimal weight: 1.9990 chunk 28 optimal weight: 0.8980 chunk 38 optimal weight: 1.9990 chunk 10 optimal weight: 0.9990 chunk 32 optimal weight: 0.0020 chunk 5 optimal weight: 1.9990 chunk 9 optimal weight: 2.9990 chunk 35 optimal weight: 0.6980 chunk 14 optimal weight: 1.9990 chunk 36 optimal weight: 2.9990 overall best weight: 0.5198 ------------------------------------------------------------------------------- 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: 0.8646 moved from start: 0.2476 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.025 3866 Z= 0.164 Angle : 0.582 7.714 5269 Z= 0.293 Chirality : 0.042 0.235 647 Planarity : 0.004 0.049 648 Dihedral : 7.368 60.903 815 Min Nonbonded Distance : 2.265 Molprobity Statistics. All-atom Clashscore : 7.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.74 % Favored : 96.26 % Rotamer: Outliers : 2.49 % Allowed : 22.69 % Favored : 74.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.07 (0.40), residues: 456 helix: 0.71 (1.21), residues: 25 sheet: 0.52 (0.42), residues: 158 loop : -0.43 (0.39), residues: 273 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP H 112 HIS 0.002 0.001 HIS A 236 PHE 0.011 0.001 PHE A 237 TYR 0.012 0.001 TYR A 222 ARG 0.009 0.001 ARG L 18 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 912 Ramachandran restraints generated. 456 Oldfield, 0 Emsley, 456 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 912 Ramachandran restraints generated. 456 Oldfield, 0 Emsley, 456 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 80 residues out of total 399 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 70 time to evaluate : 0.440 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 10 outliers final: 9 residues processed: 78 average time/residue: 0.2376 time to fit residues: 21.5720 Evaluate side-chains 79 residues out of total 399 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 70 time to evaluate : 0.442 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 116 CYS Chi-restraints excluded: chain A residue 121 VAL Chi-restraints excluded: chain A residue 135 LEU Chi-restraints excluded: chain A residue 170 SER Chi-restraints excluded: chain A residue 175 LEU Chi-restraints excluded: chain A residue 190 ILE Chi-restraints excluded: chain A residue 219 THR Chi-restraints excluded: chain H residue 52 THR Chi-restraints excluded: chain L residue 2 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 45 random chunks: chunk 4 optimal weight: 0.8980 chunk 6 optimal weight: 0.0670 chunk 31 optimal weight: 4.9990 chunk 2 optimal weight: 0.8980 chunk 25 optimal weight: 2.9990 chunk 40 optimal weight: 3.9990 chunk 24 optimal weight: 7.9990 chunk 30 optimal weight: 0.9990 chunk 1 optimal weight: 0.8980 chunk 28 optimal weight: 0.0000 chunk 27 optimal weight: 2.9990 overall best weight: 0.5522 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3059 r_free = 0.3059 target = 0.074776 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.2763 r_free = 0.2763 target = 0.059404 restraints weight = 12347.259| |-----------------------------------------------------------------------------| r_work (start): 0.2760 rms_B_bonded: 3.86 r_work: 0.2612 rms_B_bonded: 3.92 restraints_weight: 0.5000 r_work (final): 0.2612 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2622 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2622 r_free = 0.2622 target_work(ls_wunit_k1) = 0.053 | | occupancies: max = 1.00 min = 0.38 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2622 r_free = 0.2622 target_work(ls_wunit_k1) = 0.053 | | occupancies: max = 1.00 min = 0.38 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2622 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8339 moved from start: 0.2514 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.025 3866 Z= 0.170 Angle : 0.582 7.934 5269 Z= 0.292 Chirality : 0.042 0.232 647 Planarity : 0.004 0.047 648 Dihedral : 7.226 58.569 815 Min Nonbonded Distance : 2.277 Molprobity Statistics. All-atom Clashscore : 7.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.96 % Favored : 96.04 % Rotamer: Outliers : 2.24 % Allowed : 22.94 % Favored : 74.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.06 (0.40), residues: 456 helix: 0.63 (1.18), residues: 25 sheet: 0.58 (0.43), residues: 158 loop : -0.45 (0.39), residues: 273 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP H 112 HIS 0.002 0.000 HIS A 236 PHE 0.011 0.001 PHE A 237 TYR 0.012 0.001 TYR A 222 ARG 0.009 0.001 ARG L 18 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1518.97 seconds wall clock time: 27 minutes 42.88 seconds (1662.88 seconds total)