Starting phenix.real_space_refine on Sun Dec 10 06:47:38 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7p13_13154/12_2023/7p13_13154.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7p13_13154/12_2023/7p13_13154.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.29 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7p13_13154/12_2023/7p13_13154.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7p13_13154/12_2023/7p13_13154.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7p13_13154/12_2023/7p13_13154.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7p13_13154/12_2023/7p13_13154.pdb" } resolution = 2.29 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= 0.268 sd= 0.983 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians S 49 5.16 5 C 8463 2.51 5 N 2408 2.21 5 O 2653 1.98 5 H 154 0.53 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A TYR 264": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 264": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 264": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 264": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E TYR 264": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F TYR 264": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G TYR 264": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/modules/chem_data/mon_lib" Total number of atoms: 13727 Number of models: 1 Model: "" Number of chains: 7 Chain: "A" Number of atoms: 1961 Number of conformers: 1 Conformer: "" Number of residues, atoms: 249, 1961 Classifications: {'peptide': 249} Link IDs: {'PTRANS': 17, 'TRANS': 231} Chain breaks: 1 Chain: "B" Number of atoms: 1961 Number of conformers: 1 Conformer: "" Number of residues, atoms: 249, 1961 Classifications: {'peptide': 249} Link IDs: {'PTRANS': 17, 'TRANS': 231} Chain breaks: 1 Chain: "C" Number of atoms: 1961 Number of conformers: 1 Conformer: "" Number of residues, atoms: 249, 1961 Classifications: {'peptide': 249} Link IDs: {'PTRANS': 17, 'TRANS': 231} Chain breaks: 1 Chain: "D" Number of atoms: 1961 Number of conformers: 1 Conformer: "" Number of residues, atoms: 249, 1961 Classifications: {'peptide': 249} Link IDs: {'PTRANS': 17, 'TRANS': 231} Chain breaks: 1 Chain: "E" Number of atoms: 1961 Number of conformers: 1 Conformer: "" Number of residues, atoms: 249, 1961 Classifications: {'peptide': 249} Link IDs: {'PTRANS': 17, 'TRANS': 231} Chain breaks: 1 Chain: "F" Number of atoms: 1961 Number of conformers: 1 Conformer: "" Number of residues, atoms: 249, 1961 Classifications: {'peptide': 249} Link IDs: {'PTRANS': 17, 'TRANS': 231} Chain breaks: 1 Chain: "G" Number of atoms: 1961 Number of conformers: 1 Conformer: "" Number of residues, atoms: 249, 1961 Classifications: {'peptide': 249} Link IDs: {'PTRANS': 17, 'TRANS': 231} Chain breaks: 1 Time building chain proxies: 7.53, per 1000 atoms: 0.55 Number of scatterers: 13727 At special positions: 0 Unit cell: (115.092, 113.424, 102.582, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 49 16.00 O 2653 8.00 N 2408 7.00 C 8463 6.00 H 154 1.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 5.70 Conformation dependent library (CDL) restraints added in 2.7 seconds 3430 Ramachandran restraints generated. 1715 Oldfield, 0 Emsley, 1715 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3346 Finding SS restraints... Secondary structure from input PDB file: 63 helices and 0 sheets defined 71.9% alpha, 0.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.05 Creating SS restraints... Processing helix chain 'A' and resid 10 through 22 removed outlier: 3.636A pdb=" N GLU A 22 " --> pdb=" O ALA A 18 " (cutoff:3.500A) Processing helix chain 'A' and resid 39 through 79 Processing helix chain 'A' and resid 80 through 82 No H-bonds generated for 'chain 'A' and resid 80 through 82' Processing helix chain 'A' and resid 130 through 142 Processing helix chain 'A' and resid 146 through 166 Processing helix chain 'A' and resid 167 through 171 Processing helix chain 'A' and resid 179 through 223 Processing helix chain 'A' and resid 225 through 235 Processing helix chain 'A' and resid 242 through 268 Proline residue: A 248 - end of helix Processing helix chain 'B' and resid 10 through 22 removed outlier: 3.636A pdb=" N GLU B 22 " --> pdb=" O ALA B 18 " (cutoff:3.500A) Processing helix chain 'B' and resid 39 through 79 Processing helix chain 'B' and resid 80 through 82 No H-bonds generated for 'chain 'B' and resid 80 through 82' Processing helix chain 'B' and resid 130 through 142 Processing helix chain 'B' and resid 146 through 166 Processing helix chain 'B' and resid 167 through 171 Processing helix chain 'B' and resid 179 through 223 Processing helix chain 'B' and resid 225 through 235 Processing helix chain 'B' and resid 242 through 268 Proline residue: B 248 - end of helix Processing helix chain 'C' and resid 10 through 22 removed outlier: 3.636A pdb=" N GLU C 22 " --> pdb=" O ALA C 18 " (cutoff:3.500A) Processing helix chain 'C' and resid 39 through 79 Processing helix chain 'C' and resid 80 through 82 No H-bonds generated for 'chain 'C' and resid 80 through 82' Processing helix chain 'C' and resid 130 through 142 Processing helix chain 'C' and resid 146 through 166 Processing helix chain 'C' and resid 167 through 171 Processing helix chain 'C' and resid 179 through 223 Processing helix chain 'C' and resid 225 through 235 Processing helix chain 'C' and resid 242 through 268 Proline residue: C 248 - end of helix Processing helix chain 'D' and resid 10 through 22 removed outlier: 3.636A pdb=" N GLU D 22 " --> pdb=" O ALA D 18 " (cutoff:3.500A) Processing helix chain 'D' and resid 39 through 79 Processing helix chain 'D' and resid 80 through 82 No H-bonds generated for 'chain 'D' and resid 80 through 82' Processing helix chain 'D' and resid 130 through 142 Processing helix chain 'D' and resid 146 through 166 Processing helix chain 'D' and resid 167 through 171 Processing helix chain 'D' and resid 179 through 223 Processing helix chain 'D' and resid 225 through 235 Processing helix chain 'D' and resid 242 through 268 Proline residue: D 248 - end of helix Processing helix chain 'E' and resid 10 through 22 removed outlier: 3.636A pdb=" N GLU E 22 " --> pdb=" O ALA E 18 " (cutoff:3.500A) Processing helix chain 'E' and resid 39 through 79 Processing helix chain 'E' and resid 80 through 82 No H-bonds generated for 'chain 'E' and resid 80 through 82' Processing helix chain 'E' and resid 130 through 142 Processing helix chain 'E' and resid 146 through 166 Processing helix chain 'E' and resid 167 through 171 Processing helix chain 'E' and resid 179 through 223 Processing helix chain 'E' and resid 225 through 235 Processing helix chain 'E' and resid 242 through 268 Proline residue: E 248 - end of helix Processing helix chain 'F' and resid 10 through 22 removed outlier: 3.636A pdb=" N GLU F 22 " --> pdb=" O ALA F 18 " (cutoff:3.500A) Processing helix chain 'F' and resid 39 through 79 Processing helix chain 'F' and resid 80 through 82 No H-bonds generated for 'chain 'F' and resid 80 through 82' Processing helix chain 'F' and resid 130 through 142 Processing helix chain 'F' and resid 146 through 166 Processing helix chain 'F' and resid 167 through 171 Processing helix chain 'F' and resid 179 through 223 Processing helix chain 'F' and resid 225 through 235 Processing helix chain 'F' and resid 242 through 268 Proline residue: F 248 - end of helix Processing helix chain 'G' and resid 10 through 22 removed outlier: 3.636A pdb=" N GLU G 22 " --> pdb=" O ALA G 18 " (cutoff:3.500A) Processing helix chain 'G' and resid 39 through 79 Processing helix chain 'G' and resid 80 through 82 No H-bonds generated for 'chain 'G' and resid 80 through 82' Processing helix chain 'G' and resid 130 through 142 Processing helix chain 'G' and resid 146 through 166 Processing helix chain 'G' and resid 167 through 171 Processing helix chain 'G' and resid 179 through 223 Processing helix chain 'G' and resid 225 through 235 Processing helix chain 'G' and resid 242 through 268 Proline residue: G 248 - end of helix 987 hydrogen bonds defined for protein. 2919 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: 3.63 Time building geometry restraints manager: 6.15 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.83 - 1.02: 154 1.02 - 1.21: 49 1.21 - 1.41: 5677 1.41 - 1.60: 8043 1.60 - 1.80: 84 Bond restraints: 14007 Sorted by residual: bond pdb=" C LEU G 270 " pdb=" N GLU G 271 " ideal model delta sigma weight residual 1.329 1.272 0.056 1.60e-02 3.91e+03 1.24e+01 bond pdb=" C LEU E 270 " pdb=" N GLU E 271 " ideal model delta sigma weight residual 1.329 1.273 0.056 1.60e-02 3.91e+03 1.23e+01 bond pdb=" C LEU F 270 " pdb=" N GLU F 271 " ideal model delta sigma weight residual 1.329 1.273 0.056 1.60e-02 3.91e+03 1.22e+01 bond pdb=" C LEU C 270 " pdb=" N GLU C 271 " ideal model delta sigma weight residual 1.329 1.273 0.056 1.60e-02 3.91e+03 1.21e+01 bond pdb=" C LEU B 270 " pdb=" N GLU B 271 " ideal model delta sigma weight residual 1.329 1.273 0.056 1.60e-02 3.91e+03 1.21e+01 ... (remaining 14002 not shown) Histogram of bond angle deviations from ideal: 98.66 - 105.72: 424 105.72 - 112.79: 7627 112.79 - 119.85: 4861 119.85 - 126.92: 6106 126.92 - 133.99: 183 Bond angle restraints: 19201 Sorted by residual: angle pdb=" C GLU D 258 " pdb=" N LYS D 259 " pdb=" CA LYS D 259 " ideal model delta sigma weight residual 121.14 115.49 5.65 1.75e+00 3.27e-01 1.04e+01 angle pdb=" C GLU E 258 " pdb=" N LYS E 259 " pdb=" CA LYS E 259 " ideal model delta sigma weight residual 121.14 115.50 5.64 1.75e+00 3.27e-01 1.04e+01 angle pdb=" C GLU B 258 " pdb=" N LYS B 259 " pdb=" CA LYS B 259 " ideal model delta sigma weight residual 121.14 115.54 5.60 1.75e+00 3.27e-01 1.02e+01 angle pdb=" C GLU A 258 " pdb=" N LYS A 259 " pdb=" CA LYS A 259 " ideal model delta sigma weight residual 121.14 115.55 5.59 1.75e+00 3.27e-01 1.02e+01 angle pdb=" C GLU G 258 " pdb=" N LYS G 259 " pdb=" CA LYS G 259 " ideal model delta sigma weight residual 121.14 115.56 5.58 1.75e+00 3.27e-01 1.02e+01 ... (remaining 19196 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 14.99: 7475 14.99 - 29.99: 881 29.99 - 44.98: 156 44.98 - 59.97: 21 59.97 - 74.97: 42 Dihedral angle restraints: 8575 sinusoidal: 3444 harmonic: 5131 Sorted by residual: dihedral pdb=" CA PRO C 286 " pdb=" C PRO C 286 " pdb=" N PRO C 287 " pdb=" CA PRO C 287 " ideal model delta harmonic sigma weight residual -180.00 -148.65 -31.35 0 5.00e+00 4.00e-02 3.93e+01 dihedral pdb=" CA PRO E 286 " pdb=" C PRO E 286 " pdb=" N PRO E 287 " pdb=" CA PRO E 287 " ideal model delta harmonic sigma weight residual -180.00 -148.70 -31.30 0 5.00e+00 4.00e-02 3.92e+01 dihedral pdb=" CA PRO D 286 " pdb=" C PRO D 286 " pdb=" N PRO D 287 " pdb=" CA PRO D 287 " ideal model delta harmonic sigma weight residual -180.00 -148.71 -31.29 0 5.00e+00 4.00e-02 3.92e+01 ... (remaining 8572 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.055: 1238 0.055 - 0.110: 624 0.110 - 0.165: 161 0.165 - 0.221: 21 0.221 - 0.276: 7 Chirality restraints: 2051 Sorted by residual: chirality pdb=" CA GLU A 222 " pdb=" N GLU A 222 " pdb=" C GLU A 222 " pdb=" CB GLU A 222 " both_signs ideal model delta sigma weight residual False 2.51 2.23 0.28 2.00e-01 2.50e+01 1.90e+00 chirality pdb=" CA GLU E 222 " pdb=" N GLU E 222 " pdb=" C GLU E 222 " pdb=" CB GLU E 222 " both_signs ideal model delta sigma weight residual False 2.51 2.24 0.28 2.00e-01 2.50e+01 1.90e+00 chirality pdb=" CA GLU F 222 " pdb=" N GLU F 222 " pdb=" C GLU F 222 " pdb=" CB GLU F 222 " both_signs ideal model delta sigma weight residual False 2.51 2.24 0.27 2.00e-01 2.50e+01 1.89e+00 ... (remaining 2048 not shown) Planarity restraints: 2562 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C PRO D 286 " 0.050 5.00e-02 4.00e+02 7.49e-02 8.98e+00 pdb=" N PRO D 287 " -0.130 5.00e-02 4.00e+02 pdb=" CA PRO D 287 " 0.042 5.00e-02 4.00e+02 pdb=" CD PRO D 287 " 0.038 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C PRO E 286 " 0.050 5.00e-02 4.00e+02 7.47e-02 8.93e+00 pdb=" N PRO E 287 " -0.129 5.00e-02 4.00e+02 pdb=" CA PRO E 287 " 0.042 5.00e-02 4.00e+02 pdb=" CD PRO E 287 " 0.037 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C PRO A 286 " 0.050 5.00e-02 4.00e+02 7.46e-02 8.91e+00 pdb=" N PRO A 287 " -0.129 5.00e-02 4.00e+02 pdb=" CA PRO A 287 " 0.042 5.00e-02 4.00e+02 pdb=" CD PRO A 287 " 0.037 5.00e-02 4.00e+02 ... (remaining 2559 not shown) Histogram of nonbonded interaction distances: 2.10 - 2.60: 422 2.60 - 3.10: 10723 3.10 - 3.60: 17626 3.60 - 4.10: 22963 4.10 - 4.60: 36459 Nonbonded interactions: 88193 Sorted by model distance: nonbonded pdb=" HB THR D 262 " pdb=" HG1 THR D 262 " model vdw 2.103 1.816 nonbonded pdb=" HB THR E 262 " pdb=" HG1 THR E 262 " model vdw 2.105 1.816 nonbonded pdb=" HB THR C 262 " pdb=" HG1 THR C 262 " model vdw 2.105 1.816 nonbonded pdb=" HB THR B 262 " pdb=" HG1 THR B 262 " model vdw 2.119 1.816 nonbonded pdb=" HB2 GLU F 258 " pdb=" HG3 GLU F 258 " model vdw 2.133 1.952 ... (remaining 88188 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' selection = chain 'D' selection = chain 'E' selection = chain 'F' selection = chain 'G' } 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: 1.020 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: 0.350 Extract box with map and model: 4.320 Check model and map are aligned: 0.190 Set scattering table: 0.120 Process input model: 37.620 Find NCS groups from input model: 0.820 Set up NCS constraints: 0.070 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:10.860 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 55.380 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8496 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 : 0.016 0.075 13853 Z= 1.029 Angle : 1.063 11.313 18851 Z= 0.565 Chirality : 0.067 0.276 2051 Planarity : 0.008 0.075 2555 Dihedral : 14.069 74.966 5194 Min Nonbonded Distance : 2.430 Molprobity Statistics. All-atom Clashscore : 5.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.32 % Favored : 96.68 % Rotamer: Outliers : 0.00 % Allowed : 0.51 % Favored : 99.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 5.88 % 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: 2.06 (0.20), residues: 1715 helix: 1.67 (0.14), residues: 1204 sheet: None (None), residues: 0 loop : 0.86 (0.30), residues: 511 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.004 TRP C 156 HIS 0.008 0.004 HIS D 216 PHE 0.051 0.006 PHE F 130 TYR 0.029 0.006 TYR G 264 ARG 0.017 0.002 ARG E 256 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3430 Ramachandran restraints generated. 1715 Oldfield, 0 Emsley, 1715 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3430 Ramachandran restraints generated. 1715 Oldfield, 0 Emsley, 1715 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 373 residues out of total 1386 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 373 time to evaluate : 1.763 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 373 average time/residue: 1.7058 time to fit residues: 678.4305 Evaluate side-chains 250 residues out of total 1386 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 250 time to evaluate : 1.661 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 2.1648 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 168 random chunks: chunk 141 optimal weight: 2.9990 chunk 127 optimal weight: 0.8980 chunk 70 optimal weight: 0.7980 chunk 43 optimal weight: 2.9990 chunk 85 optimal weight: 0.8980 chunk 68 optimal weight: 6.9990 chunk 131 optimal weight: 1.9990 chunk 50 optimal weight: 7.9990 chunk 80 optimal weight: 1.9990 chunk 98 optimal weight: 9.9990 chunk 152 optimal weight: 0.9990 overall best weight: 1.1184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 48 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 55 ASN A 254 GLN ** B 48 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 254 GLN C 11 GLN ** C 48 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 239 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 48 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 55 ASN ** E 48 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 245 GLN E 254 GLN ** F 48 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 245 GLN F 265 ASN ** G 48 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 55 ASN G 245 GLN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8431 moved from start: 0.1814 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.025 13853 Z= 0.159 Angle : 0.507 7.459 18851 Z= 0.264 Chirality : 0.034 0.116 2051 Planarity : 0.005 0.065 2555 Dihedral : 4.060 15.630 1883 Min Nonbonded Distance : 2.037 Molprobity Statistics. All-atom Clashscore : 13.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.50 % Favored : 96.50 % Rotamer: Outliers : 1.80 % Allowed : 11.26 % Favored : 86.94 % 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: 4.31 (0.20), residues: 1715 helix: 3.62 (0.14), residues: 1190 sheet: None (None), residues: 0 loop : 1.01 (0.31), residues: 525 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP A 156 HIS 0.004 0.001 HIS A 216 PHE 0.015 0.002 PHE C 152 TYR 0.016 0.002 TYR G 236 ARG 0.003 0.000 ARG G 234 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3430 Ramachandran restraints generated. 1715 Oldfield, 0 Emsley, 1715 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3430 Ramachandran restraints generated. 1715 Oldfield, 0 Emsley, 1715 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 341 residues out of total 1386 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 316 time to evaluate : 1.733 Fit side-chains revert: symmetry clash outliers start: 25 outliers final: 12 residues processed: 331 average time/residue: 1.4383 time to fit residues: 513.9211 Evaluate side-chains 287 residues out of total 1386 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 275 time to evaluate : 1.658 Switching outliers to nearest non-outliers outliers start: 12 outliers final: 8 residues processed: 4 average time/residue: 1.2164 time to fit residues: 7.4692 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 168 random chunks: chunk 84 optimal weight: 0.5980 chunk 47 optimal weight: 3.9990 chunk 126 optimal weight: 2.9990 chunk 103 optimal weight: 0.0980 chunk 42 optimal weight: 5.9990 chunk 152 optimal weight: 1.9990 chunk 165 optimal weight: 0.9980 chunk 136 optimal weight: 8.9990 chunk 151 optimal weight: 6.9990 chunk 52 optimal weight: 6.9990 chunk 122 optimal weight: 0.9980 overall best weight: 0.9382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 48 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 265 ASN B 11 GLN ** B 48 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 254 GLN ** B 265 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 48 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 239 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 254 GLN C 265 ASN ** D 48 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 55 ASN ** E 48 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 254 GLN E 265 ASN ** F 48 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 265 ASN ** G 48 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8407 moved from start: 0.2222 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.024 13853 Z= 0.132 Angle : 0.434 5.682 18851 Z= 0.222 Chirality : 0.033 0.123 2051 Planarity : 0.004 0.051 2555 Dihedral : 3.521 11.708 1883 Min Nonbonded Distance : 2.086 Molprobity Statistics. All-atom Clashscore : 13.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.56 % Favored : 96.44 % Rotamer: Outliers : 2.16 % Allowed : 12.55 % Favored : 85.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 4.79 (0.21), residues: 1715 helix: 3.93 (0.14), residues: 1232 sheet: None (None), residues: 0 loop : 1.06 (0.32), residues: 483 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP B 156 HIS 0.003 0.001 HIS B 216 PHE 0.014 0.002 PHE C 152 TYR 0.011 0.001 TYR G 236 ARG 0.003 0.000 ARG C 234 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3430 Ramachandran restraints generated. 1715 Oldfield, 0 Emsley, 1715 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3430 Ramachandran restraints generated. 1715 Oldfield, 0 Emsley, 1715 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 330 residues out of total 1386 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 300 time to evaluate : 1.657 Fit side-chains revert: symmetry clash outliers start: 30 outliers final: 19 residues processed: 315 average time/residue: 1.4834 time to fit residues: 503.1200 Evaluate side-chains 293 residues out of total 1386 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 274 time to evaluate : 1.722 Switching outliers to nearest non-outliers outliers start: 19 outliers final: 12 residues processed: 7 average time/residue: 0.7486 time to fit residues: 8.1006 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 168 random chunks: chunk 151 optimal weight: 3.9990 chunk 114 optimal weight: 5.9990 chunk 79 optimal weight: 2.9990 chunk 16 optimal weight: 10.0000 chunk 72 optimal weight: 8.9990 chunk 102 optimal weight: 0.8980 chunk 153 optimal weight: 2.9990 chunk 162 optimal weight: 5.9990 chunk 80 optimal weight: 0.1980 chunk 145 optimal weight: 8.9990 chunk 43 optimal weight: 2.9990 overall best weight: 2.0186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 48 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 68 GLN A 265 ASN ** B 48 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 254 GLN ** B 265 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 48 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 254 GLN C 265 ASN ** D 48 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 48 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 254 GLN E 265 ASN F 48 GLN F 265 ASN ** G 48 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8434 moved from start: 0.2253 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.021 13853 Z= 0.208 Angle : 0.468 5.527 18851 Z= 0.243 Chirality : 0.035 0.117 2051 Planarity : 0.004 0.051 2555 Dihedral : 3.548 11.547 1883 Min Nonbonded Distance : 2.075 Molprobity Statistics. All-atom Clashscore : 13.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.56 % Favored : 96.44 % Rotamer: Outliers : 3.39 % Allowed : 12.99 % Favored : 83.62 % 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: 5.08 (0.21), residues: 1715 helix: 4.18 (0.14), residues: 1190 sheet: None (None), residues: 0 loop : 1.36 (0.32), residues: 525 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP E 156 HIS 0.006 0.002 HIS B 216 PHE 0.019 0.002 PHE B 152 TYR 0.014 0.002 TYR G 236 ARG 0.003 0.000 ARG C 67 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3430 Ramachandran restraints generated. 1715 Oldfield, 0 Emsley, 1715 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3430 Ramachandran restraints generated. 1715 Oldfield, 0 Emsley, 1715 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 310 residues out of total 1386 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 47 poor density : 263 time to evaluate : 1.643 Fit side-chains revert: symmetry clash outliers start: 47 outliers final: 26 residues processed: 290 average time/residue: 1.5154 time to fit residues: 472.9326 Evaluate side-chains 289 residues out of total 1386 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 263 time to evaluate : 1.604 Switching outliers to nearest non-outliers outliers start: 26 outliers final: 17 residues processed: 9 average time/residue: 0.7677 time to fit residues: 10.0126 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 168 random chunks: chunk 135 optimal weight: 7.9990 chunk 92 optimal weight: 2.9990 chunk 2 optimal weight: 0.9980 chunk 120 optimal weight: 10.0000 chunk 67 optimal weight: 4.9990 chunk 138 optimal weight: 6.9990 chunk 112 optimal weight: 10.0000 chunk 0 optimal weight: 10.0000 chunk 82 optimal weight: 5.9990 chunk 145 optimal weight: 6.9990 chunk 40 optimal weight: 10.0000 overall best weight: 4.3988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 48 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 265 ASN ** B 48 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 254 GLN ** B 265 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 48 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 254 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 265 ASN ** D 48 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 48 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 254 GLN E 265 ASN F 265 ASN ** G 48 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8475 moved from start: 0.2161 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.037 13853 Z= 0.406 Angle : 0.605 5.978 18851 Z= 0.316 Chirality : 0.041 0.117 2051 Planarity : 0.006 0.065 2555 Dihedral : 3.921 14.824 1883 Min Nonbonded Distance : 2.030 Molprobity Statistics. All-atom Clashscore : 14.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.38 % Favored : 96.62 % Rotamer: Outliers : 3.68 % Allowed : 15.01 % Favored : 81.31 % 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: 4.32 (0.21), residues: 1715 helix: 3.58 (0.14), residues: 1190 sheet: None (None), residues: 0 loop : 1.15 (0.32), residues: 525 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP E 156 HIS 0.009 0.003 HIS B 216 PHE 0.024 0.003 PHE B 152 TYR 0.016 0.003 TYR G 236 ARG 0.005 0.001 ARG C 67 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3430 Ramachandran restraints generated. 1715 Oldfield, 0 Emsley, 1715 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3430 Ramachandran restraints generated. 1715 Oldfield, 0 Emsley, 1715 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 303 residues out of total 1386 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 51 poor density : 252 time to evaluate : 1.720 Fit side-chains revert: symmetry clash outliers start: 51 outliers final: 32 residues processed: 284 average time/residue: 1.5668 time to fit residues: 478.4567 Evaluate side-chains 279 residues out of total 1386 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 247 time to evaluate : 1.580 Switching outliers to nearest non-outliers outliers start: 32 outliers final: 21 residues processed: 11 average time/residue: 0.7759 time to fit residues: 11.6988 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 168 random chunks: chunk 54 optimal weight: 0.7980 chunk 146 optimal weight: 0.9990 chunk 32 optimal weight: 1.9990 chunk 95 optimal weight: 1.9990 chunk 40 optimal weight: 7.9990 chunk 162 optimal weight: 3.9990 chunk 134 optimal weight: 5.9990 chunk 75 optimal weight: 0.7980 chunk 13 optimal weight: 5.9990 chunk 53 optimal weight: 3.9990 chunk 85 optimal weight: 3.9990 overall best weight: 1.3186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 48 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 265 ASN ** B 48 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 254 GLN ** B 265 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 48 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 254 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 265 ASN ** D 48 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 55 ASN ** E 48 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 254 GLN F 265 ASN ** G 48 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8424 moved from start: 0.2379 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.016 13853 Z= 0.145 Angle : 0.436 4.983 18851 Z= 0.227 Chirality : 0.033 0.122 2051 Planarity : 0.004 0.045 2555 Dihedral : 3.525 11.923 1883 Min Nonbonded Distance : 2.102 Molprobity Statistics. All-atom Clashscore : 14.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.27 % Favored : 96.73 % Rotamer: Outliers : 3.17 % Allowed : 16.31 % Favored : 80.52 % 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: 4.99 (0.21), residues: 1715 helix: 4.14 (0.14), residues: 1190 sheet: None (None), residues: 0 loop : 1.25 (0.32), residues: 525 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP E 156 HIS 0.004 0.001 HIS F 216 PHE 0.016 0.002 PHE C 152 TYR 0.013 0.001 TYR E 236 ARG 0.004 0.000 ARG F 234 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3430 Ramachandran restraints generated. 1715 Oldfield, 0 Emsley, 1715 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3430 Ramachandran restraints generated. 1715 Oldfield, 0 Emsley, 1715 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 313 residues out of total 1386 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 44 poor density : 269 time to evaluate : 1.725 Fit side-chains revert: symmetry clash outliers start: 44 outliers final: 23 residues processed: 297 average time/residue: 1.4993 time to fit residues: 479.5571 Evaluate side-chains 287 residues out of total 1386 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 264 time to evaluate : 1.610 Switching outliers to nearest non-outliers outliers start: 23 outliers final: 16 residues processed: 7 average time/residue: 0.6510 time to fit residues: 7.4878 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 168 random chunks: chunk 156 optimal weight: 8.9990 chunk 18 optimal weight: 0.9980 chunk 92 optimal weight: 0.2980 chunk 118 optimal weight: 3.9990 chunk 91 optimal weight: 3.9990 chunk 136 optimal weight: 7.9990 chunk 90 optimal weight: 5.9990 chunk 161 optimal weight: 0.9980 chunk 101 optimal weight: 8.9990 chunk 98 optimal weight: 0.2980 chunk 74 optimal weight: 0.0870 overall best weight: 0.5358 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 48 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 48 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 254 GLN ** B 265 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 48 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 254 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 265 ASN ** D 48 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 48 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 254 GLN F 265 ASN ** G 48 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8376 moved from start: 0.2687 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.001 0.016 13853 Z= 0.098 Angle : 0.381 4.667 18851 Z= 0.195 Chirality : 0.032 0.122 2051 Planarity : 0.003 0.031 2555 Dihedral : 3.125 11.751 1883 Min Nonbonded Distance : 2.144 Molprobity Statistics. All-atom Clashscore : 15.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.45 % Favored : 97.55 % Rotamer: Outliers : 1.88 % Allowed : 17.60 % Favored : 80.52 % 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: 5.51 (0.21), residues: 1715 helix: 4.53 (0.14), residues: 1197 sheet: None (None), residues: 0 loop : 1.40 (0.32), residues: 518 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 156 HIS 0.002 0.001 HIS F 216 PHE 0.012 0.001 PHE G 152 TYR 0.010 0.001 TYR E 236 ARG 0.005 0.000 ARG F 234 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3430 Ramachandran restraints generated. 1715 Oldfield, 0 Emsley, 1715 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3430 Ramachandran restraints generated. 1715 Oldfield, 0 Emsley, 1715 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 323 residues out of total 1386 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 297 time to evaluate : 1.653 Fit side-chains outliers start: 26 outliers final: 13 residues processed: 313 average time/residue: 1.4586 time to fit residues: 492.8355 Evaluate side-chains 297 residues out of total 1386 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 284 time to evaluate : 1.601 Switching outliers to nearest non-outliers outliers start: 13 outliers final: 10 residues processed: 3 average time/residue: 0.1179 time to fit residues: 2.7836 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 168 random chunks: chunk 100 optimal weight: 6.9990 chunk 64 optimal weight: 4.9990 chunk 96 optimal weight: 10.0000 chunk 48 optimal weight: 10.0000 chunk 31 optimal weight: 0.9990 chunk 102 optimal weight: 0.9990 chunk 110 optimal weight: 0.9990 chunk 80 optimal weight: 0.0000 chunk 15 optimal weight: 6.9990 chunk 127 optimal weight: 1.9990 chunk 147 optimal weight: 1.9990 overall best weight: 0.9992 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 48 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 48 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 254 GLN ** B 265 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 48 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 254 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 265 ASN ** D 48 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 48 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 254 GLN F 254 GLN F 265 ASN ** G 48 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8391 moved from start: 0.2696 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.018 13853 Z= 0.125 Angle : 0.401 5.758 18851 Z= 0.205 Chirality : 0.032 0.119 2051 Planarity : 0.004 0.032 2555 Dihedral : 3.117 11.224 1883 Min Nonbonded Distance : 2.146 Molprobity Statistics. All-atom Clashscore : 15.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.45 % Favored : 97.55 % Rotamer: Outliers : 1.80 % Allowed : 18.11 % Favored : 80.09 % 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: 5.55 (0.21), residues: 1715 helix: 4.53 (0.14), residues: 1197 sheet: None (None), residues: 0 loop : 1.52 (0.32), residues: 518 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A 156 HIS 0.003 0.001 HIS F 216 PHE 0.016 0.002 PHE C 152 TYR 0.012 0.001 TYR E 236 ARG 0.003 0.000 ARG A 234 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3430 Ramachandran restraints generated. 1715 Oldfield, 0 Emsley, 1715 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3430 Ramachandran restraints generated. 1715 Oldfield, 0 Emsley, 1715 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 308 residues out of total 1386 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 283 time to evaluate : 1.448 Fit side-chains outliers start: 25 outliers final: 14 residues processed: 297 average time/residue: 1.5131 time to fit residues: 483.7260 Evaluate side-chains 296 residues out of total 1386 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 282 time to evaluate : 1.745 Switching outliers to nearest non-outliers outliers start: 14 outliers final: 12 residues processed: 3 average time/residue: 0.6277 time to fit residues: 4.5080 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 168 random chunks: chunk 155 optimal weight: 9.9990 chunk 141 optimal weight: 3.9990 chunk 150 optimal weight: 1.9990 chunk 90 optimal weight: 3.9990 chunk 65 optimal weight: 3.9990 chunk 118 optimal weight: 2.9990 chunk 46 optimal weight: 2.9990 chunk 136 optimal weight: 4.9990 chunk 142 optimal weight: 2.9990 chunk 99 optimal weight: 6.9990 chunk 159 optimal weight: 3.9990 overall best weight: 2.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 48 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 265 ASN ** B 48 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 254 GLN ** B 265 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 48 GLN ** C 254 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 265 ASN ** D 48 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 48 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 254 GLN F 254 GLN F 265 ASN ** G 48 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8445 moved from start: 0.2458 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.027 13853 Z= 0.279 Angle : 0.508 4.523 18851 Z= 0.264 Chirality : 0.037 0.118 2051 Planarity : 0.005 0.046 2555 Dihedral : 3.472 12.233 1883 Min Nonbonded Distance : 2.042 Molprobity Statistics. All-atom Clashscore : 14.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.92 % Favored : 97.08 % Rotamer: Outliers : 2.02 % Allowed : 17.75 % Favored : 80.23 % 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: 4.93 (0.21), residues: 1715 helix: 4.07 (0.14), residues: 1197 sheet: None (None), residues: 0 loop : 1.24 (0.32), residues: 518 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP E 156 HIS 0.007 0.002 HIS B 216 PHE 0.022 0.003 PHE B 152 TYR 0.013 0.002 TYR E 236 ARG 0.005 0.001 ARG C 67 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3430 Ramachandran restraints generated. 1715 Oldfield, 0 Emsley, 1715 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3430 Ramachandran restraints generated. 1715 Oldfield, 0 Emsley, 1715 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 298 residues out of total 1386 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 270 time to evaluate : 1.754 Fit side-chains revert: symmetry clash outliers start: 28 outliers final: 19 residues processed: 285 average time/residue: 1.5778 time to fit residues: 484.1524 Evaluate side-chains 285 residues out of total 1386 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 266 time to evaluate : 1.758 Switching outliers to nearest non-outliers outliers start: 19 outliers final: 11 residues processed: 8 average time/residue: 1.0049 time to fit residues: 11.2751 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 168 random chunks: chunk 97 optimal weight: 5.9990 chunk 75 optimal weight: 5.9990 chunk 110 optimal weight: 1.9990 chunk 167 optimal weight: 0.9980 chunk 154 optimal weight: 5.9990 chunk 133 optimal weight: 1.9990 chunk 13 optimal weight: 4.9990 chunk 102 optimal weight: 0.7980 chunk 81 optimal weight: 0.8980 chunk 105 optimal weight: 2.9990 chunk 141 optimal weight: 6.9990 overall best weight: 1.3384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 48 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 265 ASN ** B 48 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 254 GLN ** B 265 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 254 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 48 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 55 ASN ** E 48 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 254 GLN F 254 GLN F 265 ASN ** G 48 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8416 moved from start: 0.2584 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.022 13853 Z= 0.156 Angle : 0.432 4.532 18851 Z= 0.223 Chirality : 0.033 0.120 2051 Planarity : 0.004 0.039 2555 Dihedral : 3.296 11.408 1883 Min Nonbonded Distance : 2.102 Molprobity Statistics. All-atom Clashscore : 15.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.80 % Favored : 97.20 % Rotamer: Outliers : 1.30 % Allowed : 18.76 % Favored : 79.94 % 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: 5.26 (0.21), residues: 1715 helix: 4.32 (0.14), residues: 1190 sheet: None (None), residues: 0 loop : 1.44 (0.32), residues: 525 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP D 156 HIS 0.004 0.001 HIS B 216 PHE 0.017 0.002 PHE C 152 TYR 0.011 0.001 TYR E 236 ARG 0.004 0.000 ARG F 234 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3430 Ramachandran restraints generated. 1715 Oldfield, 0 Emsley, 1715 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3430 Ramachandran restraints generated. 1715 Oldfield, 0 Emsley, 1715 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 290 residues out of total 1386 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 272 time to evaluate : 1.711 Fit side-chains outliers start: 18 outliers final: 13 residues processed: 285 average time/residue: 1.5908 time to fit residues: 487.4472 Evaluate side-chains 283 residues out of total 1386 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 270 time to evaluate : 2.082 Switching outliers to nearest non-outliers outliers start: 13 outliers final: 11 residues processed: 2 average time/residue: 0.7321 time to fit residues: 4.0255 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 168 random chunks: chunk 40 optimal weight: 10.0000 chunk 122 optimal weight: 0.8980 chunk 19 optimal weight: 4.9990 chunk 37 optimal weight: 3.9990 chunk 133 optimal weight: 0.9980 chunk 55 optimal weight: 0.7980 chunk 137 optimal weight: 8.9990 chunk 16 optimal weight: 10.0000 chunk 24 optimal weight: 10.0000 chunk 117 optimal weight: 5.9990 chunk 7 optimal weight: 0.9980 overall best weight: 1.5382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 48 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 265 ASN ** B 48 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 254 GLN ** B 265 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 254 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 265 ASN ** D 48 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 55 ASN ** E 48 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 254 GLN F 254 GLN F 265 ASN ** G 48 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3342 r_free = 0.3342 target = 0.092202 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3160 r_free = 0.3160 target = 0.083164 restraints weight = 22069.671| |-----------------------------------------------------------------------------| r_work (start): 0.3157 rms_B_bonded: 1.10 r_work: 0.3066 rms_B_bonded: 1.46 restraints_weight: 0.5000 r_work: 0.2975 rms_B_bonded: 2.57 restraints_weight: 0.2500 r_work (final): 0.2975 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8619 moved from start: 0.2595 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.021 13853 Z= 0.167 Angle : 0.434 4.679 18851 Z= 0.224 Chirality : 0.034 0.120 2051 Planarity : 0.004 0.038 2555 Dihedral : 3.275 11.012 1883 Min Nonbonded Distance : 2.106 Molprobity Statistics. All-atom Clashscore : 14.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.68 % Favored : 97.32 % Rotamer: Outliers : 1.37 % Allowed : 18.76 % Favored : 79.87 % 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: 5.19 (0.21), residues: 1715 helix: 4.30 (0.14), residues: 1197 sheet: None (None), residues: 0 loop : 1.25 (0.31), residues: 518 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP D 156 HIS 0.005 0.001 HIS F 216 PHE 0.018 0.002 PHE C 152 TYR 0.012 0.001 TYR E 236 ARG 0.004 0.000 ARG G 221 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 7107.00 seconds wall clock time: 128 minutes 17.08 seconds (7697.08 seconds total)