Starting phenix.real_space_refine on Thu Jul 18 19:05:46 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8qct_18335/07_2024/8qct_18335_neut.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8qct_18335/07_2024/8qct_18335.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.6 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8qct_18335/07_2024/8qct_18335.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8qct_18335/07_2024/8qct_18335.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8qct_18335/07_2024/8qct_18335_neut.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8qct_18335/07_2024/8qct_18335_neut.cif" } resolution = 2.6 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= 0.005 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 2167 2.51 5 N 505 2.21 5 O 569 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A GLU 136": "OE1" <-> "OE2" Residue "A ASP 169": "OD1" <-> "OD2" Residue "A GLU 233": "OE1" <-> "OE2" Residue "A TYR 279": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 362": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 398": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 447": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.01s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5388/modules/chem_data/mon_lib" Total number of atoms: 3259 Number of models: 1 Model: "" Number of chains: 2 Chain: "A" Number of atoms: 3252 Number of conformers: 1 Conformer: "" Number of residues, atoms: 418, 3252 Classifications: {'peptide': 418} Link IDs: {'PTRANS': 17, 'TRANS': 400} Chain: "A" Number of atoms: 7 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 7 Unusual residues: {'CHT': 1} Classifications: {'undetermined': 1} Time building chain proxies: 2.46, per 1000 atoms: 0.75 Number of scatterers: 3259 At special positions: 0 Unit cell: (81.366, 56.154, 65.322, 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 569 8.00 N 505 7.00 C 2167 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 1.45 Conformation dependent library (CDL) restraints added in 574.9 milliseconds 832 Ramachandran restraints generated. 416 Oldfield, 0 Emsley, 416 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 766 Finding SS restraints... Secondary structure from input PDB file: 19 helices and 0 sheets defined 85.6% alpha, 0.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.29 Creating SS restraints... Processing helix chain 'A' and resid 105 through 127 removed outlier: 4.093A pdb=" N VAL A 109 " --> pdb=" O PRO A 105 " (cutoff:3.500A) removed outlier: 3.778A pdb=" N ILE A 126 " --> pdb=" O ALA A 122 " (cutoff:3.500A) Processing helix chain 'A' and resid 128 through 130 No H-bonds generated for 'chain 'A' and resid 128 through 130' Processing helix chain 'A' and resid 131 through 140 Processing helix chain 'A' and resid 142 through 171 removed outlier: 3.712A pdb=" N ILE A 146 " --> pdb=" O THR A 142 " (cutoff:3.500A) removed outlier: 3.606A pdb=" N SER A 150 " --> pdb=" O ILE A 146 " (cutoff:3.500A) removed outlier: 5.158A pdb=" N TYR A 153 " --> pdb=" O LEU A 149 " (cutoff:3.500A) removed outlier: 4.356A pdb=" N MET A 154 " --> pdb=" O SER A 150 " (cutoff:3.500A) removed outlier: 3.522A pdb=" N TYR A 157 " --> pdb=" O TYR A 153 " (cutoff:3.500A) removed outlier: 3.738A pdb=" N VAL A 158 " --> pdb=" O MET A 154 " (cutoff:3.500A) Proline residue: A 159 - end of helix removed outlier: 5.022A pdb=" N PHE A 162 " --> pdb=" O VAL A 158 " (cutoff:3.500A) Proline residue: A 163 - end of helix Processing helix chain 'A' and resid 172 through 193 removed outlier: 3.647A pdb=" N THR A 176 " --> pdb=" O GLY A 172 " (cutoff:3.500A) removed outlier: 3.556A pdb=" N GLY A 193 " --> pdb=" O TRP A 189 " (cutoff:3.500A) Processing helix chain 'A' and resid 199 through 215 removed outlier: 3.803A pdb=" N VAL A 215 " --> pdb=" O SER A 211 " (cutoff:3.500A) Processing helix chain 'A' and resid 219 through 229 removed outlier: 4.190A pdb=" N ARG A 223 " --> pdb=" O GLY A 219 " (cutoff:3.500A) Processing helix chain 'A' and resid 233 through 260 removed outlier: 3.614A pdb=" N ASN A 245 " --> pdb=" O ALA A 241 " (cutoff:3.500A) removed outlier: 3.506A pdb=" N GLN A 246 " --> pdb=" O VAL A 242 " (cutoff:3.500A) Proline residue: A 256 - end of helix Processing helix chain 'A' and resid 266 through 296 Processing helix chain 'A' and resid 305 through 314 Processing helix chain 'A' and resid 320 through 329 Processing helix chain 'A' and resid 331 through 363 removed outlier: 5.124A pdb=" N ASN A 356 " --> pdb=" O SER A 352 " (cutoff:3.500A) removed outlier: 5.560A pdb=" N GLN A 357 " --> pdb=" O THR A 353 " (cutoff:3.500A) removed outlier: 3.775A pdb=" N TYR A 362 " --> pdb=" O MET A 358 " (cutoff:3.500A) Processing helix chain 'A' and resid 366 through 388 Processing helix chain 'A' and resid 397 through 420 Processing helix chain 'A' and resid 421 through 423 No H-bonds generated for 'chain 'A' and resid 421 through 423' Processing helix chain 'A' and resid 424 through 440 removed outlier: 3.615A pdb=" N VAL A 428 " --> pdb=" O TYR A 424 " (cutoff:3.500A) removed outlier: 3.583A pdb=" N PHE A 438 " --> pdb=" O VAL A 434 " (cutoff:3.500A) Processing helix chain 'A' and resid 442 through 450 removed outlier: 3.564A pdb=" N PHE A 447 " --> pdb=" O LEU A 443 " (cutoff:3.500A) Processing helix chain 'A' and resid 458 through 489 removed outlier: 3.556A pdb=" N SER A 462 " --> pdb=" O SER A 458 " (cutoff:3.500A) Processing helix chain 'A' and resid 489 through 510 removed outlier: 3.614A pdb=" N GLY A 493 " --> pdb=" O GLY A 489 " (cutoff:3.500A) 252 hydrogen bonds defined for protein. 756 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: 0.81 Time building geometry restraints manager: 1.51 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.34: 967 1.34 - 1.46: 779 1.46 - 1.58: 1566 1.58 - 1.69: 0 1.69 - 1.81: 28 Bond restraints: 3340 Sorted by residual: bond pdb=" N GLU A 233 " pdb=" CA GLU A 233 " ideal model delta sigma weight residual 1.455 1.487 -0.031 1.33e-02 5.65e+03 5.56e+00 bond pdb=" CG ASN A 265 " pdb=" ND2 ASN A 265 " ideal model delta sigma weight residual 1.328 1.351 -0.023 2.10e-02 2.27e+03 1.20e+00 bond pdb=" C LEU A 220 " pdb=" N PRO A 221 " ideal model delta sigma weight residual 1.334 1.348 -0.013 1.51e-02 4.39e+03 7.94e-01 bond pdb=" C TYR A 455 " pdb=" N PRO A 456 " ideal model delta sigma weight residual 1.334 1.353 -0.019 2.34e-02 1.83e+03 6.80e-01 bond pdb=" CB GLU A 298 " pdb=" CG GLU A 298 " ideal model delta sigma weight residual 1.520 1.542 -0.022 3.00e-02 1.11e+03 5.21e-01 ... (remaining 3335 not shown) Histogram of bond angle deviations from ideal: 100.38 - 107.10: 88 107.10 - 113.83: 1891 113.83 - 120.55: 1410 120.55 - 127.27: 1134 127.27 - 133.99: 33 Bond angle restraints: 4556 Sorted by residual: angle pdb=" CB GLU A 298 " pdb=" CG GLU A 298 " pdb=" CD GLU A 298 " ideal model delta sigma weight residual 112.60 116.60 -4.00 1.70e+00 3.46e-01 5.55e+00 angle pdb=" CA TYR A 117 " pdb=" CB TYR A 117 " pdb=" CG TYR A 117 " ideal model delta sigma weight residual 113.90 117.89 -3.99 1.80e+00 3.09e-01 4.91e+00 angle pdb=" N PRO A 256 " pdb=" CA PRO A 256 " pdb=" C PRO A 256 " ideal model delta sigma weight residual 110.70 113.40 -2.70 1.22e+00 6.72e-01 4.91e+00 angle pdb=" CA PRO A 256 " pdb=" C PRO A 256 " pdb=" N PRO A 257 " ideal model delta sigma weight residual 117.93 120.23 -2.30 1.20e+00 6.94e-01 3.66e+00 angle pdb=" CA GLY A 219 " pdb=" C GLY A 219 " pdb=" N LEU A 220 " ideal model delta sigma weight residual 118.41 116.05 2.36 1.29e+00 6.01e-01 3.34e+00 ... (remaining 4551 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.44: 1691 17.44 - 34.89: 171 34.89 - 52.33: 48 52.33 - 69.77: 11 69.77 - 87.22: 3 Dihedral angle restraints: 1924 sinusoidal: 721 harmonic: 1203 Sorted by residual: dihedral pdb=" CA TYR A 117 " pdb=" C TYR A 117 " pdb=" N SER A 118 " pdb=" CA SER A 118 " ideal model delta harmonic sigma weight residual 180.00 164.09 15.91 0 5.00e+00 4.00e-02 1.01e+01 dihedral pdb=" CA GLU A 459 " pdb=" CB GLU A 459 " pdb=" CG GLU A 459 " pdb=" CD GLU A 459 " ideal model delta sinusoidal sigma weight residual -180.00 -120.35 -59.65 3 1.50e+01 4.44e-03 9.48e+00 dihedral pdb=" N LEU A 173 " pdb=" CA LEU A 173 " pdb=" CB LEU A 173 " pdb=" CG LEU A 173 " ideal model delta sinusoidal sigma weight residual -60.00 -117.25 57.25 3 1.50e+01 4.44e-03 9.43e+00 ... (remaining 1921 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.029: 360 0.029 - 0.059: 126 0.059 - 0.088: 40 0.088 - 0.118: 17 0.118 - 0.147: 1 Chirality restraints: 544 Sorted by residual: chirality pdb=" CA GLU A 233 " pdb=" N GLU A 233 " pdb=" C GLU A 233 " pdb=" CB GLU A 233 " both_signs ideal model delta sigma weight residual False 2.51 2.66 -0.15 2.00e-01 2.50e+01 5.42e-01 chirality pdb=" CA LEU A 220 " pdb=" N LEU A 220 " pdb=" C LEU A 220 " pdb=" CB LEU A 220 " both_signs ideal model delta sigma weight residual False 2.51 2.40 0.12 2.00e-01 2.50e+01 3.33e-01 chirality pdb=" CA PRO A 221 " pdb=" N PRO A 221 " pdb=" C PRO A 221 " pdb=" CB PRO A 221 " both_signs ideal model delta sigma weight residual False 2.72 2.61 0.11 2.00e-01 2.50e+01 3.19e-01 ... (remaining 541 not shown) Planarity restraints: 552 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C SER A 104 " -0.034 5.00e-02 4.00e+02 5.18e-02 4.30e+00 pdb=" N PRO A 105 " 0.090 5.00e-02 4.00e+02 pdb=" CA PRO A 105 " -0.027 5.00e-02 4.00e+02 pdb=" CD PRO A 105 " -0.029 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C PHE A 162 " -0.021 5.00e-02 4.00e+02 3.21e-02 1.64e+00 pdb=" N PRO A 163 " 0.055 5.00e-02 4.00e+02 pdb=" CA PRO A 163 " -0.016 5.00e-02 4.00e+02 pdb=" CD PRO A 163 " -0.018 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C PRO A 303 " 0.019 5.00e-02 4.00e+02 2.94e-02 1.39e+00 pdb=" N PRO A 304 " -0.051 5.00e-02 4.00e+02 pdb=" CA PRO A 304 " 0.015 5.00e-02 4.00e+02 pdb=" CD PRO A 304 " 0.016 5.00e-02 4.00e+02 ... (remaining 549 not shown) Histogram of nonbonded interaction distances: 2.20 - 2.74: 288 2.74 - 3.28: 3401 3.28 - 3.82: 5718 3.82 - 4.36: 6918 4.36 - 4.90: 11519 Nonbonded interactions: 27844 Sorted by model distance: nonbonded pdb=" O ILE A 415 " pdb=" OG1 THR A 419 " model vdw 2.202 2.440 nonbonded pdb=" OG SER A 350 " pdb=" OE1 GLN A 481 " model vdw 2.223 2.440 nonbonded pdb=" OD2 ASP A 169 " pdb=" OH TYR A 321 " model vdw 2.267 2.440 nonbonded pdb=" OH TYR A 128 " pdb=" OG1 THR A 203 " model vdw 2.273 2.440 nonbonded pdb=" O THR A 263 " pdb=" OG1 THR A 263 " model vdw 2.326 2.440 ... (remaining 27839 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. 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: 0.160 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: 0.120 Check model and map are aligned: 0.020 Set scattering table: 0.030 Process input model: 13.840 Find NCS groups from input model: 0.020 Set up NCS constraints: 0.010 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:13.170 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 27.380 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8202 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 3340 Z= 0.172 Angle : 0.494 5.535 4556 Z= 0.268 Chirality : 0.036 0.147 544 Planarity : 0.004 0.052 552 Dihedral : 15.836 87.215 1158 Min Nonbonded Distance : 2.202 Molprobity Statistics. All-atom Clashscore : 7.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.92 % Favored : 98.08 % Rotamer: Outliers : 0.00 % Allowed : 21.75 % Favored : 78.25 % 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: 0.55 (0.40), residues: 416 helix: 1.04 (0.28), residues: 331 sheet: None (None), residues: 0 loop : -2.24 (0.61), residues: 85 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP A 148 HIS 0.003 0.001 HIS A 145 PHE 0.010 0.001 PHE A 114 TYR 0.018 0.001 TYR A 117 ARG 0.007 0.001 ARG A 423 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 832 Ramachandran restraints generated. 416 Oldfield, 0 Emsley, 416 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 832 Ramachandran restraints generated. 416 Oldfield, 0 Emsley, 416 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 41 residues out of total 354 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 41 time to evaluate : 0.283 Fit side-chains revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 41 average time/residue: 1.1659 time to fit residues: 49.1573 Evaluate side-chains 39 residues out of total 354 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 39 time to evaluate : 0.306 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 41 random chunks: chunk 34 optimal weight: 1.9990 chunk 31 optimal weight: 3.9990 chunk 17 optimal weight: 1.9990 chunk 10 optimal weight: 3.9990 chunk 20 optimal weight: 2.9990 chunk 16 optimal weight: 5.9990 chunk 32 optimal weight: 3.9990 chunk 12 optimal weight: 0.7980 chunk 19 optimal weight: 0.8980 chunk 23 optimal weight: 0.8980 chunk 37 optimal weight: 0.8980 overall best weight: 1.0982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 124 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 273 ASN A 306 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8184 moved from start: 0.1039 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 3340 Z= 0.224 Angle : 0.549 5.950 4556 Z= 0.294 Chirality : 0.039 0.162 544 Planarity : 0.005 0.049 552 Dihedral : 4.475 31.237 450 Min Nonbonded Distance : 2.152 Molprobity Statistics. All-atom Clashscore : 7.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.64 % Favored : 97.36 % Rotamer: Outliers : 2.26 % Allowed : 20.06 % Favored : 77.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.86 (0.43), residues: 416 helix: 1.92 (0.29), residues: 336 sheet: None (None), residues: 0 loop : -1.85 (0.72), residues: 80 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 201 HIS 0.002 0.001 HIS A 145 PHE 0.015 0.002 PHE A 114 TYR 0.023 0.001 TYR A 117 ARG 0.005 0.001 ARG A 423 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 832 Ramachandran restraints generated. 416 Oldfield, 0 Emsley, 416 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 832 Ramachandran restraints generated. 416 Oldfield, 0 Emsley, 416 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 52 residues out of total 354 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 44 time to evaluate : 0.376 Fit side-chains revert: symmetry clash REVERT: A 266 ASP cc_start: 0.7372 (t0) cc_final: 0.7100 (t0) outliers start: 8 outliers final: 6 residues processed: 48 average time/residue: 1.1133 time to fit residues: 55.1879 Evaluate side-chains 47 residues out of total 354 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 41 time to evaluate : 0.344 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 112 LEU Chi-restraints excluded: chain A residue 211 SER Chi-restraints excluded: chain A residue 220 LEU Chi-restraints excluded: chain A residue 263 THR Chi-restraints excluded: chain A residue 299 LYS Chi-restraints excluded: chain A residue 326 ARG Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 41 random chunks: chunk 20 optimal weight: 8.9990 chunk 11 optimal weight: 1.9990 chunk 30 optimal weight: 1.9990 chunk 25 optimal weight: 2.9990 chunk 10 optimal weight: 0.6980 chunk 37 optimal weight: 0.6980 chunk 40 optimal weight: 0.8980 chunk 33 optimal weight: 4.9990 chunk 36 optimal weight: 0.6980 chunk 12 optimal weight: 0.7980 chunk 29 optimal weight: 0.6980 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 124 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8159 moved from start: 0.1335 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 3340 Z= 0.172 Angle : 0.507 5.890 4556 Z= 0.269 Chirality : 0.037 0.160 544 Planarity : 0.004 0.047 552 Dihedral : 4.413 30.226 450 Min Nonbonded Distance : 2.158 Molprobity Statistics. All-atom Clashscore : 7.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.40 % Favored : 97.60 % Rotamer: Outliers : 4.80 % Allowed : 17.80 % Favored : 77.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.11 (0.43), residues: 416 helix: 2.11 (0.28), residues: 337 sheet: None (None), residues: 0 loop : -1.85 (0.71), residues: 79 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 500 HIS 0.001 0.001 HIS A 145 PHE 0.012 0.001 PHE A 114 TYR 0.024 0.001 TYR A 117 ARG 0.006 0.000 ARG A 423 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 832 Ramachandran restraints generated. 416 Oldfield, 0 Emsley, 416 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 832 Ramachandran restraints generated. 416 Oldfield, 0 Emsley, 416 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 57 residues out of total 354 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 40 time to evaluate : 0.381 Fit side-chains revert: symmetry clash REVERT: A 196 GLN cc_start: 0.8017 (OUTLIER) cc_final: 0.6924 (mt0) REVERT: A 266 ASP cc_start: 0.7236 (t0) cc_final: 0.6748 (t0) REVERT: A 326 ARG cc_start: 0.6781 (OUTLIER) cc_final: 0.5861 (mtt180) REVERT: A 400 GLN cc_start: 0.8241 (OUTLIER) cc_final: 0.6677 (tm-30) outliers start: 17 outliers final: 7 residues processed: 50 average time/residue: 0.9582 time to fit residues: 49.8057 Evaluate side-chains 52 residues out of total 354 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 42 time to evaluate : 0.315 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 112 LEU Chi-restraints excluded: chain A residue 196 GLN Chi-restraints excluded: chain A residue 211 SER Chi-restraints excluded: chain A residue 220 LEU Chi-restraints excluded: chain A residue 263 THR Chi-restraints excluded: chain A residue 299 LYS Chi-restraints excluded: chain A residue 326 ARG Chi-restraints excluded: chain A residue 345 THR Chi-restraints excluded: chain A residue 400 GLN Chi-restraints excluded: chain A residue 426 ILE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 41 random chunks: chunk 36 optimal weight: 0.6980 chunk 28 optimal weight: 0.7980 chunk 19 optimal weight: 0.7980 chunk 4 optimal weight: 0.2980 chunk 17 optimal weight: 4.9990 chunk 25 optimal weight: 1.9990 chunk 37 optimal weight: 0.9980 chunk 39 optimal weight: 6.9990 chunk 35 optimal weight: 4.9990 chunk 10 optimal weight: 2.9990 chunk 33 optimal weight: 2.9990 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 124 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8156 moved from start: 0.1545 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 3340 Z= 0.171 Angle : 0.502 5.927 4556 Z= 0.267 Chirality : 0.037 0.164 544 Planarity : 0.004 0.044 552 Dihedral : 4.386 29.851 450 Min Nonbonded Distance : 2.164 Molprobity Statistics. All-atom Clashscore : 7.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.16 % Favored : 97.84 % Rotamer: Outliers : 3.11 % Allowed : 19.49 % Favored : 77.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.19 (0.43), residues: 416 helix: 2.18 (0.28), residues: 338 sheet: None (None), residues: 0 loop : -1.99 (0.69), residues: 78 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 500 HIS 0.002 0.001 HIS A 145 PHE 0.013 0.002 PHE A 114 TYR 0.025 0.001 TYR A 117 ARG 0.003 0.000 ARG A 423 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 832 Ramachandran restraints generated. 416 Oldfield, 0 Emsley, 416 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 832 Ramachandran restraints generated. 416 Oldfield, 0 Emsley, 416 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 54 residues out of total 354 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 43 time to evaluate : 0.384 Fit side-chains revert: symmetry clash REVERT: A 196 GLN cc_start: 0.8016 (OUTLIER) cc_final: 0.6892 (mt0) REVERT: A 266 ASP cc_start: 0.7321 (t0) cc_final: 0.6744 (t0) REVERT: A 326 ARG cc_start: 0.6839 (OUTLIER) cc_final: 0.5967 (mtt180) REVERT: A 400 GLN cc_start: 0.8242 (OUTLIER) cc_final: 0.6656 (tm-30) outliers start: 11 outliers final: 5 residues processed: 50 average time/residue: 1.0729 time to fit residues: 55.4953 Evaluate side-chains 52 residues out of total 354 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 44 time to evaluate : 0.355 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 112 LEU Chi-restraints excluded: chain A residue 196 GLN Chi-restraints excluded: chain A residue 211 SER Chi-restraints excluded: chain A residue 220 LEU Chi-restraints excluded: chain A residue 263 THR Chi-restraints excluded: chain A residue 326 ARG Chi-restraints excluded: chain A residue 400 GLN Chi-restraints excluded: chain A residue 426 ILE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 41 random chunks: chunk 22 optimal weight: 2.9990 chunk 0 optimal weight: 10.0000 chunk 29 optimal weight: 4.9990 chunk 16 optimal weight: 6.9990 chunk 33 optimal weight: 4.9990 chunk 27 optimal weight: 0.6980 chunk 20 optimal weight: 0.8980 chunk 35 optimal weight: 3.9990 chunk 10 optimal weight: 0.7980 chunk 13 optimal weight: 0.7980 chunk 7 optimal weight: 0.9990 overall best weight: 0.8382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 124 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8160 moved from start: 0.1667 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 3340 Z= 0.182 Angle : 0.511 5.977 4556 Z= 0.271 Chirality : 0.037 0.170 544 Planarity : 0.004 0.041 552 Dihedral : 4.415 30.522 450 Min Nonbonded Distance : 2.162 Molprobity Statistics. All-atom Clashscore : 7.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.40 % Favored : 97.60 % Rotamer: Outliers : 3.95 % Allowed : 18.64 % Favored : 77.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.28 (0.42), residues: 416 helix: 2.30 (0.28), residues: 331 sheet: None (None), residues: 0 loop : -1.82 (0.68), residues: 85 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 500 HIS 0.002 0.001 HIS A 145 PHE 0.015 0.002 PHE A 114 TYR 0.026 0.001 TYR A 117 ARG 0.005 0.001 ARG A 301 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 832 Ramachandran restraints generated. 416 Oldfield, 0 Emsley, 416 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 832 Ramachandran restraints generated. 416 Oldfield, 0 Emsley, 416 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 56 residues out of total 354 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 42 time to evaluate : 0.326 Fit side-chains revert: symmetry clash REVERT: A 196 GLN cc_start: 0.8028 (OUTLIER) cc_final: 0.6913 (mt0) REVERT: A 266 ASP cc_start: 0.7328 (t0) cc_final: 0.6668 (t0) REVERT: A 301 ARG cc_start: 0.6613 (ttm110) cc_final: 0.6086 (mtp180) REVERT: A 326 ARG cc_start: 0.6832 (OUTLIER) cc_final: 0.5967 (mtt180) REVERT: A 400 GLN cc_start: 0.8249 (OUTLIER) cc_final: 0.6660 (tm-30) outliers start: 14 outliers final: 8 residues processed: 51 average time/residue: 1.0104 time to fit residues: 53.5289 Evaluate side-chains 56 residues out of total 354 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 45 time to evaluate : 0.354 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 112 LEU Chi-restraints excluded: chain A residue 196 GLN Chi-restraints excluded: chain A residue 211 SER Chi-restraints excluded: chain A residue 220 LEU Chi-restraints excluded: chain A residue 263 THR Chi-restraints excluded: chain A residue 299 LYS Chi-restraints excluded: chain A residue 326 ARG Chi-restraints excluded: chain A residue 345 THR Chi-restraints excluded: chain A residue 400 GLN Chi-restraints excluded: chain A residue 426 ILE Chi-restraints excluded: chain A residue 515 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 41 random chunks: chunk 23 optimal weight: 0.3980 chunk 9 optimal weight: 2.9990 chunk 39 optimal weight: 4.9990 chunk 32 optimal weight: 3.9990 chunk 18 optimal weight: 1.9990 chunk 3 optimal weight: 0.6980 chunk 13 optimal weight: 0.0270 chunk 20 optimal weight: 3.9990 chunk 38 optimal weight: 1.9990 chunk 4 optimal weight: 0.8980 chunk 22 optimal weight: 0.8980 overall best weight: 0.5838 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 124 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8143 moved from start: 0.1790 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.030 3340 Z= 0.159 Angle : 0.493 5.982 4556 Z= 0.261 Chirality : 0.037 0.164 544 Planarity : 0.004 0.039 552 Dihedral : 4.311 28.626 450 Min Nonbonded Distance : 2.165 Molprobity Statistics. All-atom Clashscore : 7.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.16 % Favored : 97.84 % Rotamer: Outliers : 3.67 % Allowed : 19.21 % Favored : 77.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.28 (0.43), residues: 416 helix: 2.25 (0.28), residues: 339 sheet: None (None), residues: 0 loop : -2.08 (0.68), residues: 77 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 500 HIS 0.001 0.001 HIS A 145 PHE 0.012 0.001 PHE A 114 TYR 0.025 0.001 TYR A 117 ARG 0.004 0.001 ARG A 423 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 832 Ramachandran restraints generated. 416 Oldfield, 0 Emsley, 416 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 832 Ramachandran restraints generated. 416 Oldfield, 0 Emsley, 416 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 61 residues out of total 354 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 48 time to evaluate : 0.348 Fit side-chains revert: symmetry clash REVERT: A 201 TRP cc_start: 0.7732 (m100) cc_final: 0.5757 (p-90) REVERT: A 266 ASP cc_start: 0.7323 (t0) cc_final: 0.6629 (t0) REVERT: A 301 ARG cc_start: 0.6642 (ttm110) cc_final: 0.6102 (mtp180) REVERT: A 326 ARG cc_start: 0.6598 (ptm160) cc_final: 0.5838 (mtt180) REVERT: A 400 GLN cc_start: 0.8230 (OUTLIER) cc_final: 0.6644 (tm-30) REVERT: A 512 LYS cc_start: 0.6556 (mmtt) cc_final: 0.6223 (pptt) outliers start: 13 outliers final: 6 residues processed: 56 average time/residue: 1.0694 time to fit residues: 61.9311 Evaluate side-chains 51 residues out of total 354 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 44 time to evaluate : 0.339 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 112 LEU Chi-restraints excluded: chain A residue 263 THR Chi-restraints excluded: chain A residue 299 LYS Chi-restraints excluded: chain A residue 345 THR Chi-restraints excluded: chain A residue 400 GLN Chi-restraints excluded: chain A residue 426 ILE Chi-restraints excluded: chain A residue 515 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 41 random chunks: chunk 28 optimal weight: 0.6980 chunk 22 optimal weight: 0.9980 chunk 33 optimal weight: 3.9990 chunk 39 optimal weight: 3.9990 chunk 24 optimal weight: 6.9990 chunk 18 optimal weight: 0.9980 chunk 15 optimal weight: 0.7980 chunk 23 optimal weight: 0.7980 chunk 11 optimal weight: 3.9990 chunk 7 optimal weight: 0.7980 chunk 25 optimal weight: 1.9990 overall best weight: 0.8180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 124 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8155 moved from start: 0.1761 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 3340 Z= 0.182 Angle : 0.511 5.947 4556 Z= 0.272 Chirality : 0.037 0.170 544 Planarity : 0.004 0.038 552 Dihedral : 4.401 30.471 450 Min Nonbonded Distance : 2.163 Molprobity Statistics. All-atom Clashscore : 7.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.40 % Favored : 97.60 % Rotamer: Outliers : 3.39 % Allowed : 19.49 % Favored : 77.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.37 (0.42), residues: 416 helix: 2.37 (0.28), residues: 331 sheet: None (None), residues: 0 loop : -1.84 (0.67), residues: 85 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A 500 HIS 0.002 0.001 HIS A 145 PHE 0.015 0.002 PHE A 114 TYR 0.026 0.001 TYR A 117 ARG 0.007 0.001 ARG A 423 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 832 Ramachandran restraints generated. 416 Oldfield, 0 Emsley, 416 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 832 Ramachandran restraints generated. 416 Oldfield, 0 Emsley, 416 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 53 residues out of total 354 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 41 time to evaluate : 0.318 Fit side-chains revert: symmetry clash REVERT: A 201 TRP cc_start: 0.7719 (m100) cc_final: 0.5748 (p-90) REVERT: A 266 ASP cc_start: 0.7339 (t0) cc_final: 0.6673 (t0) REVERT: A 326 ARG cc_start: 0.6601 (ptm160) cc_final: 0.5900 (mtt180) REVERT: A 364 GLU cc_start: 0.6990 (OUTLIER) cc_final: 0.6664 (pp20) REVERT: A 400 GLN cc_start: 0.8252 (OUTLIER) cc_final: 0.6664 (tm-30) REVERT: A 512 LYS cc_start: 0.6387 (mmtt) cc_final: 0.6155 (pptt) outliers start: 12 outliers final: 9 residues processed: 49 average time/residue: 1.0303 time to fit residues: 52.3269 Evaluate side-chains 54 residues out of total 354 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 43 time to evaluate : 0.364 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 112 LEU Chi-restraints excluded: chain A residue 211 SER Chi-restraints excluded: chain A residue 220 LEU Chi-restraints excluded: chain A residue 263 THR Chi-restraints excluded: chain A residue 299 LYS Chi-restraints excluded: chain A residue 345 THR Chi-restraints excluded: chain A residue 364 GLU Chi-restraints excluded: chain A residue 400 GLN Chi-restraints excluded: chain A residue 426 ILE Chi-restraints excluded: chain A residue 448 GLU Chi-restraints excluded: chain A residue 515 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 41 random chunks: chunk 26 optimal weight: 2.9990 chunk 19 optimal weight: 4.9990 chunk 3 optimal weight: 0.7980 chunk 31 optimal weight: 1.9990 chunk 35 optimal weight: 5.9990 chunk 37 optimal weight: 2.9990 chunk 34 optimal weight: 0.9990 chunk 36 optimal weight: 0.9990 chunk 22 optimal weight: 0.9990 chunk 16 optimal weight: 7.9990 chunk 28 optimal weight: 1.9990 overall best weight: 1.1588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 124 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8174 moved from start: 0.1741 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 3340 Z= 0.218 Angle : 0.539 6.122 4556 Z= 0.287 Chirality : 0.039 0.181 544 Planarity : 0.005 0.037 552 Dihedral : 4.524 31.816 450 Min Nonbonded Distance : 2.152 Molprobity Statistics. All-atom Clashscore : 7.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.16 % Favored : 97.84 % Rotamer: Outliers : 4.24 % Allowed : 18.08 % Favored : 77.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.26 (0.43), residues: 416 helix: 2.29 (0.28), residues: 331 sheet: None (None), residues: 0 loop : -1.84 (0.68), residues: 85 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A 500 HIS 0.003 0.001 HIS A 145 PHE 0.018 0.002 PHE A 114 TYR 0.026 0.002 TYR A 117 ARG 0.007 0.001 ARG A 301 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 832 Ramachandran restraints generated. 416 Oldfield, 0 Emsley, 416 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 832 Ramachandran restraints generated. 416 Oldfield, 0 Emsley, 416 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 58 residues out of total 354 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 43 time to evaluate : 0.268 Fit side-chains revert: symmetry clash REVERT: A 266 ASP cc_start: 0.7367 (t0) cc_final: 0.6683 (t0) REVERT: A 326 ARG cc_start: 0.6830 (OUTLIER) cc_final: 0.5962 (mtt180) REVERT: A 364 GLU cc_start: 0.6989 (OUTLIER) cc_final: 0.6664 (pp20) REVERT: A 400 GLN cc_start: 0.8259 (OUTLIER) cc_final: 0.6675 (tm-30) REVERT: A 512 LYS cc_start: 0.6439 (mmtt) cc_final: 0.6186 (pptt) outliers start: 15 outliers final: 8 residues processed: 52 average time/residue: 1.0872 time to fit residues: 58.4245 Evaluate side-chains 53 residues out of total 354 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 42 time to evaluate : 0.360 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 112 LEU Chi-restraints excluded: chain A residue 211 SER Chi-restraints excluded: chain A residue 220 LEU Chi-restraints excluded: chain A residue 263 THR Chi-restraints excluded: chain A residue 326 ARG Chi-restraints excluded: chain A residue 345 THR Chi-restraints excluded: chain A residue 364 GLU Chi-restraints excluded: chain A residue 400 GLN Chi-restraints excluded: chain A residue 426 ILE Chi-restraints excluded: chain A residue 448 GLU Chi-restraints excluded: chain A residue 515 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 41 random chunks: chunk 11 optimal weight: 2.9990 chunk 33 optimal weight: 3.9990 chunk 34 optimal weight: 0.8980 chunk 36 optimal weight: 3.9990 chunk 24 optimal weight: 0.7980 chunk 38 optimal weight: 1.9990 chunk 23 optimal weight: 0.0770 chunk 18 optimal weight: 0.7980 chunk 27 optimal weight: 1.9990 chunk 40 optimal weight: 0.9990 chunk 37 optimal weight: 0.6980 overall best weight: 0.6538 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 124 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8149 moved from start: 0.1831 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 3340 Z= 0.169 Angle : 0.506 6.211 4556 Z= 0.270 Chirality : 0.037 0.167 544 Planarity : 0.004 0.037 552 Dihedral : 4.435 31.090 450 Min Nonbonded Distance : 2.161 Molprobity Statistics. All-atom Clashscore : 7.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.16 % Favored : 97.84 % Rotamer: Outliers : 2.54 % Allowed : 19.49 % Favored : 77.97 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.39 (0.43), residues: 416 helix: 2.31 (0.29), residues: 338 sheet: None (None), residues: 0 loop : -1.84 (0.72), residues: 78 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 500 HIS 0.002 0.001 HIS A 145 PHE 0.012 0.001 PHE A 114 TYR 0.025 0.001 TYR A 117 ARG 0.006 0.000 ARG A 423 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 832 Ramachandran restraints generated. 416 Oldfield, 0 Emsley, 416 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 832 Ramachandran restraints generated. 416 Oldfield, 0 Emsley, 416 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 48 residues out of total 354 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 39 time to evaluate : 0.345 Fit side-chains revert: symmetry clash REVERT: A 201 TRP cc_start: 0.7695 (m100) cc_final: 0.5748 (p-90) REVERT: A 266 ASP cc_start: 0.7356 (t0) cc_final: 0.6654 (t0) REVERT: A 326 ARG cc_start: 0.6650 (ptm160) cc_final: 0.5855 (mtt180) REVERT: A 364 GLU cc_start: 0.6993 (OUTLIER) cc_final: 0.6667 (pp20) REVERT: A 400 GLN cc_start: 0.8252 (OUTLIER) cc_final: 0.6671 (tm-30) REVERT: A 512 LYS cc_start: 0.6343 (mmtt) cc_final: 0.6127 (pptt) outliers start: 9 outliers final: 7 residues processed: 45 average time/residue: 1.0506 time to fit residues: 49.0461 Evaluate side-chains 48 residues out of total 354 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 39 time to evaluate : 0.318 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 112 LEU Chi-restraints excluded: chain A residue 211 SER Chi-restraints excluded: chain A residue 220 LEU Chi-restraints excluded: chain A residue 263 THR Chi-restraints excluded: chain A residue 345 THR Chi-restraints excluded: chain A residue 364 GLU Chi-restraints excluded: chain A residue 400 GLN Chi-restraints excluded: chain A residue 426 ILE Chi-restraints excluded: chain A residue 515 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 41 random chunks: chunk 32 optimal weight: 4.9990 chunk 3 optimal weight: 0.9990 chunk 25 optimal weight: 0.6980 chunk 19 optimal weight: 0.0010 chunk 34 optimal weight: 0.7980 chunk 9 optimal weight: 2.9990 chunk 29 optimal weight: 7.9990 chunk 4 optimal weight: 0.9980 chunk 13 optimal weight: 1.9990 chunk 33 optimal weight: 0.8980 chunk 6 optimal weight: 0.0570 overall best weight: 0.4904 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 124 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8136 moved from start: 0.1916 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.029 3340 Z= 0.158 Angle : 0.505 6.021 4556 Z= 0.268 Chirality : 0.036 0.162 544 Planarity : 0.004 0.036 552 Dihedral : 4.267 26.474 450 Min Nonbonded Distance : 2.167 Molprobity Statistics. All-atom Clashscore : 7.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.92 % Favored : 98.08 % Rotamer: Outliers : 2.54 % Allowed : 19.49 % Favored : 77.97 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.39 (0.43), residues: 416 helix: 2.35 (0.29), residues: 339 sheet: None (None), residues: 0 loop : -2.13 (0.67), residues: 77 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A 500 HIS 0.002 0.001 HIS A 145 PHE 0.011 0.001 PHE A 496 TYR 0.025 0.001 TYR A 117 ARG 0.010 0.001 ARG A 301 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 832 Ramachandran restraints generated. 416 Oldfield, 0 Emsley, 416 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 832 Ramachandran restraints generated. 416 Oldfield, 0 Emsley, 416 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 50 residues out of total 354 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 41 time to evaluate : 0.352 Fit side-chains revert: symmetry clash REVERT: A 201 TRP cc_start: 0.7602 (m100) cc_final: 0.5702 (p-90) REVERT: A 266 ASP cc_start: 0.7331 (t0) cc_final: 0.6624 (t0) REVERT: A 326 ARG cc_start: 0.6558 (OUTLIER) cc_final: 0.5892 (mtt180) REVERT: A 400 GLN cc_start: 0.8239 (OUTLIER) cc_final: 0.6665 (tm-30) outliers start: 9 outliers final: 4 residues processed: 47 average time/residue: 1.0429 time to fit residues: 50.8690 Evaluate side-chains 45 residues out of total 354 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 39 time to evaluate : 0.350 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 211 SER Chi-restraints excluded: chain A residue 263 THR Chi-restraints excluded: chain A residue 326 ARG Chi-restraints excluded: chain A residue 345 THR Chi-restraints excluded: chain A residue 400 GLN Chi-restraints excluded: chain A residue 448 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 41 random chunks: chunk 28 optimal weight: 5.9990 chunk 1 optimal weight: 0.9990 chunk 23 optimal weight: 0.9990 chunk 37 optimal weight: 0.6980 chunk 21 optimal weight: 7.9990 chunk 27 optimal weight: 0.7980 chunk 26 optimal weight: 0.6980 chunk 24 optimal weight: 0.7980 chunk 16 optimal weight: 0.9990 chunk 15 optimal weight: 0.6980 chunk 40 optimal weight: 0.9980 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 124 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3545 r_free = 0.3545 target = 0.135800 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3156 r_free = 0.3156 target = 0.105742 restraints weight = 3820.602| |-----------------------------------------------------------------------------| r_work (start): 0.3124 rms_B_bonded: 1.53 r_work: 0.3018 rms_B_bonded: 2.26 restraints_weight: 0.5000 r_work: 0.2912 rms_B_bonded: 3.61 restraints_weight: 0.2500 r_work (final): 0.2912 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8144 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 : 0.003 0.034 3340 Z= 0.193 Angle : 0.539 6.590 4556 Z= 0.285 Chirality : 0.037 0.166 544 Planarity : 0.005 0.058 552 Dihedral : 4.375 29.202 450 Min Nonbonded Distance : 2.169 Molprobity Statistics. All-atom Clashscore : 8.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.64 % Favored : 97.36 % Rotamer: Outliers : 1.98 % Allowed : 20.06 % Favored : 77.97 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.33 (0.43), residues: 416 helix: 2.31 (0.28), residues: 339 sheet: None (None), residues: 0 loop : -2.15 (0.67), residues: 77 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A 500 HIS 0.002 0.001 HIS A 145 PHE 0.014 0.002 PHE A 114 TYR 0.025 0.001 TYR A 117 ARG 0.015 0.001 ARG A 301 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1481.20 seconds wall clock time: 28 minutes 27.65 seconds (1707.65 seconds total)