Starting phenix.real_space_refine on Fri Apr 5 14:54:22 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8hho_34805/04_2024/8hho_34805_neut_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8hho_34805/04_2024/8hho_34805.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.2 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8hho_34805/04_2024/8hho_34805.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8hho_34805/04_2024/8hho_34805.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8hho_34805/04_2024/8hho_34805_neut_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8hho_34805/04_2024/8hho_34805_neut_updated.pdb" } resolution = 3.2 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= 0.001 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians P 3 5.49 5 S 14 5.16 5 C 2083 2.51 5 N 553 2.21 5 O 621 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A PHE 54": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 121": "OE1" <-> "OE2" Residue "A TYR 132": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 160": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 161": "OE1" <-> "OE2" Residue "A TYR 220": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 226": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 253": "OD1" <-> "OD2" Residue "A GLU 283": "OE1" <-> "OE2" Residue "A GLU 288": "OE1" <-> "OE2" Residue "A GLU 366": "OE1" <-> "OE2" Residue "A PHE 381": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 385": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 400": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 408": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.01s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5288/modules/chem_data/mon_lib" Total number of atoms: 3274 Number of models: 1 Model: "" Number of chains: 1 Chain: "A" Number of atoms: 3274 Number of conformers: 1 Conformer: "" Number of residues, atoms: 417, 3274 Unusual residues: {'NAP': 1} Inner-chain residues flagged as termini: ['pdbres="LYS A 419 "'] Classifications: {'peptide': 416, 'undetermined': 1} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 9} Link IDs: {'PTRANS': 20, 'TRANS': 395, None: 1} Not linked: pdbres="LYS A 419 " pdbres="NAP A 501 " Unresolved non-hydrogen bonds: 39 Unresolved non-hydrogen angles: 44 Unresolved non-hydrogen dihedrals: 34 Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 1, 'ARG:plan': 2, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 21 Time building chain proxies: 2.41, per 1000 atoms: 0.74 Number of scatterers: 3274 At special positions: 0 Unit cell: (67.048, 72.964, 71.978, 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 14 16.00 P 3 15.00 O 621 8.00 N 553 7.00 C 2083 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: 1.31 Conformation dependent library (CDL) restraints added in 628.9 milliseconds 828 Ramachandran restraints generated. 414 Oldfield, 0 Emsley, 414 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 758 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 16 helices and 4 sheets defined 48.6% alpha, 15.1% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.74 Creating SS restraints... Processing helix chain 'A' and resid 5 through 20 removed outlier: 3.923A pdb=" N TYR A 20 " --> pdb=" O ARG A 16 " (cutoff:3.500A) Processing helix chain 'A' and resid 25 through 32 Processing helix chain 'A' and resid 80 through 96 removed outlier: 3.730A pdb=" N TRP A 92 " --> pdb=" O THR A 88 " (cutoff:3.500A) Processing helix chain 'A' and resid 117 through 134 removed outlier: 5.495A pdb=" N ASP A 133 " --> pdb=" O ARG A 129 " (cutoff:3.500A) removed outlier: 5.980A pdb=" N VAL A 134 " --> pdb=" O ALA A 130 " (cutoff:3.500A) Processing helix chain 'A' and resid 150 through 164 Processing helix chain 'A' and resid 170 through 173 Processing helix chain 'A' and resid 190 through 206 Processing helix chain 'A' and resid 222 through 234 Processing helix chain 'A' and resid 257 through 267 Processing helix chain 'A' and resid 281 through 286 removed outlier: 3.927A pdb=" N GLU A 286 " --> pdb=" O GLU A 282 " (cutoff:3.500A) Processing helix chain 'A' and resid 306 through 308 No H-bonds generated for 'chain 'A' and resid 306 through 308' Processing helix chain 'A' and resid 324 through 332 Processing helix chain 'A' and resid 340 through 343 No H-bonds generated for 'chain 'A' and resid 340 through 343' Processing helix chain 'A' and resid 346 through 360 Processing helix chain 'A' and resid 366 through 391 Processing helix chain 'A' and resid 395 through 414 Processing sheet with id= A, first strand: chain 'A' and resid 36 through 45 removed outlier: 4.451A pdb=" N THR A 55 " --> pdb=" O ILE A 109 " (cutoff:3.500A) removed outlier: 6.497A pdb=" N GLY A 103 " --> pdb=" O HIS A 61 " (cutoff:3.500A) removed outlier: 6.818A pdb=" N GLY A 104 " --> pdb=" O PRO A 67 " (cutoff:3.500A) removed outlier: 5.644A pdb=" N LYS A 69 " --> pdb=" O GLY A 104 " (cutoff:3.500A) removed outlier: 7.626A pdb=" N GLY A 106 " --> pdb=" O LYS A 69 " (cutoff:3.500A) removed outlier: 5.845A pdb=" N GLY A 71 " --> pdb=" O GLY A 106 " (cutoff:3.500A) removed outlier: 7.892A pdb=" N ILE A 108 " --> pdb=" O GLY A 71 " (cutoff:3.500A) Processing sheet with id= B, first strand: chain 'A' and resid 72 through 75 removed outlier: 7.010A pdb=" N GLY A 106 " --> pdb=" O ARG A 73 " (cutoff:3.500A) removed outlier: 7.963A pdb=" N HIS A 75 " --> pdb=" O GLY A 106 " (cutoff:3.500A) removed outlier: 5.771A pdb=" N ILE A 108 " --> pdb=" O HIS A 75 " (cutoff:3.500A) No H-bonds generated for sheet with id= B Processing sheet with id= C, first strand: chain 'A' and resid 291 through 294 removed outlier: 6.569A pdb=" N THR A 238 " --> pdb=" O ILE A 215 " (cutoff:3.500A) removed outlier: 8.056A pdb=" N VAL A 217 " --> pdb=" O THR A 238 " (cutoff:3.500A) removed outlier: 7.755A pdb=" N VAL A 240 " --> pdb=" O VAL A 217 " (cutoff:3.500A) Processing sheet with id= D, first strand: chain 'A' and resid 313 through 315 removed outlier: 6.390A pdb=" N LEU A 336 " --> pdb=" O VAL A 314 " (cutoff:3.500A) No H-bonds generated for sheet with id= D 165 hydrogen bonds defined for protein. 480 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: 0.92 Time building geometry restraints manager: 1.44 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 1047 1.34 - 1.45: 426 1.45 - 1.57: 1846 1.57 - 1.69: 5 1.69 - 1.80: 27 Bond restraints: 3351 Sorted by residual: bond pdb=" O2B NAP A 501 " pdb=" P2B NAP A 501 " ideal model delta sigma weight residual 1.736 1.611 0.125 2.00e-02 2.50e+03 3.89e+01 bond pdb=" C4A NAP A 501 " pdb=" C5A NAP A 501 " ideal model delta sigma weight residual 1.385 1.471 -0.086 2.00e-02 2.50e+03 1.84e+01 bond pdb=" C5A NAP A 501 " pdb=" C6A NAP A 501 " ideal model delta sigma weight residual 1.406 1.482 -0.076 2.00e-02 2.50e+03 1.43e+01 bond pdb=" C8A NAP A 501 " pdb=" N7A NAP A 501 " ideal model delta sigma weight residual 1.301 1.359 -0.058 2.00e-02 2.50e+03 8.27e+00 bond pdb=" C1D NAP A 501 " pdb=" O4D NAP A 501 " ideal model delta sigma weight residual 1.375 1.430 -0.055 2.00e-02 2.50e+03 7.61e+00 ... (remaining 3346 not shown) Histogram of bond angle deviations from ideal: 96.60 - 104.47: 64 104.47 - 112.35: 1722 112.35 - 120.22: 1329 120.22 - 128.10: 1413 128.10 - 135.98: 33 Bond angle restraints: 4561 Sorted by residual: angle pdb=" C VAL A 146 " pdb=" N TYR A 147 " pdb=" CA TYR A 147 " ideal model delta sigma weight residual 122.40 127.84 -5.44 1.45e+00 4.76e-01 1.41e+01 angle pdb=" N GLY A 70 " pdb=" CA GLY A 70 " pdb=" C GLY A 70 " ideal model delta sigma weight residual 110.87 116.17 -5.30 1.54e+00 4.22e-01 1.19e+01 angle pdb=" C2A NAP A 501 " pdb=" N3A NAP A 501 " pdb=" C4A NAP A 501 " ideal model delta sigma weight residual 111.82 120.85 -9.03 3.00e+00 1.11e-01 9.06e+00 angle pdb=" CA GLU A 233 " pdb=" CB GLU A 233 " pdb=" CG GLU A 233 " ideal model delta sigma weight residual 114.10 119.49 -5.39 2.00e+00 2.50e-01 7.25e+00 angle pdb=" PA NAP A 501 " pdb=" O3 NAP A 501 " pdb=" PN NAP A 501 " ideal model delta sigma weight residual 128.45 120.55 7.90 3.00e+00 1.11e-01 6.93e+00 ... (remaining 4556 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.95: 1792 17.95 - 35.90: 179 35.90 - 53.84: 53 53.84 - 71.79: 3 71.79 - 89.74: 5 Dihedral angle restraints: 2032 sinusoidal: 843 harmonic: 1189 Sorted by residual: dihedral pdb=" CA MET A 153 " pdb=" C MET A 153 " pdb=" N GLY A 154 " pdb=" CA GLY A 154 " ideal model delta harmonic sigma weight residual 180.00 161.83 18.17 0 5.00e+00 4.00e-02 1.32e+01 dihedral pdb=" CA TYR A 101 " pdb=" C TYR A 101 " pdb=" N GLY A 102 " pdb=" CA GLY A 102 " ideal model delta harmonic sigma weight residual 180.00 162.34 17.66 0 5.00e+00 4.00e-02 1.25e+01 dihedral pdb=" CB GLU A 316 " pdb=" CG GLU A 316 " pdb=" CD GLU A 316 " pdb=" OE1 GLU A 316 " ideal model delta sinusoidal sigma weight residual 0.00 89.74 -89.74 1 3.00e+01 1.11e-03 1.06e+01 ... (remaining 2029 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.044: 370 0.044 - 0.088: 89 0.088 - 0.132: 38 0.132 - 0.176: 1 0.176 - 0.220: 3 Chirality restraints: 501 Sorted by residual: chirality pdb=" C2B NAP A 501 " pdb=" C1B NAP A 501 " pdb=" C3B NAP A 501 " pdb=" O2B NAP A 501 " both_signs ideal model delta sigma weight residual False -2.75 -2.54 -0.22 2.00e-01 2.50e+01 1.21e+00 chirality pdb=" C1B NAP A 501 " pdb=" C2B NAP A 501 " pdb=" N9A NAP A 501 " pdb=" O4B NAP A 501 " both_signs ideal model delta sigma weight residual False 2.31 2.52 -0.21 2.00e-01 2.50e+01 1.15e+00 chirality pdb=" C3D NAP A 501 " pdb=" C2D NAP A 501 " pdb=" C4D NAP A 501 " pdb=" O3D NAP A 501 " both_signs ideal model delta sigma weight residual False -2.74 -2.54 -0.20 2.00e-01 2.50e+01 9.62e-01 ... (remaining 498 not shown) Planarity restraints: 579 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C HIS A 75 " -0.032 5.00e-02 4.00e+02 4.95e-02 3.91e+00 pdb=" N PRO A 76 " 0.086 5.00e-02 4.00e+02 pdb=" CA PRO A 76 " -0.025 5.00e-02 4.00e+02 pdb=" CD PRO A 76 " -0.028 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ILE A 141 " 0.026 5.00e-02 4.00e+02 3.93e-02 2.47e+00 pdb=" N PRO A 142 " -0.068 5.00e-02 4.00e+02 pdb=" CA PRO A 142 " 0.020 5.00e-02 4.00e+02 pdb=" CD PRO A 142 " 0.022 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CD ARG A 396 " -0.129 9.50e-02 1.11e+02 5.82e-02 2.33e+00 pdb=" NE ARG A 396 " 0.005 2.00e-02 2.50e+03 pdb=" CZ ARG A 396 " 0.010 2.00e-02 2.50e+03 pdb=" NH1 ARG A 396 " -0.002 2.00e-02 2.50e+03 pdb=" NH2 ARG A 396 " -0.008 2.00e-02 2.50e+03 ... (remaining 576 not shown) Histogram of nonbonded interaction distances: 2.17 - 2.72: 134 2.72 - 3.26: 3434 3.26 - 3.81: 5791 3.81 - 4.35: 7077 4.35 - 4.90: 11579 Nonbonded interactions: 28015 Sorted by model distance: nonbonded pdb=" O2N NAP A 501 " pdb=" O3D NAP A 501 " model vdw 2.169 2.440 nonbonded pdb=" NH2 ARG A 65 " pdb=" OD1 ASP A 98 " model vdw 2.268 2.520 nonbonded pdb=" ND2 ASN A 251 " pdb=" O GLY A 275 " model vdw 2.268 2.520 nonbonded pdb=" ND1 HIS A 388 " pdb=" O ILE A 393 " model vdw 2.295 2.520 nonbonded pdb=" NZ LYS A 105 " pdb=" OD2 ASP A 145 " model vdw 2.310 2.520 ... (remaining 28010 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: 1.420 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 3.440 Check model and map are aligned: 0.050 Set scattering table: 0.040 Process input model: 14.450 Find NCS groups from input model: 0.090 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: 0.000 Load rotamer database and sin/cos tables:2.850 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 22.360 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7724 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 : 0.005 0.125 3351 Z= 0.334 Angle : 0.764 9.028 4561 Z= 0.415 Chirality : 0.045 0.220 501 Planarity : 0.005 0.058 579 Dihedral : 15.654 89.740 1274 Min Nonbonded Distance : 2.169 Molprobity Statistics. All-atom Clashscore : 14.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.17 % Favored : 97.83 % Rotamer: Outliers : 0.30 % Allowed : 0.61 % Favored : 99.09 % 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: 1.56 (0.42), residues: 414 helix: 1.92 (0.37), residues: 210 sheet: 0.99 (0.69), residues: 61 loop : -0.23 (0.53), residues: 143 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 92 HIS 0.006 0.002 HIS A 388 PHE 0.004 0.001 PHE A 381 TYR 0.018 0.001 TYR A 385 ARG 0.009 0.000 ARG A 396 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 828 Ramachandran restraints generated. 414 Oldfield, 0 Emsley, 414 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 828 Ramachandran restraints generated. 414 Oldfield, 0 Emsley, 414 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 74 residues out of total 339 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 73 time to evaluate : 0.370 Fit side-chains REVERT: A 385 TYR cc_start: 0.7648 (t80) cc_final: 0.7294 (t80) outliers start: 1 outliers final: 0 residues processed: 74 average time/residue: 0.2043 time to fit residues: 18.0865 Evaluate side-chains 62 residues out of total 339 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 62 time to evaluate : 0.530 ------------------------------------------------------------------------------- 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: 4.9990 chunk 31 optimal weight: 7.9990 chunk 17 optimal weight: 9.9990 chunk 10 optimal weight: 4.9990 chunk 20 optimal weight: 0.0770 chunk 16 optimal weight: 6.9990 chunk 32 optimal weight: 0.9980 chunk 12 optimal weight: 0.7980 chunk 19 optimal weight: 0.9990 chunk 23 optimal weight: 9.9990 chunk 37 optimal weight: 1.9990 overall best weight: 0.9742 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 75 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 337 GLN A 392 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7780 moved from start: 0.1086 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 3351 Z= 0.197 Angle : 0.529 5.485 4561 Z= 0.277 Chirality : 0.044 0.143 501 Planarity : 0.004 0.041 579 Dihedral : 9.879 86.919 517 Min Nonbonded Distance : 2.147 Molprobity Statistics. All-atom Clashscore : 12.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.93 % Favored : 98.07 % Rotamer: Outliers : 2.42 % Allowed : 8.18 % Favored : 89.39 % 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: 1.69 (0.42), residues: 414 helix: 2.14 (0.36), residues: 208 sheet: 1.03 (0.69), residues: 61 loop : -0.31 (0.52), residues: 145 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.002 TRP A 263 HIS 0.005 0.002 HIS A 388 PHE 0.009 0.001 PHE A 381 TYR 0.023 0.002 TYR A 250 ARG 0.002 0.000 ARG A 396 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 828 Ramachandran restraints generated. 414 Oldfield, 0 Emsley, 414 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 828 Ramachandran restraints generated. 414 Oldfield, 0 Emsley, 414 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 74 residues out of total 339 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 66 time to evaluate : 0.385 Fit side-chains REVERT: A 263 TRP cc_start: 0.7667 (t-100) cc_final: 0.7362 (t-100) REVERT: A 396 ARG cc_start: 0.7170 (mtm180) cc_final: 0.6832 (mtm180) outliers start: 8 outliers final: 5 residues processed: 69 average time/residue: 0.1811 time to fit residues: 15.0376 Evaluate side-chains 66 residues out of total 339 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 61 time to evaluate : 0.433 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 79 THR Chi-restraints excluded: chain A residue 88 THR Chi-restraints excluded: chain A residue 222 ASN Chi-restraints excluded: chain A residue 226 TYR Chi-restraints excluded: chain A residue 302 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 41 random chunks: chunk 20 optimal weight: 0.4980 chunk 11 optimal weight: 8.9990 chunk 30 optimal weight: 1.9990 chunk 25 optimal weight: 5.9990 chunk 10 optimal weight: 0.6980 chunk 37 optimal weight: 0.9990 chunk 40 optimal weight: 3.9990 chunk 33 optimal weight: 0.6980 chunk 36 optimal weight: 2.9990 chunk 12 optimal weight: 0.6980 chunk 29 optimal weight: 7.9990 overall best weight: 0.7182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 75 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 392 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7769 moved from start: 0.1210 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 3351 Z= 0.171 Angle : 0.518 6.896 4561 Z= 0.268 Chirality : 0.043 0.135 501 Planarity : 0.004 0.039 579 Dihedral : 9.045 83.098 517 Min Nonbonded Distance : 2.204 Molprobity Statistics. All-atom Clashscore : 13.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.42 % Favored : 97.58 % Rotamer: Outliers : 1.82 % Allowed : 11.52 % Favored : 86.67 % 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: 1.67 (0.42), residues: 414 helix: 2.10 (0.36), residues: 207 sheet: 1.07 (0.70), residues: 61 loop : -0.30 (0.52), residues: 146 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP A 263 HIS 0.004 0.002 HIS A 388 PHE 0.007 0.001 PHE A 381 TYR 0.020 0.001 TYR A 250 ARG 0.001 0.000 ARG A 129 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 828 Ramachandran restraints generated. 414 Oldfield, 0 Emsley, 414 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 828 Ramachandran restraints generated. 414 Oldfield, 0 Emsley, 414 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 71 residues out of total 339 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 65 time to evaluate : 0.375 Fit side-chains REVERT: A 200 ARG cc_start: 0.8806 (ttp-170) cc_final: 0.8595 (ttp-170) REVERT: A 249 ILE cc_start: 0.7449 (mm) cc_final: 0.6879 (mt) REVERT: A 263 TRP cc_start: 0.7680 (t-100) cc_final: 0.7366 (t-100) outliers start: 6 outliers final: 5 residues processed: 68 average time/residue: 0.1768 time to fit residues: 14.4597 Evaluate side-chains 65 residues out of total 339 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 60 time to evaluate : 0.382 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 79 THR Chi-restraints excluded: chain A residue 88 THR Chi-restraints excluded: chain A residue 222 ASN Chi-restraints excluded: chain A residue 233 GLU Chi-restraints excluded: chain A residue 314 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 41 random chunks: chunk 36 optimal weight: 3.9990 chunk 28 optimal weight: 7.9990 chunk 19 optimal weight: 0.9990 chunk 4 optimal weight: 0.0770 chunk 17 optimal weight: 0.6980 chunk 25 optimal weight: 5.9990 chunk 37 optimal weight: 0.7980 chunk 39 optimal weight: 3.9990 chunk 35 optimal weight: 2.9990 chunk 10 optimal weight: 4.9990 chunk 33 optimal weight: 0.9980 overall best weight: 0.7140 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7771 moved from start: 0.1442 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 3351 Z= 0.166 Angle : 0.506 6.288 4561 Z= 0.263 Chirality : 0.043 0.133 501 Planarity : 0.004 0.039 579 Dihedral : 8.575 82.435 517 Min Nonbonded Distance : 2.214 Molprobity Statistics. All-atom Clashscore : 13.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.17 % Favored : 97.83 % Rotamer: Outliers : 2.73 % Allowed : 12.42 % Favored : 84.85 % 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: 1.68 (0.42), residues: 414 helix: 2.07 (0.36), residues: 208 sheet: 1.10 (0.70), residues: 61 loop : -0.25 (0.52), residues: 145 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP A 92 HIS 0.004 0.001 HIS A 75 PHE 0.009 0.001 PHE A 57 TYR 0.019 0.001 TYR A 250 ARG 0.002 0.000 ARG A 396 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 828 Ramachandran restraints generated. 414 Oldfield, 0 Emsley, 414 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 828 Ramachandran restraints generated. 414 Oldfield, 0 Emsley, 414 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 73 residues out of total 339 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 64 time to evaluate : 0.377 Fit side-chains REVERT: A 263 TRP cc_start: 0.7668 (t-100) cc_final: 0.7331 (t-100) outliers start: 9 outliers final: 7 residues processed: 69 average time/residue: 0.2008 time to fit residues: 16.6094 Evaluate side-chains 67 residues out of total 339 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 60 time to evaluate : 0.464 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 79 THR Chi-restraints excluded: chain A residue 88 THR Chi-restraints excluded: chain A residue 222 ASN Chi-restraints excluded: chain A residue 226 TYR Chi-restraints excluded: chain A residue 233 GLU Chi-restraints excluded: chain A residue 302 THR Chi-restraints excluded: chain A residue 314 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 41 random chunks: chunk 22 optimal weight: 4.9990 chunk 0 optimal weight: 10.0000 chunk 29 optimal weight: 8.9990 chunk 16 optimal weight: 0.0670 chunk 33 optimal weight: 0.9980 chunk 27 optimal weight: 10.0000 chunk 20 optimal weight: 5.9990 chunk 35 optimal weight: 0.4980 chunk 10 optimal weight: 4.9990 chunk 13 optimal weight: 0.4980 chunk 7 optimal weight: 5.9990 overall best weight: 1.4120 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 75 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7824 moved from start: 0.1698 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 3351 Z= 0.246 Angle : 0.560 6.374 4561 Z= 0.288 Chirality : 0.044 0.150 501 Planarity : 0.004 0.041 579 Dihedral : 8.211 81.784 517 Min Nonbonded Distance : 2.204 Molprobity Statistics. All-atom Clashscore : 14.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.42 % Favored : 97.58 % Rotamer: Outliers : 2.73 % Allowed : 13.33 % Favored : 83.94 % 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: 1.63 (0.42), residues: 414 helix: 1.99 (0.36), residues: 208 sheet: 1.10 (0.70), residues: 61 loop : -0.23 (0.52), residues: 145 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP A 92 HIS 0.004 0.002 HIS A 388 PHE 0.010 0.001 PHE A 381 TYR 0.016 0.002 TYR A 250 ARG 0.003 0.000 ARG A 396 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 828 Ramachandran restraints generated. 414 Oldfield, 0 Emsley, 414 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 828 Ramachandran restraints generated. 414 Oldfield, 0 Emsley, 414 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 73 residues out of total 339 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 64 time to evaluate : 0.341 Fit side-chains revert: symmetry clash REVERT: A 200 ARG cc_start: 0.8903 (ttp-170) cc_final: 0.8638 (ttp-170) outliers start: 9 outliers final: 7 residues processed: 69 average time/residue: 0.1698 time to fit residues: 14.2184 Evaluate side-chains 68 residues out of total 339 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 61 time to evaluate : 0.340 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 53 VAL Chi-restraints excluded: chain A residue 79 THR Chi-restraints excluded: chain A residue 88 THR Chi-restraints excluded: chain A residue 222 ASN Chi-restraints excluded: chain A residue 233 GLU Chi-restraints excluded: chain A residue 302 THR Chi-restraints excluded: chain A residue 314 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 41 random chunks: chunk 23 optimal weight: 2.9990 chunk 9 optimal weight: 1.9990 chunk 39 optimal weight: 1.9990 chunk 32 optimal weight: 2.9990 chunk 18 optimal weight: 0.9990 chunk 3 optimal weight: 0.3980 chunk 13 optimal weight: 0.6980 chunk 20 optimal weight: 0.0030 chunk 38 optimal weight: 0.9980 chunk 4 optimal weight: 0.9990 chunk 22 optimal weight: 0.8980 overall best weight: 0.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 75 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7779 moved from start: 0.1716 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 3351 Z= 0.167 Angle : 0.538 9.658 4561 Z= 0.274 Chirality : 0.043 0.143 501 Planarity : 0.004 0.042 579 Dihedral : 7.784 79.469 517 Min Nonbonded Distance : 2.245 Molprobity Statistics. All-atom Clashscore : 14.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.66 % Favored : 97.34 % Rotamer: Outliers : 1.82 % Allowed : 14.55 % Favored : 83.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.69 (0.42), residues: 414 helix: 2.15 (0.36), residues: 201 sheet: 0.78 (0.70), residues: 61 loop : -0.09 (0.52), residues: 152 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.001 TRP A 263 HIS 0.004 0.002 HIS A 388 PHE 0.009 0.001 PHE A 381 TYR 0.018 0.001 TYR A 250 ARG 0.003 0.000 ARG A 396 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 828 Ramachandran restraints generated. 414 Oldfield, 0 Emsley, 414 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 828 Ramachandran restraints generated. 414 Oldfield, 0 Emsley, 414 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 71 residues out of total 339 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 65 time to evaluate : 0.418 Fit side-chains revert: symmetry clash REVERT: A 200 ARG cc_start: 0.8863 (ttp-170) cc_final: 0.8545 (ttp-170) REVERT: A 263 TRP cc_start: 0.7679 (t-100) cc_final: 0.7440 (t-100) outliers start: 6 outliers final: 4 residues processed: 68 average time/residue: 0.1845 time to fit residues: 15.1064 Evaluate side-chains 65 residues out of total 339 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 61 time to evaluate : 0.396 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 88 THR Chi-restraints excluded: chain A residue 233 GLU Chi-restraints excluded: chain A residue 302 THR Chi-restraints excluded: chain A residue 314 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 41 random chunks: chunk 28 optimal weight: 8.9990 chunk 22 optimal weight: 1.9990 chunk 33 optimal weight: 5.9990 chunk 39 optimal weight: 4.9990 chunk 24 optimal weight: 7.9990 chunk 18 optimal weight: 1.9990 chunk 15 optimal weight: 0.7980 chunk 23 optimal weight: 0.9990 chunk 11 optimal weight: 4.9990 chunk 7 optimal weight: 8.9990 chunk 25 optimal weight: 1.9990 overall best weight: 1.5588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 75 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7844 moved from start: 0.2001 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 3351 Z= 0.274 Angle : 0.576 6.647 4561 Z= 0.299 Chirality : 0.044 0.164 501 Planarity : 0.005 0.041 579 Dihedral : 7.841 82.356 517 Min Nonbonded Distance : 2.200 Molprobity Statistics. All-atom Clashscore : 15.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.42 % Favored : 97.58 % Rotamer: Outliers : 2.73 % Allowed : 15.45 % Favored : 81.82 % 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: 1.47 (0.42), residues: 414 helix: 1.93 (0.36), residues: 202 sheet: 0.58 (0.69), residues: 61 loop : -0.10 (0.53), residues: 151 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.002 TRP A 263 HIS 0.004 0.002 HIS A 388 PHE 0.009 0.001 PHE A 381 TYR 0.016 0.002 TYR A 250 ARG 0.004 0.000 ARG A 396 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 828 Ramachandran restraints generated. 414 Oldfield, 0 Emsley, 414 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 828 Ramachandran restraints generated. 414 Oldfield, 0 Emsley, 414 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 75 residues out of total 339 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 66 time to evaluate : 0.386 Fit side-chains revert: symmetry clash REVERT: A 200 ARG cc_start: 0.8921 (ttp-170) cc_final: 0.8557 (ttp-170) REVERT: A 263 TRP cc_start: 0.7698 (t-100) cc_final: 0.7422 (t-100) outliers start: 9 outliers final: 8 residues processed: 71 average time/residue: 0.1824 time to fit residues: 15.7538 Evaluate side-chains 71 residues out of total 339 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 63 time to evaluate : 0.402 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 53 VAL Chi-restraints excluded: chain A residue 59 VAL Chi-restraints excluded: chain A residue 79 THR Chi-restraints excluded: chain A residue 88 THR Chi-restraints excluded: chain A residue 226 TYR Chi-restraints excluded: chain A residue 233 GLU Chi-restraints excluded: chain A residue 302 THR Chi-restraints excluded: chain A residue 314 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 41 random chunks: chunk 26 optimal weight: 0.8980 chunk 19 optimal weight: 0.9980 chunk 3 optimal weight: 0.9990 chunk 31 optimal weight: 0.9980 chunk 35 optimal weight: 0.8980 chunk 37 optimal weight: 2.9990 chunk 34 optimal weight: 0.9980 chunk 36 optimal weight: 0.9980 chunk 22 optimal weight: 2.9990 chunk 16 optimal weight: 0.0970 chunk 28 optimal weight: 8.9990 overall best weight: 0.7778 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 75 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7793 moved from start: 0.1968 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 3351 Z= 0.191 Angle : 0.550 7.866 4561 Z= 0.284 Chirality : 0.043 0.152 501 Planarity : 0.005 0.043 579 Dihedral : 7.681 80.741 517 Min Nonbonded Distance : 2.158 Molprobity Statistics. All-atom Clashscore : 14.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.90 % Favored : 97.10 % Rotamer: Outliers : 2.73 % Allowed : 16.06 % Favored : 81.21 % 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: 1.54 (0.42), residues: 414 helix: 2.01 (0.36), residues: 201 sheet: 0.73 (0.71), residues: 61 loop : -0.14 (0.52), residues: 152 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP A 263 HIS 0.010 0.003 HIS A 75 PHE 0.009 0.001 PHE A 381 TYR 0.017 0.001 TYR A 250 ARG 0.004 0.000 ARG A 396 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 828 Ramachandran restraints generated. 414 Oldfield, 0 Emsley, 414 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 828 Ramachandran restraints generated. 414 Oldfield, 0 Emsley, 414 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 76 residues out of total 339 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 67 time to evaluate : 0.485 Fit side-chains REVERT: A 200 ARG cc_start: 0.8890 (ttp-170) cc_final: 0.8542 (ttp-170) REVERT: A 263 TRP cc_start: 0.7722 (t-100) cc_final: 0.7432 (t-100) REVERT: A 396 ARG cc_start: 0.7271 (mtm180) cc_final: 0.6620 (mtm180) outliers start: 9 outliers final: 7 residues processed: 72 average time/residue: 0.1861 time to fit residues: 16.0454 Evaluate side-chains 71 residues out of total 339 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 64 time to evaluate : 0.380 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 53 VAL Chi-restraints excluded: chain A residue 59 VAL Chi-restraints excluded: chain A residue 79 THR Chi-restraints excluded: chain A residue 88 THR Chi-restraints excluded: chain A residue 233 GLU Chi-restraints excluded: chain A residue 302 THR Chi-restraints excluded: chain A residue 314 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 41 random chunks: chunk 11 optimal weight: 0.5980 chunk 33 optimal weight: 1.9990 chunk 34 optimal weight: 0.0670 chunk 36 optimal weight: 3.9990 chunk 24 optimal weight: 0.9990 chunk 38 optimal weight: 4.9990 chunk 23 optimal weight: 0.9990 chunk 18 optimal weight: 1.9990 chunk 27 optimal weight: 4.9990 chunk 40 optimal weight: 0.9990 chunk 37 optimal weight: 0.6980 overall best weight: 0.6722 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7776 moved from start: 0.2022 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 3351 Z= 0.186 Angle : 0.561 7.988 4561 Z= 0.289 Chirality : 0.043 0.139 501 Planarity : 0.005 0.045 579 Dihedral : 7.621 80.767 517 Min Nonbonded Distance : 2.120 Molprobity Statistics. All-atom Clashscore : 14.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.66 % Favored : 97.34 % Rotamer: Outliers : 2.73 % Allowed : 17.58 % Favored : 79.70 % 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: 1.60 (0.42), residues: 414 helix: 2.07 (0.36), residues: 201 sheet: 0.79 (0.71), residues: 61 loop : -0.15 (0.52), residues: 152 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.048 0.002 TRP A 92 HIS 0.007 0.001 HIS A 388 PHE 0.015 0.001 PHE A 381 TYR 0.017 0.001 TYR A 250 ARG 0.003 0.000 ARG A 396 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 828 Ramachandran restraints generated. 414 Oldfield, 0 Emsley, 414 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 828 Ramachandran restraints generated. 414 Oldfield, 0 Emsley, 414 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 76 residues out of total 339 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 67 time to evaluate : 0.381 Fit side-chains REVERT: A 200 ARG cc_start: 0.8888 (ttp-170) cc_final: 0.8536 (ttp-170) REVERT: A 263 TRP cc_start: 0.7597 (t-100) cc_final: 0.7291 (t-100) REVERT: A 396 ARG cc_start: 0.7212 (mtm180) cc_final: 0.6589 (mtm180) outliers start: 9 outliers final: 7 residues processed: 73 average time/residue: 0.1695 time to fit residues: 14.9447 Evaluate side-chains 74 residues out of total 339 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 67 time to evaluate : 0.373 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 53 VAL Chi-restraints excluded: chain A residue 59 VAL Chi-restraints excluded: chain A residue 79 THR Chi-restraints excluded: chain A residue 88 THR Chi-restraints excluded: chain A residue 233 GLU Chi-restraints excluded: chain A residue 302 THR Chi-restraints excluded: chain A residue 314 VAL 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: 1.9990 chunk 25 optimal weight: 6.9990 chunk 19 optimal weight: 0.7980 chunk 34 optimal weight: 0.7980 chunk 9 optimal weight: 0.9980 chunk 29 optimal weight: 0.6980 chunk 4 optimal weight: 0.9980 chunk 13 optimal weight: 0.0000 chunk 33 optimal weight: 0.9990 chunk 6 optimal weight: 0.3980 overall best weight: 0.5384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7746 moved from start: 0.2046 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 3351 Z= 0.170 Angle : 0.568 7.804 4561 Z= 0.289 Chirality : 0.043 0.144 501 Planarity : 0.004 0.045 579 Dihedral : 7.522 80.144 517 Min Nonbonded Distance : 2.122 Molprobity Statistics. All-atom Clashscore : 14.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.90 % Favored : 97.10 % Rotamer: Outliers : 2.12 % Allowed : 18.18 % Favored : 79.70 % 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: 1.59 (0.42), residues: 414 helix: 2.11 (0.37), residues: 201 sheet: 0.82 (0.72), residues: 61 loop : -0.25 (0.51), residues: 152 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.042 0.002 TRP A 92 HIS 0.006 0.001 HIS A 388 PHE 0.013 0.001 PHE A 381 TYR 0.018 0.001 TYR A 250 ARG 0.002 0.000 ARG A 396 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 828 Ramachandran restraints generated. 414 Oldfield, 0 Emsley, 414 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 828 Ramachandran restraints generated. 414 Oldfield, 0 Emsley, 414 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 75 residues out of total 339 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 68 time to evaluate : 0.377 Fit side-chains REVERT: A 200 ARG cc_start: 0.8886 (ttp-170) cc_final: 0.8555 (ttp-170) REVERT: A 263 TRP cc_start: 0.7641 (t-100) cc_final: 0.7283 (t-100) REVERT: A 396 ARG cc_start: 0.7217 (mtm180) cc_final: 0.6655 (mtm180) outliers start: 7 outliers final: 7 residues processed: 73 average time/residue: 0.1544 time to fit residues: 13.7538 Evaluate side-chains 74 residues out of total 339 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 67 time to evaluate : 0.387 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 53 VAL Chi-restraints excluded: chain A residue 59 VAL Chi-restraints excluded: chain A residue 79 THR Chi-restraints excluded: chain A residue 88 THR Chi-restraints excluded: chain A residue 233 GLU Chi-restraints excluded: chain A residue 302 THR Chi-restraints excluded: chain A residue 314 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 41 random chunks: chunk 28 optimal weight: 4.9990 chunk 1 optimal weight: 0.7980 chunk 23 optimal weight: 0.5980 chunk 37 optimal weight: 4.9990 chunk 21 optimal weight: 1.9990 chunk 27 optimal weight: 0.3980 chunk 26 optimal weight: 5.9990 chunk 24 optimal weight: 20.0000 chunk 16 optimal weight: 3.9990 chunk 15 optimal weight: 0.8980 chunk 40 optimal weight: 0.7980 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3920 r_free = 0.3920 target = 0.140505 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3611 r_free = 0.3611 target = 0.119815 restraints weight = 6915.810| |-----------------------------------------------------------------------------| r_work (start): 0.3605 rms_B_bonded: 2.63 r_work: 0.3498 rms_B_bonded: 3.38 restraints_weight: 0.5000 r_work (final): 0.3498 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7911 moved from start: 0.2071 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 3351 Z= 0.183 Angle : 0.563 7.579 4561 Z= 0.288 Chirality : 0.043 0.124 501 Planarity : 0.005 0.045 579 Dihedral : 7.515 80.217 517 Min Nonbonded Distance : 2.137 Molprobity Statistics. All-atom Clashscore : 14.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.42 % Favored : 97.58 % Rotamer: Outliers : 2.12 % Allowed : 18.79 % Favored : 79.09 % 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: 1.54 (0.42), residues: 414 helix: 2.09 (0.36), residues: 202 sheet: 0.78 (0.71), residues: 61 loop : -0.33 (0.51), residues: 151 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.042 0.002 TRP A 92 HIS 0.006 0.002 HIS A 388 PHE 0.014 0.001 PHE A 381 TYR 0.014 0.001 TYR A 160 ARG 0.003 0.000 ARG A 396 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1237.62 seconds wall clock time: 22 minutes 56.17 seconds (1376.17 seconds total)