Starting phenix.real_space_refine on Sun Mar 10 16:41:06 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8hiq_34826/03_2024/8hiq_34826_neut_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8hiq_34826/03_2024/8hiq_34826.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/8hiq_34826/03_2024/8hiq_34826.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8hiq_34826/03_2024/8hiq_34826.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8hiq_34826/03_2024/8hiq_34826_neut_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8hiq_34826/03_2024/8hiq_34826_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 ASP 47": "OD1" <-> "OD2" Residue "A GLU 78": "OE1" <-> "OE2" Residue "A TYR 147": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 160": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 226": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 250": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 258": "OD1" <-> "OD2" Residue "A TYR 363": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 381": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 397": "OD1" <-> "OD2" Residue "A TYR 400": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.01s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/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: 2.43, per 1000 atoms: 0.74 Number of scatterers: 3274 At special positions: 0 Unit cell: (68.034, 71.978, 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: 1.41 Conformation dependent library (CDL) restraints added in 536.7 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 48.8% alpha, 13.9% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.70 Creating SS restraints... Processing helix chain 'A' and resid 5 through 20 removed outlier: 4.275A 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 Processing helix chain 'A' and resid 117 through 134 removed outlier: 5.809A pdb=" N ASP A 133 " --> pdb=" O ARG A 129 " (cutoff:3.500A) removed outlier: 6.115A 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 235 Processing helix chain 'A' and resid 257 through 267 Processing helix chain 'A' and resid 281 through 285 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 345 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: 4.553A pdb=" N THR A 55 " --> pdb=" O ILE A 109 " (cutoff:3.500A) removed outlier: 4.221A pdb=" N GLY A 71 " --> pdb=" O GLY A 104 " (cutoff:3.500A) Processing sheet with id= B, first strand: chain 'A' and resid 67 through 69 Processing sheet with id= C, first strand: chain 'A' and resid 291 through 294 removed outlier: 6.630A pdb=" N THR A 238 " --> pdb=" O ILE A 215 " (cutoff:3.500A) removed outlier: 8.464A pdb=" N VAL A 217 " --> pdb=" O THR A 238 " (cutoff:3.500A) removed outlier: 8.219A 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: 6.739A pdb=" N LEU A 336 " --> pdb=" O VAL A 314 " (cutoff:3.500A) No H-bonds generated for sheet with id= D 174 hydrogen bonds defined for protein. 504 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: 0.91 Time building geometry restraints manager: 1.54 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: 1062 1.34 - 1.46: 666 1.46 - 1.57: 1591 1.57 - 1.69: 5 1.69 - 1.81: 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 1.614 0.122 2.00e-02 2.50e+03 3.69e+01 bond pdb=" C1D NAP A 501 " pdb=" O4D NAP A 501 " ideal model delta sigma weight residual 1.375 1.428 -0.053 2.00e-02 2.50e+03 7.04e+00 bond pdb=" C5D NAP A 501 " pdb=" O5D NAP A 501 " ideal model delta sigma weight residual 1.403 1.450 -0.047 2.00e-02 2.50e+03 5.54e+00 bond pdb=" O5D NAP A 501 " pdb=" PN NAP A 501 " ideal model delta sigma weight residual 1.649 1.604 0.045 2.00e-02 2.50e+03 5.05e+00 bond pdb=" O3 NAP A 501 " pdb=" PA NAP A 501 " ideal model delta sigma weight residual 1.647 1.604 0.043 2.00e-02 2.50e+03 4.53e+00 ... (remaining 3346 not shown) Histogram of bond angle deviations from ideal: 99.78 - 106.64: 123 106.64 - 113.49: 1835 113.49 - 120.34: 1218 120.34 - 127.20: 1331 127.20 - 134.05: 54 Bond angle restraints: 4561 Sorted by residual: angle pdb=" CA MET A 153 " pdb=" CB MET A 153 " pdb=" CG MET A 153 " ideal model delta sigma weight residual 114.10 107.08 7.02 2.00e+00 2.50e-01 1.23e+01 angle pdb=" N GLY A 219 " pdb=" CA GLY A 219 " pdb=" C GLY A 219 " ideal model delta sigma weight residual 113.18 105.81 7.37 2.37e+00 1.78e-01 9.68e+00 angle pdb=" C VAL A 146 " pdb=" N TYR A 147 " pdb=" CA TYR A 147 " ideal model delta sigma weight residual 123.05 127.73 -4.68 1.57e+00 4.06e-01 8.89e+00 angle pdb=" N ARG A 166 " pdb=" CA ARG A 166 " pdb=" CB ARG A 166 " ideal model delta sigma weight residual 113.65 109.78 3.87 1.47e+00 4.63e-01 6.92e+00 angle pdb=" C2B NAP A 501 " pdb=" O2B NAP A 501 " pdb=" P2B NAP A 501 " ideal model delta sigma weight residual 117.19 109.33 7.86 3.00e+00 1.11e-01 6.87e+00 ... (remaining 4556 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.85: 1791 17.85 - 35.71: 175 35.71 - 53.56: 40 53.56 - 71.41: 19 71.41 - 89.27: 7 Dihedral angle restraints: 2032 sinusoidal: 843 harmonic: 1189 Sorted by residual: 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 180.00 161.37 18.63 0 5.00e+00 4.00e-02 1.39e+01 dihedral pdb=" CB GLU A 45 " pdb=" CG GLU A 45 " pdb=" CD GLU A 45 " pdb=" OE1 GLU A 45 " ideal model delta sinusoidal sigma weight residual 0.00 88.75 -88.75 1 3.00e+01 1.11e-03 1.04e+01 dihedral pdb=" CA LYS A 213 " pdb=" C LYS A 213 " pdb=" N LYS A 214 " pdb=" CA LYS A 214 " ideal model delta harmonic sigma weight residual 180.00 -163.96 -16.04 0 5.00e+00 4.00e-02 1.03e+01 ... (remaining 2029 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.025: 267 0.025 - 0.050: 126 0.050 - 0.075: 55 0.075 - 0.099: 30 0.099 - 0.124: 23 Chirality restraints: 501 Sorted by residual: chirality pdb=" CA ILE A 108 " pdb=" N ILE A 108 " pdb=" C ILE A 108 " pdb=" CB ILE A 108 " both_signs ideal model delta sigma weight residual False 2.43 2.56 -0.12 2.00e-01 2.50e+01 3.86e-01 chirality pdb=" CA ILE A 338 " pdb=" N ILE A 338 " pdb=" C ILE A 338 " pdb=" CB ILE A 338 " both_signs ideal model delta sigma weight residual False 2.43 2.56 -0.12 2.00e-01 2.50e+01 3.71e-01 chirality pdb=" CA ILE A 174 " pdb=" N ILE A 174 " pdb=" C ILE A 174 " pdb=" CB ILE A 174 " both_signs ideal model delta sigma weight residual False 2.43 2.55 -0.12 2.00e-01 2.50e+01 3.68e-01 ... (remaining 498 not shown) Planarity restraints: 579 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C1D NAP A 501 " -0.021 2.00e-02 2.50e+03 7.61e-02 1.16e+02 pdb=" C2N NAP A 501 " -0.071 2.00e-02 2.50e+03 pdb=" C3N NAP A 501 " -0.033 2.00e-02 2.50e+03 pdb=" C4N NAP A 501 " -0.125 2.00e-02 2.50e+03 pdb=" C5N NAP A 501 " 0.023 2.00e-02 2.50e+03 pdb=" C6N NAP A 501 " 0.108 2.00e-02 2.50e+03 pdb=" C7N NAP A 501 " 0.109 2.00e-02 2.50e+03 pdb=" N1N NAP A 501 " 0.008 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C ILE A 141 " 0.034 5.00e-02 4.00e+02 5.11e-02 4.17e+00 pdb=" N PRO A 142 " -0.088 5.00e-02 4.00e+02 pdb=" CA PRO A 142 " 0.027 5.00e-02 4.00e+02 pdb=" CD PRO A 142 " 0.028 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C THR A 323 " -0.026 5.00e-02 4.00e+02 4.01e-02 2.57e+00 pdb=" N PRO A 324 " 0.069 5.00e-02 4.00e+02 pdb=" CA PRO A 324 " -0.020 5.00e-02 4.00e+02 pdb=" CD PRO A 324 " -0.022 5.00e-02 4.00e+02 ... (remaining 576 not shown) Histogram of nonbonded interaction distances: 2.28 - 2.81: 888 2.81 - 3.33: 3402 3.33 - 3.85: 5893 3.85 - 4.38: 6794 4.38 - 4.90: 11291 Nonbonded interactions: 28268 Sorted by model distance: nonbonded pdb=" OG1 THR A 68 " pdb=" OD1 ASP A 140 " model vdw 2.284 2.440 nonbonded pdb=" NZ LYS A 177 " pdb=" OD1 ASN A 358 " model vdw 2.300 2.520 nonbonded pdb=" O ASN A 308 " pdb=" NZ LYS A 310 " model vdw 2.319 2.520 nonbonded pdb=" OD1 ASN A 319 " pdb=" ND2 ASN A 344 " model vdw 2.320 2.520 nonbonded pdb=" NE2 GLN A 60 " pdb=" O VAL A 134 " model vdw 2.328 2.520 ... (remaining 28263 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: 0.960 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.000 Extract box with map and model: 3.450 Check model and map are aligned: 0.050 Set scattering table: 0.030 Process input model: 14.150 Find NCS groups from input model: 0.070 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:2.790 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 21.520 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7578 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 0.122 3351 Z= 0.323 Angle : 0.739 8.787 4561 Z= 0.405 Chirality : 0.043 0.124 501 Planarity : 0.006 0.076 579 Dihedral : 17.055 89.266 1274 Min Nonbonded Distance : 2.284 Molprobity Statistics. All-atom Clashscore : 14.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.86 % Favored : 96.14 % Rotamer: Outliers : 0.00 % Allowed : 0.30 % Favored : 99.70 % 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: 1.52 (0.43), residues: 414 helix: 1.97 (0.36), residues: 209 sheet: -0.06 (0.62), residues: 70 loop : 0.19 (0.58), residues: 135 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 89 HIS 0.002 0.001 HIS A 388 PHE 0.009 0.001 PHE A 341 TYR 0.010 0.001 TYR A 363 ARG 0.007 0.001 ARG A 200 *********************** 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 62 residues out of total 339 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 62 time to evaluate : 0.347 Fit side-chains REVERT: A 166 ARG cc_start: 0.5204 (ttt-90) cc_final: 0.4757 (ttt-90) REVERT: A 388 HIS cc_start: 0.6928 (t70) cc_final: 0.6714 (t-170) outliers start: 0 outliers final: 0 residues processed: 62 average time/residue: 0.2248 time to fit residues: 16.1999 Evaluate side-chains 52 residues out of total 339 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 52 time to evaluate : 0.398 ------------------------------------------------------------------------------- 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: 10.0000 chunk 17 optimal weight: 3.9990 chunk 10 optimal weight: 4.9990 chunk 20 optimal weight: 8.9990 chunk 16 optimal weight: 3.9990 chunk 32 optimal weight: 3.9990 chunk 12 optimal weight: 0.9990 chunk 19 optimal weight: 0.9990 chunk 23 optimal weight: 4.9990 chunk 37 optimal weight: 0.8980 overall best weight: 2.1788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 357 GLN A 409 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7640 moved from start: 0.1054 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.097 3351 Z= 0.315 Angle : 0.572 7.501 4561 Z= 0.293 Chirality : 0.043 0.167 501 Planarity : 0.005 0.052 579 Dihedral : 10.003 58.783 517 Min Nonbonded Distance : 2.194 Molprobity Statistics. All-atom Clashscore : 14.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.11 % Favored : 95.89 % Rotamer: Outliers : 0.61 % Allowed : 6.97 % Favored : 92.42 % 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: 1.33 (0.42), residues: 414 helix: 1.89 (0.35), residues: 212 sheet: -0.14 (0.68), residues: 60 loop : -0.12 (0.55), residues: 142 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 89 HIS 0.004 0.001 HIS A 388 PHE 0.008 0.001 PHE A 341 TYR 0.008 0.001 TYR A 101 ARG 0.005 0.000 ARG A 331 *********************** 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 53 residues out of total 339 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 51 time to evaluate : 0.368 Fit side-chains REVERT: A 157 MET cc_start: 0.7559 (tmm) cc_final: 0.7331 (tmm) REVERT: A 166 ARG cc_start: 0.5291 (ttt-90) cc_final: 0.4965 (ttt-90) REVERT: A 366 GLU cc_start: 0.8456 (tp30) cc_final: 0.8248 (tp30) REVERT: A 377 MET cc_start: 0.6658 (mmt) cc_final: 0.6296 (mmt) outliers start: 2 outliers final: 2 residues processed: 53 average time/residue: 0.2257 time to fit residues: 14.0008 Evaluate side-chains 50 residues out of total 339 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 48 time to evaluate : 0.402 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 133 ASP Chi-restraints excluded: chain A residue 184 SER Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 41 random chunks: chunk 20 optimal weight: 7.9990 chunk 11 optimal weight: 3.9990 chunk 30 optimal weight: 0.9990 chunk 25 optimal weight: 8.9990 chunk 10 optimal weight: 0.9980 chunk 37 optimal weight: 0.9990 chunk 40 optimal weight: 6.9990 chunk 33 optimal weight: 8.9990 chunk 36 optimal weight: 1.9990 chunk 12 optimal weight: 0.7980 chunk 29 optimal weight: 10.0000 overall best weight: 1.1586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 386 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7601 moved from start: 0.1144 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.053 3351 Z= 0.202 Angle : 0.504 7.291 4561 Z= 0.260 Chirality : 0.042 0.133 501 Planarity : 0.005 0.053 579 Dihedral : 9.019 53.374 517 Min Nonbonded Distance : 2.236 Molprobity Statistics. All-atom Clashscore : 12.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.62 % Favored : 96.38 % Rotamer: Outliers : 0.61 % Allowed : 9.70 % Favored : 89.70 % 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: 1.43 (0.42), residues: 414 helix: 2.06 (0.35), residues: 212 sheet: -0.20 (0.68), residues: 60 loop : -0.18 (0.55), residues: 142 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 74 HIS 0.002 0.001 HIS A 388 PHE 0.008 0.001 PHE A 341 TYR 0.006 0.001 TYR A 408 ARG 0.004 0.000 ARG A 331 *********************** 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 54 residues out of total 339 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 52 time to evaluate : 0.373 Fit side-chains REVERT: A 157 MET cc_start: 0.7660 (tmm) cc_final: 0.7447 (tmm) REVERT: A 166 ARG cc_start: 0.5197 (ttt-90) cc_final: 0.4873 (ttt-90) REVERT: A 366 GLU cc_start: 0.8537 (tp30) cc_final: 0.8332 (tp30) REVERT: A 377 MET cc_start: 0.6600 (mmt) cc_final: 0.6264 (mmt) outliers start: 2 outliers final: 2 residues processed: 54 average time/residue: 0.2262 time to fit residues: 14.2288 Evaluate side-chains 51 residues out of total 339 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 49 time to evaluate : 0.369 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 53 VAL Chi-restraints excluded: chain A residue 133 ASP Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 41 random chunks: chunk 36 optimal weight: 4.9990 chunk 28 optimal weight: 10.0000 chunk 19 optimal weight: 0.8980 chunk 4 optimal weight: 0.7980 chunk 17 optimal weight: 0.0040 chunk 25 optimal weight: 2.9990 chunk 37 optimal weight: 0.9980 chunk 39 optimal weight: 1.9990 chunk 35 optimal weight: 0.8980 chunk 10 optimal weight: 0.9990 chunk 33 optimal weight: 7.9990 overall best weight: 0.7192 ------------------------------------------------------------------------------- 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: 0.7569 moved from start: 0.1267 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 3351 Z= 0.167 Angle : 0.482 6.952 4561 Z= 0.249 Chirality : 0.041 0.133 501 Planarity : 0.005 0.051 579 Dihedral : 8.339 49.420 517 Min Nonbonded Distance : 2.266 Molprobity Statistics. All-atom Clashscore : 12.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.38 % Favored : 96.62 % Rotamer: Outliers : 0.91 % Allowed : 12.12 % Favored : 86.97 % 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: 1.53 (0.42), residues: 414 helix: 2.25 (0.35), residues: 211 sheet: -0.17 (0.68), residues: 60 loop : -0.29 (0.54), residues: 143 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A 89 HIS 0.002 0.001 HIS A 394 PHE 0.008 0.001 PHE A 341 TYR 0.007 0.001 TYR A 250 ARG 0.006 0.000 ARG A 118 *********************** 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 56 residues out of total 339 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 53 time to evaluate : 0.347 Fit side-chains REVERT: A 166 ARG cc_start: 0.5165 (ttt-90) cc_final: 0.4843 (ttt-90) outliers start: 3 outliers final: 3 residues processed: 56 average time/residue: 0.2279 time to fit residues: 14.8942 Evaluate side-chains 53 residues out of total 339 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 50 time to evaluate : 0.335 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 53 VAL Chi-restraints excluded: chain A residue 133 ASP Chi-restraints excluded: chain A residue 184 SER Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 41 random chunks: chunk 22 optimal weight: 8.9990 chunk 0 optimal weight: 10.0000 chunk 29 optimal weight: 8.9990 chunk 16 optimal weight: 4.9990 chunk 33 optimal weight: 3.9990 chunk 27 optimal weight: 8.9990 chunk 20 optimal weight: 3.9990 chunk 35 optimal weight: 2.9990 chunk 10 optimal weight: 7.9990 chunk 13 optimal weight: 1.9990 chunk 7 optimal weight: 0.9980 overall best weight: 2.7988 ------------------------------------------------------------------------------- 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: 0.7667 moved from start: 0.1585 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.107 3351 Z= 0.376 Angle : 0.593 7.684 4561 Z= 0.305 Chirality : 0.044 0.134 501 Planarity : 0.005 0.052 579 Dihedral : 8.509 50.257 517 Min Nonbonded Distance : 2.179 Molprobity Statistics. All-atom Clashscore : 15.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.35 % Favored : 95.65 % Rotamer: Outliers : 1.21 % Allowed : 13.94 % 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: 1.31 (0.42), residues: 414 helix: 2.01 (0.35), residues: 211 sheet: -0.46 (0.65), residues: 67 loop : -0.15 (0.56), residues: 136 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 364 HIS 0.004 0.001 HIS A 388 PHE 0.011 0.002 PHE A 341 TYR 0.007 0.001 TYR A 101 ARG 0.007 0.001 ARG A 118 *********************** 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 55 residues out of total 339 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 51 time to evaluate : 0.367 Fit side-chains REVERT: A 377 MET cc_start: 0.6682 (mmt) cc_final: 0.6337 (mmt) outliers start: 4 outliers final: 3 residues processed: 55 average time/residue: 0.2162 time to fit residues: 13.9526 Evaluate side-chains 50 residues out of total 339 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 47 time to evaluate : 0.369 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 53 VAL Chi-restraints excluded: chain A residue 184 SER Chi-restraints excluded: chain A residue 238 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 41 random chunks: chunk 23 optimal weight: 8.9990 chunk 9 optimal weight: 1.9990 chunk 39 optimal weight: 0.9980 chunk 32 optimal weight: 0.8980 chunk 18 optimal weight: 0.0770 chunk 3 optimal weight: 3.9990 chunk 13 optimal weight: 2.9990 chunk 20 optimal weight: 3.9990 chunk 38 optimal weight: 0.9990 chunk 4 optimal weight: 0.7980 chunk 22 optimal weight: 2.9990 overall best weight: 0.7540 ------------------------------------------------------------------------------- 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: 0.7580 moved from start: 0.1552 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 3351 Z= 0.174 Angle : 0.507 7.042 4561 Z= 0.261 Chirality : 0.041 0.131 501 Planarity : 0.005 0.053 579 Dihedral : 8.092 51.861 517 Min Nonbonded Distance : 2.254 Molprobity Statistics. All-atom Clashscore : 13.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.38 % Favored : 96.62 % Rotamer: Outliers : 1.52 % Allowed : 13.94 % Favored : 84.55 % 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: 1.48 (0.42), residues: 414 helix: 2.26 (0.35), residues: 211 sheet: -0.26 (0.68), residues: 60 loop : -0.37 (0.54), residues: 143 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 63 HIS 0.002 0.001 HIS A 388 PHE 0.008 0.001 PHE A 341 TYR 0.009 0.001 TYR A 147 ARG 0.007 0.001 ARG A 118 *********************** 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 57 residues out of total 339 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 52 time to evaluate : 0.390 Fit side-chains REVERT: A 287 LEU cc_start: 0.6206 (OUTLIER) cc_final: 0.6000 (tt) outliers start: 5 outliers final: 4 residues processed: 57 average time/residue: 0.2078 time to fit residues: 13.9747 Evaluate side-chains 56 residues out of total 339 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 51 time to evaluate : 0.340 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 53 VAL Chi-restraints excluded: chain A residue 133 ASP Chi-restraints excluded: chain A residue 184 SER Chi-restraints excluded: chain A residue 238 THR Chi-restraints excluded: chain A residue 287 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 41 random chunks: chunk 28 optimal weight: 0.9990 chunk 22 optimal weight: 6.9990 chunk 33 optimal weight: 1.9990 chunk 39 optimal weight: 1.9990 chunk 24 optimal weight: 5.9990 chunk 18 optimal weight: 7.9990 chunk 15 optimal weight: 0.8980 chunk 23 optimal weight: 6.9990 chunk 11 optimal weight: 1.9990 chunk 7 optimal weight: 0.7980 chunk 25 optimal weight: 0.9980 overall best weight: 1.1384 ------------------------------------------------------------------------------- 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: 0.7592 moved from start: 0.1589 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.057 3351 Z= 0.210 Angle : 0.533 7.391 4561 Z= 0.273 Chirality : 0.042 0.134 501 Planarity : 0.005 0.051 579 Dihedral : 8.028 51.899 517 Min Nonbonded Distance : 2.238 Molprobity Statistics. All-atom Clashscore : 13.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.11 % Favored : 95.89 % Rotamer: Outliers : 1.21 % Allowed : 15.15 % 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: 1.54 (0.42), residues: 414 helix: 2.26 (0.35), residues: 211 sheet: -0.27 (0.67), residues: 68 loop : -0.23 (0.56), residues: 135 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A 74 HIS 0.002 0.001 HIS A 388 PHE 0.009 0.001 PHE A 341 TYR 0.009 0.001 TYR A 250 ARG 0.006 0.001 ARG A 118 *********************** 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 56 residues out of total 339 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 52 time to evaluate : 0.381 Fit side-chains REVERT: A 287 LEU cc_start: 0.6096 (OUTLIER) cc_final: 0.5870 (tt) outliers start: 4 outliers final: 3 residues processed: 56 average time/residue: 0.2179 time to fit residues: 14.3072 Evaluate side-chains 54 residues out of total 339 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 50 time to evaluate : 0.372 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 53 VAL Chi-restraints excluded: chain A residue 184 SER Chi-restraints excluded: chain A residue 238 THR Chi-restraints excluded: chain A residue 287 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 41 random chunks: chunk 26 optimal weight: 9.9990 chunk 19 optimal weight: 0.9990 chunk 3 optimal weight: 0.9990 chunk 31 optimal weight: 2.9990 chunk 35 optimal weight: 1.9990 chunk 37 optimal weight: 0.7980 chunk 34 optimal weight: 0.9980 chunk 36 optimal weight: 0.4980 chunk 22 optimal weight: 1.9990 chunk 16 optimal weight: 6.9990 chunk 28 optimal weight: 3.9990 overall best weight: 0.8584 ------------------------------------------------------------------------------- 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: 0.7567 moved from start: 0.1747 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 3351 Z= 0.189 Angle : 0.535 7.347 4561 Z= 0.275 Chirality : 0.042 0.144 501 Planarity : 0.005 0.051 579 Dihedral : 7.864 52.469 517 Min Nonbonded Distance : 2.254 Molprobity Statistics. All-atom Clashscore : 14.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.11 % Favored : 95.89 % Rotamer: Outliers : 1.52 % Allowed : 15.76 % Favored : 82.73 % 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: 1.55 (0.42), residues: 414 helix: 2.28 (0.34), residues: 211 sheet: -0.17 (0.67), residues: 68 loop : -0.29 (0.56), residues: 135 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 74 HIS 0.002 0.001 HIS A 388 PHE 0.008 0.001 PHE A 341 TYR 0.026 0.001 TYR A 20 ARG 0.007 0.001 ARG A 118 *********************** 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 54 residues out of total 339 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 49 time to evaluate : 0.372 Fit side-chains REVERT: A 287 LEU cc_start: 0.6032 (OUTLIER) cc_final: 0.5721 (tt) outliers start: 5 outliers final: 3 residues processed: 53 average time/residue: 0.2246 time to fit residues: 13.9416 Evaluate side-chains 53 residues out of total 339 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 49 time to evaluate : 0.382 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 53 VAL Chi-restraints excluded: chain A residue 184 SER Chi-restraints excluded: chain A residue 238 THR Chi-restraints excluded: chain A residue 287 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 41 random chunks: chunk 11 optimal weight: 0.8980 chunk 33 optimal weight: 4.9990 chunk 34 optimal weight: 4.9990 chunk 36 optimal weight: 0.0770 chunk 24 optimal weight: 0.4980 chunk 38 optimal weight: 1.9990 chunk 23 optimal weight: 10.0000 chunk 18 optimal weight: 5.9990 chunk 27 optimal weight: 0.0010 chunk 40 optimal weight: 0.7980 chunk 37 optimal weight: 1.9990 overall best weight: 0.4544 ------------------------------------------------------------------------------- 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: 0.7526 moved from start: 0.1882 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.038 3351 Z= 0.165 Angle : 0.534 6.789 4561 Z= 0.277 Chirality : 0.042 0.140 501 Planarity : 0.005 0.050 579 Dihedral : 7.670 52.852 517 Min Nonbonded Distance : 2.272 Molprobity Statistics. All-atom Clashscore : 13.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.86 % Favored : 96.14 % Rotamer: Outliers : 1.21 % Allowed : 16.06 % Favored : 82.73 % 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: 1.55 (0.42), residues: 414 helix: 2.31 (0.34), residues: 211 sheet: -0.04 (0.68), residues: 68 loop : -0.43 (0.56), residues: 135 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 63 HIS 0.001 0.000 HIS A 388 PHE 0.009 0.001 PHE A 197 TYR 0.018 0.001 TYR A 20 ARG 0.007 0.001 ARG A 118 *********************** 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 52 residues out of total 339 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 48 time to evaluate : 0.362 Fit side-chains REVERT: A 287 LEU cc_start: 0.5921 (OUTLIER) cc_final: 0.5687 (tt) REVERT: A 400 TYR cc_start: 0.7887 (OUTLIER) cc_final: 0.6491 (t80) outliers start: 4 outliers final: 2 residues processed: 52 average time/residue: 0.2407 time to fit residues: 14.8060 Evaluate side-chains 52 residues out of total 339 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 48 time to evaluate : 0.386 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 53 VAL Chi-restraints excluded: chain A residue 184 SER Chi-restraints excluded: chain A residue 287 LEU Chi-restraints excluded: chain A residue 400 TYR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 41 random chunks: chunk 32 optimal weight: 6.9990 chunk 3 optimal weight: 0.8980 chunk 25 optimal weight: 3.9990 chunk 19 optimal weight: 0.9980 chunk 34 optimal weight: 0.9990 chunk 9 optimal weight: 0.0980 chunk 29 optimal weight: 3.9990 chunk 4 optimal weight: 0.5980 chunk 13 optimal weight: 1.9990 chunk 33 optimal weight: 5.9990 chunk 6 optimal weight: 0.9980 overall best weight: 0.7180 ------------------------------------------------------------------------------- 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: 0.7534 moved from start: 0.1935 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 3351 Z= 0.191 Angle : 0.558 7.244 4561 Z= 0.286 Chirality : 0.042 0.155 501 Planarity : 0.005 0.054 579 Dihedral : 7.554 52.982 517 Min Nonbonded Distance : 2.276 Molprobity Statistics. All-atom Clashscore : 13.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.59 % Favored : 95.41 % Rotamer: Outliers : 1.21 % Allowed : 16.06 % Favored : 82.73 % 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 (0.43), residues: 414 helix: 2.38 (0.35), residues: 211 sheet: 0.01 (0.68), residues: 68 loop : -0.40 (0.56), residues: 135 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 63 HIS 0.003 0.001 HIS A 388 PHE 0.009 0.001 PHE A 341 TYR 0.014 0.001 TYR A 20 ARG 0.007 0.001 ARG A 200 ********************** 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 52 residues out of total 339 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 48 time to evaluate : 0.369 Fit side-chains REVERT: A 166 ARG cc_start: 0.5215 (ttt-90) cc_final: 0.5011 (ttt-90) REVERT: A 287 LEU cc_start: 0.5953 (OUTLIER) cc_final: 0.5709 (tt) REVERT: A 400 TYR cc_start: 0.7872 (OUTLIER) cc_final: 0.6475 (t80) outliers start: 4 outliers final: 2 residues processed: 52 average time/residue: 0.2376 time to fit residues: 14.3399 Evaluate side-chains 53 residues out of total 339 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 49 time to evaluate : 0.372 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 53 VAL Chi-restraints excluded: chain A residue 184 SER Chi-restraints excluded: chain A residue 287 LEU Chi-restraints excluded: chain A residue 400 TYR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 41 random chunks: chunk 28 optimal weight: 3.9990 chunk 1 optimal weight: 2.9990 chunk 23 optimal weight: 4.9990 chunk 37 optimal weight: 0.3980 chunk 21 optimal weight: 0.9990 chunk 27 optimal weight: 5.9990 chunk 26 optimal weight: 10.0000 chunk 24 optimal weight: 8.9990 chunk 16 optimal weight: 7.9990 chunk 15 optimal weight: 0.9980 chunk 40 optimal weight: 0.8980 overall best weight: 1.2584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 19 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4166 r_free = 0.4166 target = 0.157529 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3811 r_free = 0.3811 target = 0.132770 restraints weight = 7084.833| |-----------------------------------------------------------------------------| r_work (start): 0.3800 rms_B_bonded: 2.69 r_work: 0.3693 rms_B_bonded: 3.43 restraints_weight: 0.5000 r_work (final): 0.3693 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7746 moved from start: 0.1874 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.057 3351 Z= 0.226 Angle : 0.565 7.431 4561 Z= 0.291 Chirality : 0.043 0.152 501 Planarity : 0.005 0.059 579 Dihedral : 7.613 53.079 517 Min Nonbonded Distance : 2.255 Molprobity Statistics. All-atom Clashscore : 13.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.35 % Favored : 95.65 % Rotamer: Outliers : 1.21 % Allowed : 16.36 % Favored : 82.42 % 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 (0.43), residues: 414 helix: 2.35 (0.35), residues: 211 sheet: -0.03 (0.68), residues: 69 loop : -0.39 (0.56), residues: 134 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 30 HIS 0.003 0.001 HIS A 388 PHE 0.009 0.001 PHE A 341 TYR 0.033 0.001 TYR A 20 ARG 0.008 0.001 ARG A 118 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1134.05 seconds wall clock time: 21 minutes 24.00 seconds (1284.00 seconds total)