Starting phenix.real_space_refine (version: 1.21rc1) on Mon Jul 3 18:15:50 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8hj9_34835/07_2023/8hj9_34835_neut_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8hj9_34835/07_2023/8hj9_34835.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.12 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8hj9_34835/07_2023/8hj9_34835.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8hj9_34835/07_2023/8hj9_34835.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8hj9_34835/07_2023/8hj9_34835_neut_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8hj9_34835/07_2023/8hj9_34835_neut_updated.pdb" } resolution = 3.12 write_initial_geo_file = False refinement { macro_cycles = 10 } 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 ------------------------------------------------------------------------------- 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 GLU 8": "OE1" <-> "OE2" Residue "A GLU 15": "OE1" <-> "OE2" Residue "A GLU 25": "OE1" <-> "OE2" Residue "A ASP 48": "OD1" <-> "OD2" Residue "A PHE 57": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 78": "OE1" <-> "OE2" Residue "A TYR 132": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 160": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 250": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 283": "OE1" <-> "OE2" Residue "A PHE 353": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 354": "OE1" <-> "OE2" Residue "A TYR 363": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 381": "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-1.21rc1-5013/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: 1.91, per 1000 atoms: 0.58 Number of scatterers: 3274 At special positions: 0 Unit cell: (67.048, 75.922, 70.992, 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: 1.32 Conformation dependent library (CDL) restraints added in 549.2 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 3 sheets defined 49.5% alpha, 13.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.36 Creating SS restraints... Processing helix chain 'A' and resid 5 through 20 removed outlier: 4.114A 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 95 Processing helix chain 'A' and resid 112 through 114 No H-bonds generated for 'chain 'A' and resid 112 through 114' Processing helix chain 'A' and resid 117 through 134 removed outlier: 5.598A pdb=" N ASP A 133 " --> pdb=" O ARG A 129 " (cutoff:3.500A) removed outlier: 5.943A 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 Processing helix chain 'A' and resid 303 through 305 No H-bonds generated for 'chain 'A' and resid 303 through 305' Processing helix chain 'A' and resid 324 through 332 Processing helix chain 'A' and resid 340 through 360 removed outlier: 3.536A pdb=" N ASN A 344 " --> pdb=" O ASP A 340 " (cutoff:3.500A) removed outlier: 3.591A pdb=" N ALA A 345 " --> pdb=" O PHE A 341 " (cutoff:3.500A) removed outlier: 5.025A pdb=" N GLY A 346 " --> pdb=" O LEU A 342 " (cutoff:3.500A) removed outlier: 6.178A pdb=" N GLY A 347 " --> pdb=" O CYS A 343 " (cutoff:3.500A) removed outlier: 4.479A pdb=" N VAL A 348 " --> pdb=" O ASN A 344 " (cutoff:3.500A) 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: 6.376A pdb=" N GLY A 103 " --> pdb=" O HIS A 61 " (cutoff:3.500A) removed outlier: 6.915A pdb=" N GLY A 104 " --> pdb=" O PRO A 67 " (cutoff:3.500A) removed outlier: 5.535A pdb=" N LYS A 69 " --> pdb=" O GLY A 104 " (cutoff:3.500A) removed outlier: 7.386A pdb=" N GLY A 106 " --> pdb=" O LYS A 69 " (cutoff:3.500A) removed outlier: 5.949A pdb=" N GLY A 71 " --> pdb=" O GLY A 106 " (cutoff:3.500A) removed outlier: 8.056A pdb=" N ILE A 108 " --> pdb=" O GLY A 71 " (cutoff:3.500A) Processing sheet with id= B, first strand: chain 'A' and resid 291 through 294 removed outlier: 6.648A pdb=" N THR A 238 " --> pdb=" O ILE A 215 " (cutoff:3.500A) removed outlier: 8.245A pdb=" N VAL A 217 " --> pdb=" O THR A 238 " (cutoff:3.500A) removed outlier: 8.076A pdb=" N VAL A 240 " --> pdb=" O VAL A 217 " (cutoff:3.500A) Processing sheet with id= C, first strand: chain 'A' and resid 313 through 315 removed outlier: 6.884A pdb=" N LEU A 336 " --> pdb=" O VAL A 314 " (cutoff:3.500A) No H-bonds generated for sheet with id= C 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: 0.89 Time building geometry restraints manager: 1.43 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: 1063 1.34 - 1.46: 676 1.46 - 1.57: 1580 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 1.615 0.121 2.00e-02 2.50e+03 3.67e+01 bond pdb=" C1D NAP A 501 " pdb=" O4D NAP A 501 " ideal model delta sigma weight residual 1.375 1.427 -0.052 2.00e-02 2.50e+03 6.80e+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 5.07e+00 bond pdb=" O3 NAP A 501 " pdb=" PA NAP A 501 " ideal model delta sigma weight residual 1.647 1.605 0.042 2.00e-02 2.50e+03 4.48e+00 ... (remaining 3346 not shown) Histogram of bond angle deviations from ideal: 99.63 - 106.51: 115 106.51 - 113.39: 1835 113.39 - 120.27: 1171 120.27 - 127.15: 1385 127.15 - 134.04: 55 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 123.47 127.83 -4.36 1.53e+00 4.27e-01 8.13e+00 angle pdb=" C2B NAP A 501 " pdb=" O2B NAP A 501 " pdb=" P2B NAP A 501 " ideal model delta sigma weight residual 117.19 109.40 7.79 3.00e+00 1.11e-01 6.75e+00 angle pdb=" N GLY A 219 " pdb=" CA GLY A 219 " pdb=" C GLY A 219 " ideal model delta sigma weight residual 113.18 107.69 5.49 2.37e+00 1.78e-01 5.37e+00 angle pdb=" N VAL A 97 " pdb=" CA VAL A 97 " pdb=" C VAL A 97 " ideal model delta sigma weight residual 112.83 110.54 2.29 9.90e-01 1.02e+00 5.34e+00 angle pdb=" N ASP A 145 " pdb=" CA ASP A 145 " pdb=" C ASP A 145 " ideal model delta sigma weight residual 108.19 110.98 -2.79 1.29e+00 6.01e-01 4.69e+00 ... (remaining 4556 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.07: 1763 17.07 - 34.15: 163 34.15 - 51.22: 41 51.22 - 68.29: 10 68.29 - 85.36: 9 Dihedral angle restraints: 1986 sinusoidal: 797 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 180.00 162.79 17.21 0 5.00e+00 4.00e-02 1.18e+01 dihedral pdb=" CB LYS A 32 " pdb=" CG LYS A 32 " pdb=" CD LYS A 32 " pdb=" CE LYS A 32 " ideal model delta sinusoidal sigma weight residual -180.00 -122.52 -57.48 3 1.50e+01 4.44e-03 9.44e+00 dihedral pdb=" CG LYS A 214 " pdb=" CD LYS A 214 " pdb=" CE LYS A 214 " pdb=" NZ LYS A 214 " ideal model delta sinusoidal sigma weight residual -60.00 -115.05 55.05 3 1.50e+01 4.44e-03 9.32e+00 ... (remaining 1983 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.027: 290 0.027 - 0.054: 120 0.054 - 0.081: 43 0.081 - 0.108: 37 0.108 - 0.135: 11 Chirality restraints: 501 Sorted by residual: chirality pdb=" CA ILE A 37 " pdb=" N ILE A 37 " pdb=" C ILE A 37 " pdb=" CB ILE A 37 " both_signs ideal model delta sigma weight residual False 2.43 2.57 -0.13 2.00e-01 2.50e+01 4.53e-01 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 2.55 -0.12 2.00e-01 2.50e+01 3.66e-01 chirality pdb=" CA ILE A 313 " pdb=" N ILE A 313 " pdb=" C ILE A 313 " pdb=" CB ILE A 313 " both_signs ideal model delta sigma weight residual False 2.43 2.55 -0.12 2.00e-01 2.50e+01 3.44e-01 ... (remaining 498 not shown) Planarity restraints: 579 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C1D NAP A 501 " -0.032 2.00e-02 2.50e+03 7.06e-02 9.96e+01 pdb=" C2N NAP A 501 " 0.113 2.00e-02 2.50e+03 pdb=" C3N NAP A 501 " 0.032 2.00e-02 2.50e+03 pdb=" C4N NAP A 501 " 0.087 2.00e-02 2.50e+03 pdb=" C5N NAP A 501 " -0.037 2.00e-02 2.50e+03 pdb=" C6N NAP A 501 " -0.059 2.00e-02 2.50e+03 pdb=" C7N NAP A 501 " -0.113 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 " 0.029 5.00e-02 4.00e+02 4.34e-02 3.02e+00 pdb=" N PRO A 142 " -0.075 5.00e-02 4.00e+02 pdb=" CA PRO A 142 " 0.023 5.00e-02 4.00e+02 pdb=" CD PRO A 142 " 0.024 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ASN A 149 " -0.024 5.00e-02 4.00e+02 3.63e-02 2.11e+00 pdb=" N PRO A 150 " 0.063 5.00e-02 4.00e+02 pdb=" CA PRO A 150 " -0.018 5.00e-02 4.00e+02 pdb=" CD PRO A 150 " -0.020 5.00e-02 4.00e+02 ... (remaining 576 not shown) Histogram of nonbonded interaction distances: 2.23 - 2.77: 554 2.77 - 3.30: 3341 3.30 - 3.83: 5865 3.83 - 4.37: 6757 4.37 - 4.90: 11539 Nonbonded interactions: 28056 Sorted by model distance: nonbonded pdb=" OH TYR A 408 " pdb=" O LYS A 419 " model vdw 2.234 2.440 nonbonded pdb=" NE1 TRP A 263 " pdb=" O LYS A 271 " model vdw 2.255 2.520 nonbonded pdb=" OG1 THR A 68 " pdb=" OD1 ASP A 140 " model vdw 2.257 2.440 nonbonded pdb=" OD2 ASP A 244 " pdb=" OG SER A 269 " model vdw 2.281 2.440 nonbonded pdb=" O ASP A 209 " pdb=" NZ LYS A 213 " model vdw 2.290 2.520 ... (remaining 28051 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: 0.770 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.000 Extract box with map and model: 3.560 Check model and map are aligned: 0.050 Set scattering table: 0.030 Process input model: 13.080 Find NCS groups from input model: 0.080 Set up NCS constraints: 0.010 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.750 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 20.340 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7503 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.121 3351 Z= 0.280 Angle : 0.648 7.795 4561 Z= 0.363 Chirality : 0.042 0.135 501 Planarity : 0.005 0.071 579 Dihedral : 15.542 85.364 1228 Min Nonbonded Distance : 2.234 Molprobity Statistics. All-atom Clashscore : 10.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.66 % Favored : 97.34 % Rotamer Outliers : 0.00 % 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: 1.80 (0.43), residues: 414 helix: 2.39 (0.35), residues: 205 sheet: 0.15 (0.69), residues: 64 loop : -0.00 (0.57), residues: 145 *********************** 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 56 residues out of total 339 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 56 time to evaluate : 0.380 Fit side-chains revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 56 average time/residue: 0.1319 time to fit residues: 9.5271 Evaluate side-chains 43 residues out of total 339 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 43 time to evaluate : 0.381 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.5156 ------------------------------------------------------------------------------- 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: 3.9990 chunk 31 optimal weight: 9.9990 chunk 17 optimal weight: 1.9990 chunk 10 optimal weight: 6.9990 chunk 20 optimal weight: 10.0000 chunk 16 optimal weight: 2.9990 chunk 32 optimal weight: 2.9990 chunk 12 optimal weight: 0.7980 chunk 19 optimal weight: 1.9990 chunk 23 optimal weight: 10.0000 chunk 37 optimal weight: 0.6980 overall best weight: 1.6986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 111 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7616 moved from start: 0.1109 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.027 3351 Z= 0.243 Angle : 0.486 6.472 4561 Z= 0.248 Chirality : 0.042 0.133 501 Planarity : 0.004 0.047 579 Dihedral : 7.425 89.613 471 Min Nonbonded Distance : 2.164 Molprobity Statistics. All-atom Clashscore : 12.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.14 % Favored : 96.86 % Rotamer Outliers : 1.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.59 (0.43), residues: 414 helix: 2.18 (0.35), residues: 210 sheet: 0.12 (0.72), residues: 60 loop : -0.16 (0.57), residues: 144 *********************** 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 47 residues out of total 339 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 42 time to evaluate : 0.391 Fit side-chains revert: symmetry clash outliers start: 5 outliers final: 3 residues processed: 43 average time/residue: 0.1295 time to fit residues: 7.4119 Evaluate side-chains 45 residues out of total 339 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 42 time to evaluate : 0.385 Switching outliers to nearest non-outliers outliers start: 3 outliers final: 0 residues processed: 3 average time/residue: 0.0372 time to fit residues: 0.7231 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 41 random chunks: chunk 20 optimal weight: 0.8980 chunk 11 optimal weight: 6.9990 chunk 30 optimal weight: 0.0570 chunk 25 optimal weight: 6.9990 chunk 10 optimal weight: 0.5980 chunk 37 optimal weight: 0.9980 chunk 40 optimal weight: 2.9990 chunk 33 optimal weight: 0.9980 chunk 36 optimal weight: 0.6980 chunk 12 optimal weight: 0.7980 chunk 29 optimal weight: 10.0000 overall best weight: 0.6098 ------------------------------------------------------------------------------- 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: 0.7557 moved from start: 0.1010 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.022 3351 Z= 0.136 Angle : 0.430 6.839 4561 Z= 0.220 Chirality : 0.040 0.132 501 Planarity : 0.004 0.050 579 Dihedral : 6.425 75.766 471 Min Nonbonded Distance : 2.214 Molprobity Statistics. All-atom Clashscore : 10.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.17 % Favored : 97.83 % Rotamer Outliers : 0.61 % 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: 1.70 (0.43), residues: 414 helix: 2.27 (0.35), residues: 210 sheet: 0.26 (0.72), residues: 60 loop : -0.15 (0.57), residues: 144 *********************** 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 52 residues out of total 339 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 50 time to evaluate : 0.382 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 2 outliers final: 0 residues processed: 50 average time/residue: 0.1417 time to fit residues: 9.1050 Evaluate side-chains 42 residues out of total 339 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 42 time to evaluate : 0.387 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.5620 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 41 random chunks: chunk 36 optimal weight: 0.8980 chunk 28 optimal weight: 4.9990 chunk 19 optimal weight: 0.9980 chunk 4 optimal weight: 0.5980 chunk 17 optimal weight: 1.9990 chunk 25 optimal weight: 1.9990 chunk 37 optimal weight: 0.9990 chunk 39 optimal weight: 3.9990 chunk 35 optimal weight: 2.9990 chunk 10 optimal weight: 2.9990 chunk 33 optimal weight: 5.9990 overall best weight: 1.0984 ------------------------------------------------------------------------------- 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: 0.7590 moved from start: 0.1235 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.021 3351 Z= 0.177 Angle : 0.454 7.124 4561 Z= 0.229 Chirality : 0.041 0.129 501 Planarity : 0.004 0.050 579 Dihedral : 5.691 63.540 471 Min Nonbonded Distance : 2.200 Molprobity Statistics. All-atom Clashscore : 11.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.66 % Favored : 97.34 % Rotamer Outliers : 1.82 % 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: 1.62 (0.43), residues: 414 helix: 2.21 (0.35), residues: 210 sheet: 0.23 (0.71), residues: 62 loop : -0.21 (0.57), residues: 142 *********************** 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 50 residues out of total 339 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 44 time to evaluate : 0.384 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 6 outliers final: 2 residues processed: 47 average time/residue: 0.1264 time to fit residues: 7.8488 Evaluate side-chains 45 residues out of total 339 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 43 time to evaluate : 0.394 Switching outliers to nearest non-outliers outliers start: 2 outliers final: 0 residues processed: 2 average time/residue: 0.0352 time to fit residues: 0.6453 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 41 random chunks: chunk 22 optimal weight: 0.8980 chunk 0 optimal weight: 10.0000 chunk 29 optimal weight: 9.9990 chunk 16 optimal weight: 7.9990 chunk 33 optimal weight: 4.9990 chunk 27 optimal weight: 5.9990 chunk 20 optimal weight: 1.9990 chunk 35 optimal weight: 0.9980 chunk 10 optimal weight: 3.9990 chunk 13 optimal weight: 0.7980 chunk 7 optimal weight: 1.9990 overall best weight: 1.3384 ------------------------------------------------------------------------------- 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: 0.7608 moved from start: 0.1343 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.022 3351 Z= 0.198 Angle : 0.479 7.555 4561 Z= 0.241 Chirality : 0.042 0.128 501 Planarity : 0.004 0.051 579 Dihedral : 5.256 53.841 471 Min Nonbonded Distance : 2.184 Molprobity Statistics. All-atom Clashscore : 11.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.14 % Favored : 96.86 % Rotamer Outliers : 1.21 % 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: 1.53 (0.43), residues: 414 helix: 2.12 (0.34), residues: 210 sheet: -0.18 (0.66), residues: 70 loop : -0.00 (0.59), residues: 134 *********************** 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 50 residues out of total 339 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 46 time to evaluate : 0.369 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 4 outliers final: 1 residues processed: 48 average time/residue: 0.1201 time to fit residues: 7.7451 Evaluate side-chains 45 residues out of total 339 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 44 time to evaluate : 0.395 Switching outliers to nearest non-outliers outliers start: 1 outliers final: 0 residues processed: 1 average time/residue: 0.0375 time to fit residues: 0.6011 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 41 random chunks: chunk 23 optimal weight: 9.9990 chunk 9 optimal weight: 2.9990 chunk 39 optimal weight: 0.9980 chunk 32 optimal weight: 0.5980 chunk 18 optimal weight: 0.5980 chunk 3 optimal weight: 0.7980 chunk 13 optimal weight: 0.9990 chunk 20 optimal weight: 0.9980 chunk 38 optimal weight: 0.7980 chunk 4 optimal weight: 0.5980 chunk 22 optimal weight: 0.9990 overall best weight: 0.6780 ------------------------------------------------------------------------------- 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: 0.7565 moved from start: 0.1334 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.021 3351 Z= 0.144 Angle : 0.459 7.907 4561 Z= 0.230 Chirality : 0.041 0.128 501 Planarity : 0.004 0.051 579 Dihedral : 4.978 47.495 471 Min Nonbonded Distance : 2.213 Molprobity Statistics. All-atom Clashscore : 10.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.66 % Favored : 97.34 % Rotamer Outliers : 1.21 % 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: 1.62 (0.43), residues: 414 helix: 2.18 (0.34), residues: 210 sheet: 0.17 (0.68), residues: 67 loop : -0.12 (0.58), residues: 137 *********************** 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 51 residues out of total 339 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 47 time to evaluate : 0.387 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 4 outliers final: 1 residues processed: 50 average time/residue: 0.1106 time to fit residues: 7.5067 Evaluate side-chains 45 residues out of total 339 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 44 time to evaluate : 0.376 Switching outliers to nearest non-outliers outliers start: 1 outliers final: 0 residues processed: 1 average time/residue: 0.0359 time to fit residues: 0.5830 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 41 random chunks: chunk 28 optimal weight: 10.0000 chunk 22 optimal weight: 0.9980 chunk 33 optimal weight: 0.8980 chunk 39 optimal weight: 0.8980 chunk 24 optimal weight: 9.9990 chunk 18 optimal weight: 0.4980 chunk 15 optimal weight: 4.9990 chunk 23 optimal weight: 6.9990 chunk 11 optimal weight: 4.9990 chunk 7 optimal weight: 2.9990 chunk 25 optimal weight: 5.9990 overall best weight: 1.2582 ------------------------------------------------------------------------------- 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: 0.7596 moved from start: 0.1454 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.023 3351 Z= 0.195 Angle : 0.501 7.200 4561 Z= 0.254 Chirality : 0.042 0.128 501 Planarity : 0.004 0.052 579 Dihedral : 5.006 44.750 471 Min Nonbonded Distance : 2.202 Molprobity Statistics. All-atom Clashscore : 11.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.66 % Favored : 97.34 % Rotamer Outliers : 0.91 % 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 (0.43), residues: 414 helix: 2.10 (0.35), residues: 210 sheet: -0.12 (0.66), residues: 70 loop : 0.02 (0.59), residues: 134 *********************** 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 49 residues out of total 339 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 46 time to evaluate : 0.382 Fit side-chains revert: symmetry clash outliers start: 3 outliers final: 0 residues processed: 48 average time/residue: 0.1297 time to fit residues: 8.1651 Evaluate side-chains 43 residues out of total 339 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 43 time to evaluate : 0.373 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.6036 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 41 random chunks: chunk 26 optimal weight: 0.9980 chunk 19 optimal weight: 0.9980 chunk 3 optimal weight: 2.9990 chunk 31 optimal weight: 9.9990 chunk 35 optimal weight: 0.9990 chunk 37 optimal weight: 0.8980 chunk 34 optimal weight: 0.7980 chunk 36 optimal weight: 0.7980 chunk 22 optimal weight: 7.9990 chunk 16 optimal weight: 0.4980 chunk 28 optimal weight: 4.9990 overall best weight: 0.7980 ------------------------------------------------------------------------------- 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: 0.7568 moved from start: 0.1477 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.024 3351 Z= 0.164 Angle : 0.512 8.269 4561 Z= 0.257 Chirality : 0.042 0.143 501 Planarity : 0.004 0.052 579 Dihedral : 4.997 42.352 471 Min Nonbonded Distance : 2.211 Molprobity Statistics. All-atom Clashscore : 11.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.90 % Favored : 97.10 % Rotamer Outliers : 0.30 % 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: 1.58 (0.43), residues: 414 helix: 2.13 (0.35), residues: 210 sheet: -0.02 (0.68), residues: 70 loop : -0.00 (0.59), residues: 134 *********************** 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 47 residues out of total 339 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 46 time to evaluate : 0.383 Fit side-chains outliers start: 1 outliers final: 1 residues processed: 47 average time/residue: 0.1235 time to fit residues: 7.7828 Evaluate side-chains 44 residues out of total 339 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 43 time to evaluate : 0.377 Switching outliers to nearest non-outliers outliers start: 1 outliers final: 0 residues processed: 1 average time/residue: 0.0351 time to fit residues: 0.5598 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 41 random chunks: chunk 11 optimal weight: 4.9990 chunk 33 optimal weight: 0.8980 chunk 34 optimal weight: 5.9990 chunk 36 optimal weight: 0.9990 chunk 24 optimal weight: 8.9990 chunk 38 optimal weight: 0.8980 chunk 23 optimal weight: 5.9990 chunk 18 optimal weight: 0.9980 chunk 27 optimal weight: 7.9990 chunk 40 optimal weight: 3.9990 chunk 37 optimal weight: 0.8980 overall best weight: 0.9382 ------------------------------------------------------------------------------- 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: 0.7573 moved from start: 0.1536 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.022 3351 Z= 0.178 Angle : 0.532 8.331 4561 Z= 0.265 Chirality : 0.042 0.156 501 Planarity : 0.004 0.052 579 Dihedral : 5.015 41.046 471 Min Nonbonded Distance : 2.206 Molprobity Statistics. All-atom Clashscore : 12.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.90 % Favored : 97.10 % Rotamer Outliers : 0.30 % 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: 1.50 (0.43), residues: 414 helix: 2.08 (0.35), residues: 210 sheet: 0.06 (0.68), residues: 69 loop : -0.15 (0.58), residues: 135 *********************** 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 47 residues out of total 339 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 46 time to evaluate : 0.379 Fit side-chains outliers start: 1 outliers final: 1 residues processed: 46 average time/residue: 0.1218 time to fit residues: 7.5289 Evaluate side-chains 44 residues out of total 339 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 43 time to evaluate : 0.379 Switching outliers to nearest non-outliers outliers start: 1 outliers final: 0 residues processed: 1 average time/residue: 0.0359 time to fit residues: 0.5870 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 41 random chunks: chunk 32 optimal weight: 3.9990 chunk 3 optimal weight: 3.9990 chunk 25 optimal weight: 4.9990 chunk 19 optimal weight: 0.9990 chunk 34 optimal weight: 0.5980 chunk 9 optimal weight: 0.7980 chunk 29 optimal weight: 8.9990 chunk 4 optimal weight: 0.0980 chunk 13 optimal weight: 0.9990 chunk 33 optimal weight: 0.8980 chunk 6 optimal weight: 0.9980 overall best weight: 0.6780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 234 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7550 moved from start: 0.1565 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.021 3351 Z= 0.159 Angle : 0.522 8.407 4561 Z= 0.261 Chirality : 0.042 0.160 501 Planarity : 0.004 0.052 579 Dihedral : 4.997 39.728 471 Min Nonbonded Distance : 2.212 Molprobity Statistics. All-atom Clashscore : 12.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.66 % Favored : 97.34 % Rotamer Outliers : 0.00 % 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: 1.50 (0.43), residues: 414 helix: 2.12 (0.35), residues: 210 sheet: -0.13 (0.67), residues: 68 loop : -0.10 (0.58), residues: 136 ********************** 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 45 residues out of total 339 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 45 time to evaluate : 0.380 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 45 average time/residue: 0.1134 time to fit residues: 7.0716 Evaluate side-chains 45 residues out of total 339 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 45 time to evaluate : 0.354 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.5204 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Traceback (most recent call last): File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5013/build/../modules/phenix/phenix/command_line/real_space_refine.py", line 8, in run_program(real_space_refine.Program) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5013/modules/cctbx_project/iotbx/cli_parser.py", line 872, in run_program task.run() File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5013/modules/phenix/phenix/programs/real_space_refine.py", line 192, in run log = self.logger) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5013/modules/phenix/phenix/refinement/rsr/wrappers.py", line 58, in __init__ log = log) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5013/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 297, in __init__ self.caller(self.refine_xyz) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5013/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 312, in caller func() File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5013/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 673, in refine_xyz self.minimization_no_ncs() File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5013/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 737, in minimization_no_ncs log = self.log) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5013/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 51, in __init__ gradients_method = gradients_method) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5013/modules/cctbx_project/mmtbx/refinement/real_space/weight.py", line 87, in __init__ rms_angles_limit = rms_angles_limit) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5013/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 368, in refine rms_angles_limit = rms_angles_limit) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5013/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 235, in __init__ weight = weight) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5013/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 112, in refine states_collector = self.states_accumulator) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5013/modules/cctbx_project/cctbx/maptbx/real_space_refinement_simple.py", line 174, in __init__ exception_handling_params=lbfgs_exception_handling_params) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5013/modules/cctbx_project/scitbx/lbfgs/__init__.py", line 278, in run line_search) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5013/modules/cctbx_project/scitbx/lbfgs/__init__.py", line 131, in run_c_plus_plus f, g = target_evaluator.compute_functional_and_gradients() File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5013/modules/cctbx_project/cctbx/maptbx/real_space_refinement_simple.py", line 245, in compute_functional_and_gradients compute_gradients=True) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5013/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1479, in energies_sites flags=flags, sites_cart=sites_cart, site_labels=site_labels) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5013/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1381, in pair_proxies check_bonded_distance_cutoff(sites_frac=sites_frac) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5013/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1262, in check_bonded_distance_cutoff raise RuntimeError(msg) RuntimeError: Bond distance > max_reasonable_bond_distance: 59.3792 > 50: distance: 32 - 75: 13.251 distance: 34 - 39: 19.844 distance: 35 - 72: 5.321 distance: 39 - 40: 4.123 distance: 40 - 41: 6.006 distance: 40 - 43: 12.592 distance: 41 - 42: 7.704 distance: 41 - 45: 14.961 distance: 43 - 44: 21.967 distance: 45 - 46: 23.238 distance: 46 - 47: 25.376 distance: 46 - 49: 21.307 distance: 47 - 48: 16.194 distance: 47 - 53: 12.844 distance: 49 - 50: 24.338 distance: 50 - 51: 24.174 distance: 50 - 52: 24.072 distance: 53 - 54: 14.080 distance: 54 - 55: 13.032 distance: 54 - 57: 15.875 distance: 55 - 56: 9.934 distance: 55 - 59: 13.041 distance: 57 - 58: 13.551 distance: 59 - 60: 5.093 distance: 60 - 61: 7.802 distance: 60 - 63: 14.209 distance: 61 - 62: 19.020 distance: 61 - 64: 15.567 distance: 64 - 65: 12.540 distance: 65 - 66: 15.213 distance: 66 - 67: 5.931 distance: 66 - 68: 21.106 distance: 68 - 69: 12.669 distance: 68 - 176: 9.906 distance: 69 - 70: 17.405 distance: 70 - 71: 3.453 distance: 70 - 72: 19.087 distance: 71 - 173: 18.727 distance: 72 - 73: 9.867 distance: 73 - 74: 5.707 distance: 73 - 76: 11.285 distance: 74 - 75: 6.213 distance: 74 - 80: 9.998 distance: 76 - 77: 5.358 distance: 76 - 78: 19.864 distance: 77 - 79: 11.589 distance: 80 - 81: 7.138 distance: 80 - 162: 7.132 distance: 81 - 82: 30.789 distance: 81 - 84: 30.440 distance: 82 - 83: 34.797 distance: 82 - 92: 24.856 distance: 83 - 159: 33.336 distance: 84 - 85: 17.163 distance: 85 - 86: 26.462 distance: 85 - 87: 15.565 distance: 86 - 88: 11.891 distance: 87 - 89: 18.416 distance: 88 - 90: 5.142 distance: 89 - 90: 30.314 distance: 90 - 91: 5.872 distance: 92 - 93: 22.722 distance: 93 - 94: 12.249 distance: 93 - 96: 25.467 distance: 94 - 95: 14.766 distance: 94 - 100: 15.049 distance: 96 - 97: 8.433 distance: 97 - 98: 11.430 distance: 97 - 99: 8.185 distance: 100 - 101: 17.553 distance: 100 - 106: 19.759 distance: 101 - 102: 13.686 distance: 101 - 104: 26.389 distance: 102 - 103: 8.022 distance: 102 - 107: 7.708 distance: 104 - 105: 3.444 distance: 105 - 106: 8.171