Starting phenix.real_space_refine on Tue Feb 13 05:13:49 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8xd1_38262/02_2024/8xd1_38262_neut_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8xd1_38262/02_2024/8xd1_38262.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.96 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8xd1_38262/02_2024/8xd1_38262.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8xd1_38262/02_2024/8xd1_38262.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8xd1_38262/02_2024/8xd1_38262_neut_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8xd1_38262/02_2024/8xd1_38262_neut_updated.pdb" } resolution = 2.96 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= 0.002 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 2097 2.51 5 N 562 2.21 5 O 631 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A GLU 29": "OE1" <-> "OE2" Residue "A GLU 78": "OE1" <-> "OE2" Residue "A TYR 101": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 114": "OE1" <-> "OE2" Residue "A TYR 147": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 209": "OD1" <-> "OD2" Residue "A ASP 244": "OD1" <-> "OD2" Residue "A ASP 253": "OD1" <-> "OD2" Residue "A ASP 327": "OD1" <-> "OD2" Residue "A ASP 340": "OD1" <-> "OD2" Residue "A GLU 354": "OE1" <-> "OE2" Residue "A TYR 362": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 368": "OE1" <-> "OE2" Residue "A GLU 371": "OE1" <-> "OE2" Residue "A GLU 383": "OE1" <-> "OE2" 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-5238/modules/chem_data/mon_lib" Total number of atoms: 3307 Number of models: 1 Model: "" Number of chains: 2 Chain: "A" Number of atoms: 3267 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 416, 3261 Classifications: {'peptide': 416} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 20, 'TRANS': 395} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 4 Conformer: "B" Number of residues, atoms: 416, 3261 Classifications: {'peptide': 416} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 20, 'TRANS': 395} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 4 bond proxies already assigned to first conformer: 3327 Chain: "A" Number of atoms: 40 Number of conformers: 1 Conformer: "" Number of residues, atoms: 10, 40 Unusual residues: {'NAP': 1} Classifications: {'undetermined': 1, 'water': 9} Link IDs: {None: 9} Unresolved non-hydrogen bonds: 19 Unresolved non-hydrogen angles: 28 Unresolved non-hydrogen dihedrals: 40 Unresolved non-hydrogen chiralities: 4 Planarities with less than four sites: {'NAP:plan-2': 1, 'NAP:plan-4': 1} Unresolved non-hydrogen planarities: 12 Time building chain proxies: 3.87, per 1000 atoms: 1.17 Number of scatterers: 3307 At special positions: 0 Unit cell: (67.68, 73.696, 71.44, 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 631 8.00 N 562 7.00 C 2097 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: 1.07 Conformation dependent library (CDL) restraints added in 1.2 seconds 830 Ramachandran restraints generated. 415 Oldfield, 0 Emsley, 415 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 760 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 16 helices and 4 sheets defined 47.6% alpha, 13.5% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.82 Creating SS restraints... Processing helix chain 'A' and resid 6 through 20 removed outlier: 3.795A pdb=" N TYR A 20 " --> pdb=" O ARG A 16 " (cutoff:3.500A) Processing helix chain 'A' and resid 25 through 31 Processing helix chain 'A' and resid 80 through 96 removed outlier: 3.523A pdb=" N TRP A 92 " --> pdb=" O THR A 88 " (cutoff:3.500A) 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: 5.813A pdb=" N ASP A 133 " --> pdb=" O ARG A 129 " (cutoff:3.500A) removed outlier: 6.176A 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 removed outlier: 3.537A pdb=" N VAL A 173 " --> pdb=" O ALA A 170 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 170 through 173' Processing helix chain 'A' and resid 190 through 206 Processing helix chain 'A' and resid 224 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 324 through 332 Processing helix chain 'A' and resid 340 through 343 No H-bonds generated for 'chain 'A' and resid 340 through 343' Processing helix chain 'A' and resid 346 through 360 Processing helix chain 'A' and resid 366 through 391 Processing helix chain 'A' and resid 395 through 414 Processing sheet with id= A, first strand: chain 'A' and resid 36 through 45 removed outlier: 4.543A pdb=" N THR A 55 " --> pdb=" O ILE A 109 " (cutoff:3.500A) removed outlier: 6.489A pdb=" N GLY A 103 " --> pdb=" O HIS A 61 " (cutoff:3.500A) removed outlier: 6.890A pdb=" N GLY A 104 " --> pdb=" O PRO A 67 " (cutoff:3.500A) removed outlier: 5.187A pdb=" N LYS A 69 " --> pdb=" O GLY A 104 " (cutoff:3.500A) removed outlier: 7.276A pdb=" N GLY A 106 " --> pdb=" O LYS A 69 " (cutoff:3.500A) Processing sheet with id= B, first strand: chain 'A' and resid 72 through 75 removed outlier: 7.110A pdb=" N GLY A 106 " --> pdb=" O ARG A 73 " (cutoff:3.500A) removed outlier: 7.996A pdb=" N HIS A 75 " --> pdb=" O GLY A 106 " (cutoff:3.500A) removed outlier: 5.911A pdb=" N ILE A 108 " --> pdb=" O HIS A 75 " (cutoff:3.500A) No H-bonds generated for sheet with id= B Processing sheet with id= C, first strand: chain 'A' and resid 291 through 294 removed outlier: 6.711A pdb=" N THR A 238 " --> pdb=" O ILE A 215 " (cutoff:3.500A) removed outlier: 8.503A pdb=" N VAL A 217 " --> pdb=" O THR A 238 " (cutoff:3.500A) removed outlier: 8.551A 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: 6.588A pdb=" N LEU A 336 " --> pdb=" O VAL A 314 " (cutoff:3.500A) No H-bonds generated for sheet with id= D 157 hydrogen bonds defined for protein. 458 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: 0.90 Time building geometry restraints manager: 1.17 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.32: 584 1.32 - 1.44: 841 1.44 - 1.57: 1918 1.57 - 1.69: 4 1.69 - 1.81: 27 Bond restraints: 3374 Sorted by residual: bond pdb=" O2B NAP A 500 " pdb=" P2B NAP A 500 " ideal model delta sigma weight residual 1.736 1.567 0.169 2.00e-02 2.50e+03 7.17e+01 bond pdb=" C4A NAP A 500 " pdb=" N3A NAP A 500 " ideal model delta sigma weight residual 1.332 1.439 -0.107 2.00e-02 2.50e+03 2.85e+01 bond pdb=" C6A NAP A 500 " pdb=" N6A NAP A 500 " ideal model delta sigma weight residual 1.335 1.436 -0.101 2.00e-02 2.50e+03 2.56e+01 bond pdb=" C8A NAP A 500 " pdb=" N7A NAP A 500 " ideal model delta sigma weight residual 1.301 1.399 -0.098 2.00e-02 2.50e+03 2.42e+01 bond pdb=" N LYS A 204 " pdb=" CA BLYS A 204 " ideal model delta sigma weight residual 1.459 1.402 0.057 1.23e-02 6.61e+03 2.16e+01 ... (remaining 3369 not shown) Histogram of bond angle deviations from ideal: 99.76 - 106.62: 108 106.62 - 113.48: 1852 113.48 - 120.33: 1192 120.33 - 127.19: 1380 127.19 - 134.05: 51 Bond angle restraints: 4583 Sorted by residual: angle pdb=" N GLN A 234 " pdb=" CA GLN A 234 " pdb=" C GLN A 234 " ideal model delta sigma weight residual 111.07 116.91 -5.84 1.07e+00 8.73e-01 2.98e+01 angle pdb=" N VAL A 270 " pdb=" CA VAL A 270 " pdb=" C VAL A 270 " ideal model delta sigma weight residual 106.21 111.30 -5.09 1.07e+00 8.73e-01 2.26e+01 angle pdb=" C ASP A 5 " pdb=" N PRO A 6 " pdb=" CA PRO A 6 " ideal model delta sigma weight residual 118.85 123.76 -4.91 1.09e+00 8.42e-01 2.03e+01 angle pdb=" N ARG A 396 " pdb=" CA ARG A 396 " pdb=" C ARG A 396 " ideal model delta sigma weight residual 111.07 106.32 4.75 1.07e+00 8.73e-01 1.97e+01 angle pdb=" O1A NAP A 500 " pdb=" PA NAP A 500 " pdb=" O2A NAP A 500 " ideal model delta sigma weight residual 121.77 109.72 12.05 3.00e+00 1.11e-01 1.61e+01 ... (remaining 4578 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.85: 1781 17.85 - 35.71: 165 35.71 - 53.56: 60 53.56 - 71.41: 26 71.41 - 89.27: 8 Dihedral angle restraints: 2040 sinusoidal: 847 harmonic: 1193 Sorted by residual: dihedral pdb=" CB GLU A 286 " pdb=" CG GLU A 286 " pdb=" CD GLU A 286 " pdb=" OE1 GLU A 286 " ideal model delta sinusoidal sigma weight residual 0.00 84.44 -84.44 1 3.00e+01 1.11e-03 9.63e+00 dihedral pdb=" CB GLU A 78 " pdb=" CG GLU A 78 " pdb=" CD GLU A 78 " pdb=" OE1 GLU A 78 " ideal model delta sinusoidal sigma weight residual 0.00 -84.26 84.26 1 3.00e+01 1.11e-03 9.60e+00 dihedral pdb=" N ASP A 290 " pdb=" CA ASP A 290 " pdb=" CB ASP A 290 " pdb=" CG ASP A 290 " ideal model delta sinusoidal sigma weight residual -60.00 -119.64 59.64 3 1.50e+01 4.44e-03 9.48e+00 ... (remaining 2037 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.059: 417 0.059 - 0.118: 76 0.118 - 0.177: 3 0.177 - 0.236: 1 0.236 - 0.295: 1 Chirality restraints: 498 Sorted by residual: chirality pdb=" C2B NAP A 500 " pdb=" C1B NAP A 500 " pdb=" C3B NAP A 500 " pdb=" O2B NAP A 500 " both_signs ideal model delta sigma weight residual False -2.75 -2.46 -0.29 2.00e-01 2.50e+01 2.18e+00 chirality pdb=" CA GLN A 234 " pdb=" N GLN A 234 " pdb=" C GLN A 234 " pdb=" CB GLN A 234 " both_signs ideal model delta sigma weight residual False 2.51 2.33 0.18 2.00e-01 2.50e+01 8.18e-01 chirality pdb=" C4B NAP A 500 " pdb=" C3B NAP A 500 " pdb=" C5B NAP A 500 " pdb=" O4B NAP A 500 " both_signs ideal model delta sigma weight residual False -2.54 -2.40 -0.14 2.00e-01 2.50e+01 5.21e-01 ... (remaining 495 not shown) Planarity restraints: 583 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ILE A 338 " 0.047 5.00e-02 4.00e+02 7.08e-02 8.01e+00 pdb=" N PRO A 339 " -0.122 5.00e-02 4.00e+02 pdb=" CA PRO A 339 " 0.037 5.00e-02 4.00e+02 pdb=" CD PRO A 339 " 0.039 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ASN A 251 " -0.046 5.00e-02 4.00e+02 7.05e-02 7.95e+00 pdb=" N PRO A 252 " 0.122 5.00e-02 4.00e+02 pdb=" CA PRO A 252 " -0.037 5.00e-02 4.00e+02 pdb=" CD PRO A 252 " -0.039 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ASN A 149 " -0.026 5.00e-02 4.00e+02 3.93e-02 2.48e+00 pdb=" N PRO A 150 " 0.068 5.00e-02 4.00e+02 pdb=" CA PRO A 150 " -0.020 5.00e-02 4.00e+02 pdb=" CD PRO A 150 " -0.022 5.00e-02 4.00e+02 ... (remaining 580 not shown) Histogram of nonbonded interaction distances: 2.37 - 2.88: 1218 2.88 - 3.38: 3166 3.38 - 3.89: 5800 3.89 - 4.39: 6529 4.39 - 4.90: 11054 Nonbonded interactions: 27767 Sorted by model distance: nonbonded pdb=" NZ LYS A 105 " pdb=" OD2 ASP A 145 " model vdw 2.373 2.520 nonbonded pdb=" NH2 ARG A 118 " pdb=" OE1 GLU A 121 " model vdw 2.516 2.520 nonbonded pdb=" O ILE A 174 " pdb=" NZ LYS A 177 " model vdw 2.523 2.520 nonbonded pdb=" O ILE A 109 " pdb=" O HOH A 601 " model vdw 2.524 2.440 nonbonded pdb=" O ALA A 223 " pdb=" OG1 THR A 227 " model vdw 2.528 2.440 ... (remaining 27762 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=0.50 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: 0.690 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 3.510 Check model and map are aligned: 0.050 Set scattering table: 0.030 Process input model: 15.870 Find NCS groups from input model: 0.090 Set up NCS constraints: 0.020 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:11.290 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 31.560 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8190 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 : 0.007 0.169 3374 Z= 0.435 Angle : 0.830 12.050 4583 Z= 0.465 Chirality : 0.046 0.295 498 Planarity : 0.006 0.071 583 Dihedral : 18.201 89.266 1280 Min Nonbonded Distance : 2.373 Molprobity Statistics. All-atom Clashscore : 6.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.62 % Favored : 96.38 % Rotamer: Outliers : 6.49 % Allowed : 4.42 % Favored : 89.09 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.90 (0.43), residues: 415 helix: 1.98 (0.36), residues: 209 sheet: -0.69 (0.78), residues: 50 loop : -0.87 (0.50), residues: 156 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 30 HIS 0.002 0.000 HIS A 75 PHE 0.008 0.001 PHE A 381 TYR 0.006 0.001 TYR A 408 ARG 0.001 0.000 ARG A 246 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 830 Ramachandran restraints generated. 415 Oldfield, 0 Emsley, 415 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 830 Ramachandran restraints generated. 415 Oldfield, 0 Emsley, 415 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 91 residues out of total 338 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 70 time to evaluate : 0.377 Fit side-chains revert: symmetry clash REVERT: A 230 LEU cc_start: 0.8157 (mp) cc_final: 0.7882 (mp) REVERT: A 290 ASP cc_start: 0.7179 (OUTLIER) cc_final: 0.6897 (m-30) outliers start: 21 outliers final: 4 residues processed: 80 average time/residue: 1.3247 time to fit residues: 108.6789 Evaluate side-chains 59 residues out of total 338 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 54 time to evaluate : 0.374 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 9 MET Chi-restraints excluded: chain A residue 208 ILE Chi-restraints excluded: chain A residue 210 LEU Chi-restraints excluded: chain A residue 265 ARG Chi-restraints excluded: chain A residue 290 ASP 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: 0.0570 chunk 17 optimal weight: 3.9990 chunk 10 optimal weight: 3.9990 chunk 20 optimal weight: 0.5980 chunk 16 optimal weight: 3.9990 chunk 32 optimal weight: 8.9990 chunk 12 optimal weight: 0.9990 chunk 19 optimal weight: 0.9980 chunk 23 optimal weight: 8.9990 chunk 37 optimal weight: 0.9990 overall best weight: 0.7302 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 13 GLN A 218 GLN A 234 GLN A 337 GLN A 388 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8226 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 : 0.002 0.019 3374 Z= 0.146 Angle : 0.498 6.348 4583 Z= 0.253 Chirality : 0.042 0.126 498 Planarity : 0.006 0.062 583 Dihedral : 11.301 60.896 504 Min Nonbonded Distance : 2.305 Molprobity Statistics. All-atom Clashscore : 5.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.90 % Favored : 97.10 % Rotamer: Outliers : 2.65 % Allowed : 15.04 % Favored : 82.30 % 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: 1.35 (0.43), residues: 415 helix: 2.20 (0.37), residues: 209 sheet: 0.30 (0.73), residues: 60 loop : -0.79 (0.50), residues: 146 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.001 TRP A 263 HIS 0.004 0.001 HIS A 394 PHE 0.008 0.001 PHE A 381 TYR 0.015 0.001 TYR A 250 ARG 0.008 0.000 ARG A 370 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 830 Ramachandran restraints generated. 415 Oldfield, 0 Emsley, 415 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 830 Ramachandran restraints generated. 415 Oldfield, 0 Emsley, 415 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 71 residues out of total 338 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 63 time to evaluate : 0.399 Fit side-chains revert: symmetry clash REVERT: A 230 LEU cc_start: 0.8260 (mp) cc_final: 0.7846 (mp) REVERT: A 271 LYS cc_start: 0.6150 (OUTLIER) cc_final: 0.5803 (ptmt) REVERT: A 290 ASP cc_start: 0.7430 (OUTLIER) cc_final: 0.7042 (t70) outliers start: 8 outliers final: 4 residues processed: 68 average time/residue: 1.2556 time to fit residues: 87.8275 Evaluate side-chains 60 residues out of total 338 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 54 time to evaluate : 0.377 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 9 MET Chi-restraints excluded: chain A residue 210 LEU Chi-restraints excluded: chain A residue 270 VAL Chi-restraints excluded: chain A residue 271 LYS Chi-restraints excluded: chain A residue 272 ASP Chi-restraints excluded: chain A residue 290 ASP Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 41 random chunks: chunk 20 optimal weight: 9.9990 chunk 11 optimal weight: 4.9990 chunk 30 optimal weight: 10.0000 chunk 25 optimal weight: 3.9990 chunk 10 optimal weight: 0.0970 chunk 37 optimal weight: 7.9990 chunk 40 optimal weight: 1.9990 chunk 33 optimal weight: 2.9990 chunk 36 optimal weight: 0.6980 chunk 12 optimal weight: 1.9990 chunk 29 optimal weight: 5.9990 overall best weight: 1.5584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 218 GLN A 234 GLN ** A 267 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 388 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8266 moved from start: 0.1653 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.020 3374 Z= 0.189 Angle : 0.494 6.173 4583 Z= 0.253 Chirality : 0.042 0.122 498 Planarity : 0.006 0.058 583 Dihedral : 9.568 54.261 498 Min Nonbonded Distance : 2.300 Molprobity Statistics. All-atom Clashscore : 6.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.14 % Favored : 96.86 % Rotamer: Outliers : 1.77 % Allowed : 17.70 % Favored : 80.53 % 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 (0.43), residues: 415 helix: 2.17 (0.37), residues: 209 sheet: 0.21 (0.69), residues: 65 loop : -0.74 (0.52), residues: 141 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP A 263 HIS 0.005 0.001 HIS A 394 PHE 0.009 0.001 PHE A 381 TYR 0.008 0.001 TYR A 226 ARG 0.007 0.000 ARG A 370 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 830 Ramachandran restraints generated. 415 Oldfield, 0 Emsley, 415 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 830 Ramachandran restraints generated. 415 Oldfield, 0 Emsley, 415 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 65 residues out of total 338 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 60 time to evaluate : 0.393 Fit side-chains revert: symmetry clash REVERT: A 290 ASP cc_start: 0.7472 (OUTLIER) cc_final: 0.7125 (t70) outliers start: 5 outliers final: 4 residues processed: 65 average time/residue: 1.1729 time to fit residues: 78.4961 Evaluate side-chains 59 residues out of total 338 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 54 time to evaluate : 0.368 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 208 ILE Chi-restraints excluded: chain A residue 210 LEU Chi-restraints excluded: chain A residue 270 VAL Chi-restraints excluded: chain A residue 272 ASP Chi-restraints excluded: chain A residue 290 ASP Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 41 random chunks: chunk 36 optimal weight: 3.9990 chunk 28 optimal weight: 10.0000 chunk 19 optimal weight: 0.9980 chunk 4 optimal weight: 4.9990 chunk 17 optimal weight: 0.2980 chunk 25 optimal weight: 0.7980 chunk 37 optimal weight: 0.9990 chunk 39 optimal weight: 1.9990 chunk 35 optimal weight: 0.9980 chunk 10 optimal weight: 0.9980 chunk 33 optimal weight: 2.9990 overall best weight: 0.8180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 218 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 267 HIS A 388 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8234 moved from start: 0.1767 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.014 3374 Z= 0.134 Angle : 0.465 6.561 4583 Z= 0.233 Chirality : 0.042 0.124 498 Planarity : 0.005 0.052 583 Dihedral : 8.986 59.054 495 Min Nonbonded Distance : 2.359 Molprobity Statistics. All-atom Clashscore : 6.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.38 % Favored : 96.62 % Rotamer: Outliers : 2.06 % Allowed : 18.29 % Favored : 79.65 % 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: 1.38 (0.43), residues: 415 helix: 2.27 (0.37), residues: 208 sheet: 0.15 (0.68), residues: 65 loop : -0.75 (0.52), residues: 142 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 263 HIS 0.004 0.001 HIS A 394 PHE 0.008 0.001 PHE A 381 TYR 0.022 0.001 TYR A 250 ARG 0.008 0.000 ARG A 370 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 830 Ramachandran restraints generated. 415 Oldfield, 0 Emsley, 415 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 830 Ramachandran restraints generated. 415 Oldfield, 0 Emsley, 415 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 64 residues out of total 338 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 58 time to evaluate : 0.376 Fit side-chains revert: symmetry clash REVERT: A 290 ASP cc_start: 0.7451 (OUTLIER) cc_final: 0.7168 (t70) outliers start: 6 outliers final: 2 residues processed: 63 average time/residue: 1.1624 time to fit residues: 75.5078 Evaluate side-chains 57 residues out of total 338 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 54 time to evaluate : 0.343 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 208 ILE Chi-restraints excluded: chain A residue 270 VAL Chi-restraints excluded: chain A residue 290 ASP Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 41 random chunks: chunk 22 optimal weight: 10.0000 chunk 0 optimal weight: 10.0000 chunk 29 optimal weight: 10.0000 chunk 16 optimal weight: 1.9990 chunk 33 optimal weight: 0.0010 chunk 27 optimal weight: 10.0000 chunk 20 optimal weight: 4.9990 chunk 35 optimal weight: 3.9990 chunk 10 optimal weight: 0.6980 chunk 13 optimal weight: 0.3980 chunk 7 optimal weight: 7.9990 overall best weight: 1.4190 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 218 GLN A 388 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8261 moved from start: 0.1838 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.019 3374 Z= 0.177 Angle : 0.489 6.801 4583 Z= 0.246 Chirality : 0.043 0.119 498 Planarity : 0.005 0.050 583 Dihedral : 8.305 56.597 493 Min Nonbonded Distance : 2.307 Molprobity Statistics. All-atom Clashscore : 6.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.38 % Favored : 96.62 % Rotamer: Outliers : 1.77 % Allowed : 20.35 % Favored : 77.88 % 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: 1.38 (0.43), residues: 415 helix: 2.28 (0.36), residues: 208 sheet: 0.11 (0.68), residues: 65 loop : -0.78 (0.51), residues: 142 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.001 TRP A 263 HIS 0.005 0.001 HIS A 394 PHE 0.009 0.001 PHE A 381 TYR 0.007 0.001 TYR A 226 ARG 0.008 0.000 ARG A 370 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 830 Ramachandran restraints generated. 415 Oldfield, 0 Emsley, 415 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 830 Ramachandran restraints generated. 415 Oldfield, 0 Emsley, 415 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 62 residues out of total 338 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 57 time to evaluate : 0.367 Fit side-chains revert: symmetry clash REVERT: A 290 ASP cc_start: 0.7489 (OUTLIER) cc_final: 0.7229 (t70) outliers start: 5 outliers final: 4 residues processed: 62 average time/residue: 1.2688 time to fit residues: 80.9198 Evaluate side-chains 61 residues out of total 338 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 56 time to evaluate : 0.359 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 208 ILE Chi-restraints excluded: chain A residue 270 VAL Chi-restraints excluded: chain A residue 271 LYS Chi-restraints excluded: chain A residue 272 ASP Chi-restraints excluded: chain A residue 290 ASP Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 41 random chunks: chunk 23 optimal weight: 10.0000 chunk 9 optimal weight: 0.7980 chunk 39 optimal weight: 10.0000 chunk 32 optimal weight: 20.0000 chunk 18 optimal weight: 5.9990 chunk 3 optimal weight: 0.9980 chunk 13 optimal weight: 3.9990 chunk 20 optimal weight: 6.9990 chunk 38 optimal weight: 0.9990 chunk 4 optimal weight: 2.9990 chunk 22 optimal weight: 2.9990 overall best weight: 1.7586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 218 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 388 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8277 moved from start: 0.1998 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.022 3374 Z= 0.203 Angle : 0.499 6.910 4583 Z= 0.251 Chirality : 0.043 0.119 498 Planarity : 0.005 0.049 583 Dihedral : 7.650 58.125 493 Min Nonbonded Distance : 2.297 Molprobity Statistics. All-atom Clashscore : 6.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.14 % Favored : 96.86 % Rotamer: Outliers : 1.47 % Allowed : 20.06 % Favored : 78.47 % 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: 1.37 (0.43), residues: 415 helix: 2.30 (0.37), residues: 208 sheet: 0.06 (0.67), residues: 65 loop : -0.81 (0.51), residues: 142 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP A 263 HIS 0.005 0.002 HIS A 394 PHE 0.008 0.001 PHE A 381 TYR 0.024 0.001 TYR A 250 ARG 0.008 0.000 ARG A 370 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 830 Ramachandran restraints generated. 415 Oldfield, 0 Emsley, 415 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 830 Ramachandran restraints generated. 415 Oldfield, 0 Emsley, 415 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 62 residues out of total 338 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 58 time to evaluate : 0.372 Fit side-chains revert: symmetry clash outliers start: 4 outliers final: 2 residues processed: 62 average time/residue: 1.2266 time to fit residues: 78.2830 Evaluate side-chains 59 residues out of total 338 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 57 time to evaluate : 0.372 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 210 LEU Chi-restraints excluded: chain A residue 270 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 41 random chunks: chunk 28 optimal weight: 7.9990 chunk 22 optimal weight: 7.9990 chunk 33 optimal weight: 4.9990 chunk 39 optimal weight: 0.9980 chunk 24 optimal weight: 8.9990 chunk 18 optimal weight: 2.9990 chunk 15 optimal weight: 5.9990 chunk 23 optimal weight: 5.9990 chunk 11 optimal weight: 1.9990 chunk 7 optimal weight: 5.9990 chunk 25 optimal weight: 7.9990 overall best weight: 3.3988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 218 GLN A 388 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8326 moved from start: 0.2216 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.036 3374 Z= 0.347 Angle : 0.567 7.087 4583 Z= 0.290 Chirality : 0.045 0.129 498 Planarity : 0.006 0.050 583 Dihedral : 7.207 57.792 491 Min Nonbonded Distance : 2.250 Molprobity Statistics. All-atom Clashscore : 6.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.14 % Favored : 96.86 % Rotamer: Outliers : 1.77 % Allowed : 19.17 % Favored : 79.06 % 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: 1.12 (0.43), residues: 415 helix: 2.24 (0.37), residues: 206 sheet: -0.44 (0.63), residues: 72 loop : -0.90 (0.54), residues: 137 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.002 TRP A 263 HIS 0.006 0.002 HIS A 394 PHE 0.011 0.002 PHE A 341 TYR 0.016 0.002 TYR A 226 ARG 0.008 0.001 ARG A 370 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 830 Ramachandran restraints generated. 415 Oldfield, 0 Emsley, 415 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 830 Ramachandran restraints generated. 415 Oldfield, 0 Emsley, 415 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 59 residues out of total 338 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 54 time to evaluate : 0.410 Fit side-chains revert: symmetry clash outliers start: 5 outliers final: 3 residues processed: 59 average time/residue: 1.1854 time to fit residues: 72.1142 Evaluate side-chains 56 residues out of total 338 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 53 time to evaluate : 0.375 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 210 LEU Chi-restraints excluded: chain A residue 270 VAL Chi-restraints excluded: chain A residue 272 ASP Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 41 random chunks: chunk 26 optimal weight: 1.9990 chunk 19 optimal weight: 0.9980 chunk 3 optimal weight: 0.5980 chunk 31 optimal weight: 6.9990 chunk 35 optimal weight: 0.6980 chunk 37 optimal weight: 0.9990 chunk 34 optimal weight: 1.9990 chunk 36 optimal weight: 0.6980 chunk 22 optimal weight: 3.9990 chunk 16 optimal weight: 0.9990 chunk 28 optimal weight: 6.9990 overall best weight: 0.7982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 218 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 388 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8249 moved from start: 0.2092 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.020 3374 Z= 0.143 Angle : 0.503 7.618 4583 Z= 0.253 Chirality : 0.042 0.121 498 Planarity : 0.005 0.048 583 Dihedral : 6.408 55.165 491 Min Nonbonded Distance : 2.118 Molprobity Statistics. All-atom Clashscore : 6.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.14 % Favored : 96.86 % Rotamer: Outliers : 1.18 % Allowed : 20.06 % Favored : 78.76 % 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 (0.43), residues: 415 helix: 2.28 (0.37), residues: 209 sheet: -0.09 (0.67), residues: 67 loop : -0.85 (0.53), residues: 139 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A 263 HIS 0.005 0.001 HIS A 394 PHE 0.010 0.001 PHE A 381 TYR 0.021 0.001 TYR A 250 ARG 0.009 0.000 ARG A 370 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 830 Ramachandran restraints generated. 415 Oldfield, 0 Emsley, 415 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 830 Ramachandran restraints generated. 415 Oldfield, 0 Emsley, 415 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 59 residues out of total 338 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 56 time to evaluate : 0.378 Fit side-chains revert: symmetry clash outliers start: 3 outliers final: 2 residues processed: 59 average time/residue: 1.2014 time to fit residues: 73.0740 Evaluate side-chains 52 residues out of total 338 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 50 time to evaluate : 0.351 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 210 LEU Chi-restraints excluded: chain A residue 270 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 41 random chunks: chunk 11 optimal weight: 2.9990 chunk 33 optimal weight: 0.7980 chunk 34 optimal weight: 6.9990 chunk 36 optimal weight: 3.9990 chunk 24 optimal weight: 5.9990 chunk 38 optimal weight: 2.9990 chunk 23 optimal weight: 3.9990 chunk 18 optimal weight: 4.9990 chunk 27 optimal weight: 1.9990 chunk 40 optimal weight: 0.9990 chunk 37 optimal weight: 1.9990 overall best weight: 1.7588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 388 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8283 moved from start: 0.2150 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.021 3374 Z= 0.206 Angle : 0.517 7.143 4583 Z= 0.262 Chirality : 0.043 0.122 498 Planarity : 0.005 0.047 583 Dihedral : 6.369 55.002 491 Min Nonbonded Distance : 2.124 Molprobity Statistics. All-atom Clashscore : 6.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.90 % Favored : 97.10 % Rotamer: Outliers : 0.88 % Allowed : 20.35 % Favored : 78.76 % 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: 1.32 (0.43), residues: 415 helix: 2.31 (0.37), residues: 208 sheet: -0.10 (0.67), residues: 67 loop : -0.83 (0.52), residues: 140 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP A 263 HIS 0.006 0.001 HIS A 394 PHE 0.009 0.001 PHE A 381 TYR 0.009 0.001 TYR A 226 ARG 0.008 0.000 ARG A 370 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 830 Ramachandran restraints generated. 415 Oldfield, 0 Emsley, 415 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 830 Ramachandran restraints generated. 415 Oldfield, 0 Emsley, 415 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 54 residues out of total 338 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 52 time to evaluate : 0.360 Fit side-chains revert: symmetry clash outliers start: 2 outliers final: 2 residues processed: 54 average time/residue: 1.2518 time to fit residues: 69.5806 Evaluate side-chains 53 residues out of total 338 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 51 time to evaluate : 0.342 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 210 LEU Chi-restraints excluded: chain A residue 270 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 41 random chunks: chunk 32 optimal weight: 0.7980 chunk 3 optimal weight: 3.9990 chunk 25 optimal weight: 0.6980 chunk 19 optimal weight: 0.8980 chunk 34 optimal weight: 0.9980 chunk 9 optimal weight: 0.9990 chunk 29 optimal weight: 9.9990 chunk 4 optimal weight: 3.9990 chunk 13 optimal weight: 5.9990 chunk 33 optimal weight: 0.9980 chunk 6 optimal weight: 0.8980 overall best weight: 0.8580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 388 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8248 moved from start: 0.2137 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.020 3374 Z= 0.145 Angle : 0.496 7.602 4583 Z= 0.249 Chirality : 0.042 0.121 498 Planarity : 0.005 0.047 583 Dihedral : 6.213 54.673 491 Min Nonbonded Distance : 2.140 Molprobity Statistics. All-atom Clashscore : 6.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.14 % Favored : 96.86 % Rotamer: Outliers : 0.88 % Allowed : 20.06 % Favored : 79.06 % 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: 1.40 (0.43), residues: 415 helix: 2.34 (0.37), residues: 209 sheet: -0.01 (0.68), residues: 67 loop : -0.79 (0.52), residues: 139 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A 263 HIS 0.005 0.001 HIS A 394 PHE 0.009 0.001 PHE A 381 TYR 0.021 0.001 TYR A 250 ARG 0.009 0.000 ARG A 370 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 830 Ramachandran restraints generated. 415 Oldfield, 0 Emsley, 415 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 830 Ramachandran restraints generated. 415 Oldfield, 0 Emsley, 415 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 57 residues out of total 338 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 55 time to evaluate : 0.381 Fit side-chains revert: symmetry clash outliers start: 2 outliers final: 1 residues processed: 57 average time/residue: 1.1620 time to fit residues: 68.3476 Evaluate side-chains 51 residues out of total 338 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 50 time to evaluate : 0.394 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 270 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 41 random chunks: chunk 28 optimal weight: 6.9990 chunk 1 optimal weight: 2.9990 chunk 23 optimal weight: 0.0670 chunk 37 optimal weight: 1.9990 chunk 21 optimal weight: 0.4980 chunk 27 optimal weight: 6.9990 chunk 26 optimal weight: 5.9990 chunk 24 optimal weight: 5.9990 chunk 16 optimal weight: 0.6980 chunk 15 optimal weight: 0.9990 chunk 40 optimal weight: 2.9990 overall best weight: 0.8522 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 388 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3538 r_free = 0.3538 target = 0.140755 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3024 r_free = 0.3024 target = 0.104384 restraints weight = 11059.157| |-----------------------------------------------------------------------------| r_work (start): 0.2999 rms_B_bonded: 3.09 r_work: 0.2848 rms_B_bonded: 3.32 restraints_weight: 0.5000 r_work (final): 0.2848 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2863 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2863 r_free = 0.2863 target_work(ls_wunit_k1) = 0.094 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2863 r_free = 0.2863 target_work(ls_wunit_k1) = 0.094 | | occupancies: max = 1.00 min = 0.48 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2863 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8551 moved from start: 0.2155 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.021 3374 Z= 0.144 Angle : 0.494 7.710 4583 Z= 0.248 Chirality : 0.043 0.119 498 Planarity : 0.005 0.047 583 Dihedral : 6.105 53.958 491 Min Nonbonded Distance : 2.145 Molprobity Statistics. All-atom Clashscore : 6.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.90 % Favored : 97.10 % Rotamer: Outliers : 0.88 % Allowed : 20.35 % Favored : 78.76 % 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: 1.45 (0.43), residues: 415 helix: 2.36 (0.37), residues: 209 sheet: 0.03 (0.67), residues: 67 loop : -0.73 (0.53), residues: 139 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP A 263 HIS 0.005 0.001 HIS A 394 PHE 0.008 0.001 PHE A 381 TYR 0.007 0.001 TYR A 363 ARG 0.009 0.000 ARG A 370 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1846.84 seconds wall clock time: 33 minutes 34.83 seconds (2014.83 seconds total)