Starting phenix.real_space_refine on Thu Jul 18 20:54:20 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8xd1_38262/07_2024/8xd1_38262_neut.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8xd1_38262/07_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_38262/07_2024/8xd1_38262.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8xd1_38262/07_2024/8xd1_38262.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8xd1_38262/07_2024/8xd1_38262_neut.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8xd1_38262/07_2024/8xd1_38262_neut.cif" } 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-5388/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: 4.33, per 1000 atoms: 1.31 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: 2.48 Conformation dependent library (CDL) restraints added in 1.9 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... Secondary structure from input PDB file: 17 helices and 2 sheets defined 54.8% alpha, 13.7% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.41 Creating SS restraints... Processing helix chain 'A' and resid 5 through 19 Processing helix chain 'A' and resid 24 through 32 Processing helix chain 'A' and resid 79 through 97 removed outlier: 3.523A pdb=" N TRP A 92 " --> pdb=" O THR A 88 " (cutoff:3.500A) removed outlier: 3.859A pdb=" N VAL A 97 " --> pdb=" O LYS A 93 " (cutoff:3.500A) Processing helix chain 'A' and resid 111 through 115 Processing helix chain 'A' and resid 116 through 132 Processing helix chain 'A' and resid 133 through 135 No H-bonds generated for 'chain 'A' and resid 133 through 135' Processing helix chain 'A' and resid 149 through 165 Processing helix chain 'A' and resid 169 through 174 removed outlier: 3.537A pdb=" N VAL A 173 " --> pdb=" O ALA A 170 " (cutoff:3.500A) removed outlier: 3.843A pdb=" N ILE A 174 " --> pdb=" O PHE A 171 " (cutoff:3.500A) Processing helix chain 'A' and resid 189 through 207 Processing helix chain 'A' and resid 223 through 235 Processing helix chain 'A' and resid 256 through 268 removed outlier: 3.571A pdb=" N VAL A 260 " --> pdb=" O ASP A 256 " (cutoff:3.500A) Processing helix chain 'A' and resid 280 through 287 Processing helix chain 'A' and resid 323 through 333 Processing helix chain 'A' and resid 339 through 344 removed outlier: 3.607A pdb=" N ASN A 344 " --> pdb=" O ASP A 340 " (cutoff:3.500A) Processing helix chain 'A' and resid 345 through 361 Processing helix chain 'A' and resid 365 through 392 Processing helix chain 'A' and resid 394 through 415 Processing sheet with id=AA1, 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: 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) removed outlier: 6.007A pdb=" N GLY A 71 " --> pdb=" O GLY A 106 " (cutoff:3.500A) removed outlier: 7.982A pdb=" N ILE A 108 " --> pdb=" O GLY A 71 " (cutoff:3.500A) removed outlier: 6.331A pdb=" N ARG A 73 " --> pdb=" O ILE A 108 " (cutoff:3.500A) removed outlier: 6.851A pdb=" N THR A 68 " --> pdb=" O ILE A 141 " (cutoff:3.500A) removed outlier: 8.087A pdb=" N ALA A 143 " --> pdb=" O THR A 68 " (cutoff:3.500A) removed outlier: 6.882A pdb=" N GLY A 70 " --> pdb=" O ALA A 143 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 277 through 279 removed outlier: 6.318A pdb=" N ILE A 215 " --> pdb=" O VAL A 239 " (cutoff:3.500A) removed outlier: 3.753A pdb=" N ALA A 241 " --> pdb=" O ILE A 215 " (cutoff:3.500A) removed outlier: 6.793A pdb=" N LYS A 214 " --> pdb=" O VAL A 291 " (cutoff:3.500A) removed outlier: 8.277A pdb=" N ALA A 293 " --> pdb=" O LYS A 214 " (cutoff:3.500A) removed outlier: 6.897A pdb=" N ALA A 216 " --> pdb=" O ALA A 293 " (cutoff:3.500A) removed outlier: 7.059A pdb=" N VAL A 314 " --> pdb=" O ILE A 338 " (cutoff:3.500A) 183 hydrogen bonds defined for protein. 530 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: 1.15 Time building geometry restraints manager: 1.44 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 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: 1210 2.88 - 3.38: 3145 3.38 - 3.89: 5768 3.89 - 4.39: 6487 4.39 - 4.90: 11053 Nonbonded interactions: 27663 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 27658 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: 0.010 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.040 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.000 Extract box with map and model: 0.150 Check model and map are aligned: 0.030 Set scattering table: 0.040 Process input model: 17.360 Find NCS groups from input model: 0.040 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:12.760 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 31.450 ------------------------------------------------------------------------------- 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= 0.473 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 : 0.381 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: 1.2632 time to fit residues: 103.7554 Evaluate side-chains 59 residues out of total 338 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 54 time to evaluate : 0.383 ------------------------------------------------------------------------------- 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: 0.6980 chunk 17 optimal weight: 3.9990 chunk 10 optimal weight: 2.9990 chunk 20 optimal weight: 0.9990 chunk 16 optimal weight: 2.9990 chunk 32 optimal weight: 2.9990 chunk 12 optimal weight: 0.9990 chunk 19 optimal weight: 0.8980 chunk 23 optimal weight: 3.9990 chunk 37 optimal weight: 0.9980 overall best weight: 0.9184 ------------------------------------------------------------------------------- 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 388 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8229 moved from start: 0.1464 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= 0.156 Angle : 0.511 6.354 4583 Z= 0.262 Chirality : 0.042 0.126 498 Planarity : 0.006 0.061 583 Dihedral : 11.258 60.910 504 Min Nonbonded Distance : 2.312 Molprobity Statistics. All-atom Clashscore : 6.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.14 % Favored : 96.86 % Rotamer: Outliers : 2.36 % Allowed : 15.04 % Favored : 82.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.47 (0.43), residues: 415 helix: 2.26 (0.37), residues: 210 sheet: 0.20 (0.70), residues: 65 loop : -0.62 (0.53), residues: 140 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.001 TRP A 263 HIS 0.004 0.001 HIS A 394 PHE 0.008 0.001 PHE A 57 TYR 0.015 0.001 TYR A 250 ARG 0.007 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 66 residues out of total 338 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 59 time to evaluate : 0.431 Fit side-chains revert: symmetry clash REVERT: A 271 LYS cc_start: 0.6181 (OUTLIER) cc_final: 0.5758 (ptmt) outliers start: 7 outliers final: 3 residues processed: 64 average time/residue: 1.1795 time to fit residues: 77.8689 Evaluate side-chains 58 residues out of total 338 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 54 time to evaluate : 0.407 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 9 MET Chi-restraints excluded: chain A residue 270 VAL Chi-restraints excluded: chain A residue 271 LYS Chi-restraints excluded: chain A residue 272 ASP Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 41 random chunks: chunk 20 optimal weight: 4.9990 chunk 11 optimal weight: 0.7980 chunk 30 optimal weight: 5.9990 chunk 25 optimal weight: 0.9980 chunk 10 optimal weight: 7.9990 chunk 37 optimal weight: 0.6980 chunk 40 optimal weight: 1.9990 chunk 33 optimal weight: 0.5980 chunk 36 optimal weight: 0.8980 chunk 12 optimal weight: 2.9990 chunk 29 optimal weight: 0.4980 overall best weight: 0.6980 ------------------------------------------------------------------------------- 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: 0.8214 moved from start: 0.1798 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.024 3374 Z= 0.138 Angle : 0.488 6.459 4583 Z= 0.249 Chirality : 0.042 0.126 498 Planarity : 0.005 0.057 583 Dihedral : 8.978 53.498 494 Min Nonbonded Distance : 2.341 Molprobity Statistics. All-atom Clashscore : 5.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.14 % Favored : 96.86 % Rotamer: Outliers : 1.77 % Allowed : 16.81 % Favored : 81.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.54 (0.43), residues: 415 helix: 2.43 (0.37), residues: 205 sheet: 0.26 (0.70), residues: 65 loop : -0.69 (0.52), residues: 145 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP A 263 HIS 0.004 0.001 HIS A 394 PHE 0.008 0.001 PHE A 381 TYR 0.006 0.001 TYR A 363 ARG 0.008 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 62 residues out of total 338 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 57 time to evaluate : 0.392 Fit side-chains REVERT: A 230 LEU cc_start: 0.8127 (mp) cc_final: 0.7634 (mp) outliers start: 5 outliers final: 4 residues processed: 62 average time/residue: 1.0576 time to fit residues: 67.8912 Evaluate side-chains 58 residues out of total 338 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 54 time to evaluate : 0.446 ------------------------------------------------------------------------------- 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 Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 41 random chunks: chunk 36 optimal weight: 0.5980 chunk 28 optimal weight: 8.9990 chunk 19 optimal weight: 7.9990 chunk 4 optimal weight: 2.9990 chunk 17 optimal weight: 0.9990 chunk 25 optimal weight: 1.9990 chunk 37 optimal weight: 0.6980 chunk 39 optimal weight: 4.9990 chunk 35 optimal weight: 0.6980 chunk 10 optimal weight: 7.9990 chunk 33 optimal weight: 0.9990 overall best weight: 0.7984 ------------------------------------------------------------------------------- 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: 0.8215 moved from start: 0.1963 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= 0.134 Angle : 0.464 6.396 4583 Z= 0.234 Chirality : 0.042 0.128 498 Planarity : 0.005 0.052 583 Dihedral : 8.547 59.068 491 Min Nonbonded Distance : 2.370 Molprobity Statistics. All-atom Clashscore : 5.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.90 % Favored : 97.10 % Rotamer: Outliers : 1.18 % Allowed : 17.11 % Favored : 81.71 % 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: 415 helix: 2.50 (0.37), residues: 205 sheet: 0.24 (0.71), residues: 65 loop : -0.72 (0.52), residues: 145 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 263 HIS 0.005 0.001 HIS A 394 PHE 0.008 0.001 PHE A 381 TYR 0.024 0.001 TYR A 250 ARG 0.007 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 62 residues out of total 338 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 59 time to evaluate : 0.393 Fit side-chains REVERT: A 230 LEU cc_start: 0.8125 (mp) cc_final: 0.7571 (mp) outliers start: 3 outliers final: 2 residues processed: 62 average time/residue: 1.1395 time to fit residues: 72.8620 Evaluate side-chains 57 residues out of total 338 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 55 time to evaluate : 0.321 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 208 ILE Chi-restraints excluded: chain A residue 270 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 41 random chunks: chunk 22 optimal weight: 9.9990 chunk 0 optimal weight: 10.0000 chunk 29 optimal weight: 9.9990 chunk 16 optimal weight: 0.7980 chunk 33 optimal weight: 5.9990 chunk 27 optimal weight: 10.0000 chunk 20 optimal weight: 2.9990 chunk 35 optimal weight: 5.9990 chunk 10 optimal weight: 7.9990 chunk 13 optimal weight: 0.5980 chunk 7 optimal weight: 0.8980 overall best weight: 2.2584 ------------------------------------------------------------------------------- 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 388 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8283 moved from start: 0.2056 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.028 3374 Z= 0.243 Angle : 0.515 6.346 4583 Z= 0.264 Chirality : 0.043 0.122 498 Planarity : 0.005 0.052 583 Dihedral : 7.974 56.109 491 Min Nonbonded Distance : 2.278 Molprobity Statistics. All-atom Clashscore : 6.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.14 % Favored : 96.86 % Rotamer: Outliers : 1.77 % Allowed : 18.58 % 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: 1.50 (0.44), residues: 415 helix: 2.34 (0.37), residues: 210 sheet: 0.10 (0.70), residues: 65 loop : -0.64 (0.53), residues: 140 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 263 HIS 0.006 0.001 HIS A 394 PHE 0.009 0.001 PHE A 341 TYR 0.010 0.001 TYR A 226 ARG 0.007 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 63 residues out of total 338 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 58 time to evaluate : 0.482 Fit side-chains REVERT: A 230 LEU cc_start: 0.8231 (mp) cc_final: 0.7653 (mp) outliers start: 5 outliers final: 2 residues processed: 63 average time/residue: 1.2961 time to fit residues: 83.9568 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 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 210 LEU Chi-restraints excluded: chain A residue 270 VAL 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: 0.0030 chunk 39 optimal weight: 8.9990 chunk 32 optimal weight: 5.9990 chunk 18 optimal weight: 0.9980 chunk 3 optimal weight: 2.9990 chunk 13 optimal weight: 0.9980 chunk 20 optimal weight: 6.9990 chunk 38 optimal weight: 1.9990 chunk 4 optimal weight: 1.9990 chunk 22 optimal weight: 4.9990 overall best weight: 1.1994 ------------------------------------------------------------------------------- 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: 0.8250 moved from start: 0.2125 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.018 3374 Z= 0.160 Angle : 0.508 7.238 4583 Z= 0.256 Chirality : 0.042 0.125 498 Planarity : 0.005 0.049 583 Dihedral : 7.041 56.993 491 Min Nonbonded Distance : 2.131 Molprobity Statistics. All-atom Clashscore : 6.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.38 % Favored : 96.62 % Rotamer: Outliers : 1.47 % Allowed : 20.94 % Favored : 77.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.48 (0.44), residues: 415 helix: 2.37 (0.36), residues: 210 sheet: -0.11 (0.69), residues: 67 loop : -0.64 (0.54), residues: 138 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 92 HIS 0.006 0.001 HIS A 394 PHE 0.009 0.001 PHE A 381 TYR 0.022 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 55 residues out of total 338 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 51 time to evaluate : 0.388 Fit side-chains REVERT: A 230 LEU cc_start: 0.8190 (mp) cc_final: 0.7586 (mp) outliers start: 4 outliers final: 2 residues processed: 55 average time/residue: 1.2348 time to fit residues: 70.0325 Evaluate side-chains 54 residues out of total 338 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 52 time to evaluate : 0.398 ------------------------------------------------------------------------------- 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: 6.9990 chunk 22 optimal weight: 10.0000 chunk 33 optimal weight: 5.9990 chunk 39 optimal weight: 4.9990 chunk 24 optimal weight: 7.9990 chunk 18 optimal weight: 2.9990 chunk 15 optimal weight: 8.9990 chunk 23 optimal weight: 5.9990 chunk 11 optimal weight: 4.9990 chunk 7 optimal weight: 2.9990 chunk 25 optimal weight: 4.9990 overall best weight: 4.1990 ------------------------------------------------------------------------------- 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: 0.8328 moved from start: 0.2330 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.043 3374 Z= 0.398 Angle : 0.603 6.461 4583 Z= 0.309 Chirality : 0.046 0.125 498 Planarity : 0.006 0.052 583 Dihedral : 7.000 56.200 491 Min Nonbonded Distance : 2.119 Molprobity Statistics. All-atom Clashscore : 6.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.90 % Favored : 97.10 % Rotamer: Outliers : 2.36 % Allowed : 19.76 % 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: 1.20 (0.44), residues: 415 helix: 2.16 (0.37), residues: 210 sheet: -0.34 (0.67), residues: 68 loop : -0.74 (0.55), residues: 137 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP A 263 HIS 0.007 0.002 HIS A 394 PHE 0.011 0.002 PHE A 341 TYR 0.016 0.002 TYR A 226 ARG 0.010 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 60 residues out of total 338 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 53 time to evaluate : 0.422 Fit side-chains revert: symmetry clash REVERT: A 230 LEU cc_start: 0.8302 (mp) cc_final: 0.7773 (mp) outliers start: 7 outliers final: 4 residues processed: 59 average time/residue: 1.2591 time to fit residues: 76.6144 Evaluate side-chains 56 residues out of total 338 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 52 time to evaluate : 0.393 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 210 LEU Chi-restraints excluded: chain A residue 267 HIS 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: 8.9990 chunk 19 optimal weight: 0.9990 chunk 3 optimal weight: 0.5980 chunk 31 optimal weight: 0.8980 chunk 35 optimal weight: 0.7980 chunk 37 optimal weight: 0.9980 chunk 34 optimal weight: 0.7980 chunk 36 optimal weight: 0.6980 chunk 22 optimal weight: 3.9990 chunk 16 optimal weight: 2.9990 chunk 28 optimal weight: 5.9990 overall best weight: 0.7580 ------------------------------------------------------------------------------- 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: 0.8242 moved from start: 0.2186 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.024 3374 Z= 0.145 Angle : 0.514 7.464 4583 Z= 0.259 Chirality : 0.042 0.123 498 Planarity : 0.005 0.051 583 Dihedral : 6.467 55.122 491 Min Nonbonded Distance : 2.178 Molprobity Statistics. All-atom Clashscore : 6.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.66 % Favored : 97.34 % Rotamer: Outliers : 1.18 % Allowed : 21.24 % Favored : 77.58 % 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: 1.42 (0.44), residues: 415 helix: 2.33 (0.36), residues: 210 sheet: -0.15 (0.68), residues: 67 loop : -0.66 (0.55), residues: 138 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 92 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 0.011 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 57 residues out of total 338 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 54 time to evaluate : 0.385 Fit side-chains revert: symmetry clash REVERT: A 230 LEU cc_start: 0.8221 (mp) cc_final: 0.7629 (mp) outliers start: 3 outliers final: 3 residues processed: 57 average time/residue: 1.3113 time to fit residues: 76.8929 Evaluate side-chains 53 residues out of total 338 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 50 time to evaluate : 0.343 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 210 LEU Chi-restraints excluded: chain A residue 267 HIS 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: 0.9980 chunk 33 optimal weight: 4.9990 chunk 34 optimal weight: 4.9990 chunk 36 optimal weight: 0.9980 chunk 24 optimal weight: 9.9990 chunk 38 optimal weight: 6.9990 chunk 23 optimal weight: 4.9990 chunk 18 optimal weight: 6.9990 chunk 27 optimal weight: 5.9990 chunk 40 optimal weight: 3.9990 chunk 37 optimal weight: 1.9990 overall best weight: 2.5986 ------------------------------------------------------------------------------- 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: 0.8301 moved from start: 0.2274 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.030 3374 Z= 0.271 Angle : 0.556 7.009 4583 Z= 0.281 Chirality : 0.044 0.121 498 Planarity : 0.005 0.054 583 Dihedral : 6.488 53.456 491 Min Nonbonded Distance : 2.167 Molprobity Statistics. All-atom Clashscore : 7.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.14 % Favored : 96.86 % 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 (0.44), residues: 415 helix: 2.33 (0.37), residues: 210 sheet: -0.27 (0.68), residues: 67 loop : -0.68 (0.55), residues: 138 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A 263 HIS 0.007 0.001 HIS A 394 PHE 0.009 0.002 PHE A 341 TYR 0.011 0.001 TYR A 226 ARG 0.012 0.001 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 55 residues out of total 338 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 50 time to evaluate : 0.399 Fit side-chains revert: symmetry clash REVERT: A 230 LEU cc_start: 0.8256 (mp) cc_final: 0.7703 (mp) outliers start: 5 outliers final: 3 residues processed: 55 average time/residue: 1.1519 time to fit residues: 65.4498 Evaluate side-chains 52 residues out of total 338 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 49 time to evaluate : 0.383 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 210 LEU Chi-restraints excluded: chain A residue 267 HIS 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: 5.9990 chunk 3 optimal weight: 0.9980 chunk 25 optimal weight: 0.0870 chunk 19 optimal weight: 0.9990 chunk 34 optimal weight: 0.7980 chunk 9 optimal weight: 0.0270 chunk 29 optimal weight: 0.2980 chunk 4 optimal weight: 0.0070 chunk 13 optimal weight: 0.0770 chunk 33 optimal weight: 0.0980 chunk 6 optimal weight: 0.9990 overall best weight: 0.0592 ------------------------------------------------------------------------------- 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: 0.8189 moved from start: 0.2353 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.028 3374 Z= 0.124 Angle : 0.512 7.786 4583 Z= 0.256 Chirality : 0.042 0.130 498 Planarity : 0.005 0.049 583 Dihedral : 6.213 53.789 491 Min Nonbonded Distance : 2.197 Molprobity Statistics. All-atom Clashscore : 6.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.42 % Favored : 97.58 % Rotamer: Outliers : 1.18 % Allowed : 20.94 % 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: 1.48 (0.43), residues: 415 helix: 2.37 (0.36), residues: 210 sheet: -0.03 (0.70), residues: 67 loop : -0.68 (0.54), residues: 138 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP A 92 HIS 0.004 0.001 HIS A 394 PHE 0.009 0.001 PHE A 381 TYR 0.024 0.001 TYR A 250 ARG 0.011 0.001 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: 3 poor density : 54 time to evaluate : 0.368 Fit side-chains revert: symmetry clash REVERT: A 118 ARG cc_start: 0.8054 (mmp80) cc_final: 0.7845 (mmp80) REVERT: A 230 LEU cc_start: 0.8170 (mp) cc_final: 0.7578 (mp) outliers start: 3 outliers final: 3 residues processed: 57 average time/residue: 1.2220 time to fit residues: 71.8392 Evaluate side-chains 55 residues out of total 338 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 52 time to evaluate : 0.384 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 210 LEU Chi-restraints excluded: chain A residue 267 HIS 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: 8.9990 chunk 37 optimal weight: 1.9990 chunk 21 optimal weight: 6.9990 chunk 27 optimal weight: 10.0000 chunk 26 optimal weight: 9.9990 chunk 24 optimal weight: 7.9990 chunk 16 optimal weight: 0.1980 chunk 15 optimal weight: 0.8980 chunk 40 optimal weight: 2.9990 overall best weight: 1.8186 ------------------------------------------------------------------------------- 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 = 0.3512 r_free = 0.3512 target = 0.138347 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.2991 r_free = 0.2991 target = 0.101910 restraints weight = 11236.259| |-----------------------------------------------------------------------------| r_work (start): 0.2981 rms_B_bonded: 3.10 r_work: 0.2828 rms_B_bonded: 3.37 restraints_weight: 0.5000 r_work (final): 0.2828 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2763 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2763 r_free = 0.2763 target_work(ls_wunit_k1) = 0.088 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2763 r_free = 0.2763 target_work(ls_wunit_k1) = 0.088 | | occupancies: max = 1.00 min = 0.46 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2763 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8589 moved from start: 0.2260 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.023 3374 Z= 0.208 Angle : 0.536 7.404 4583 Z= 0.271 Chirality : 0.043 0.126 498 Planarity : 0.005 0.055 583 Dihedral : 6.228 52.645 491 Min Nonbonded Distance : 2.188 Molprobity Statistics. All-atom Clashscore : 6.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.38 % Favored : 96.62 % Rotamer: Outliers : 1.18 % Allowed : 21.24 % Favored : 77.58 % 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: 1.57 (0.44), residues: 415 helix: 2.45 (0.37), residues: 210 sheet: -0.16 (0.68), residues: 67 loop : -0.54 (0.55), residues: 138 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 0.008 0.001 PHE A 341 TYR 0.009 0.001 TYR A 363 ARG 0.012 0.001 ARG A 370 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1837.10 seconds wall clock time: 32 minutes 41.16 seconds (1961.16 seconds total)