Starting phenix.real_space_refine on Mon Jan 13 18:41:45 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8xd1_38262/01_2025/8xd1_38262_neut.cif Found real_map, /net/cci-nas-00/data/ceres_data/8xd1_38262/01_2025/8xd1_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/cci-nas-00/data/ceres_data/8xd1_38262/01_2025/8xd1_38262.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8xd1_38262/01_2025/8xd1_38262.map" model { file = "/net/cci-nas-00/data/ceres_data/8xd1_38262/01_2025/8xd1_38262_neut.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8xd1_38262/01_2025/8xd1_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. Time to flip 16 residue(s): 0.01s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/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: 4.60, per 1000 atoms: 1.39 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 - 3.00 Amino acid : True - 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: 0.83 Conformation dependent library (CDL) restraints added in 729.0 milliseconds 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: 0.34 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: 0.89 Time building geometry restraints manager: 0.98 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: 0.00 - 2.41: 4491 2.41 - 4.82: 71 4.82 - 7.23: 12 7.23 - 9.64: 7 9.64 - 12.05: 2 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 3.120 nonbonded pdb=" NH2 ARG A 118 " pdb=" OE1 GLU A 121 " model vdw 2.516 3.120 nonbonded pdb=" O ILE A 174 " pdb=" NZ LYS A 177 " model vdw 2.523 3.120 nonbonded pdb=" O ILE A 109 " pdb=" O HOH A 601 " model vdw 2.524 3.040 nonbonded pdb=" O ALA A 223 " pdb=" OG1 THR A 227 " model vdw 2.528 3.040 ... (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: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.710 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: 0.140 Check model and map are aligned: 0.020 Set scattering table: 0.030 Process input model: 14.880 Find NCS groups from input model: 0.070 Set up NCS constraints: 0.030 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:13.310 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 29.200 ------------------------------------------------------------------------------- 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 to be fit. rotamer outliers: 21 poor density : 70 time to evaluate : 0.490 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: 1.3881 time to fit residues: 114.0700 Evaluate side-chains 59 residues out of total 338 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 54 time to evaluate : 0.343 ------------------------------------------------------------------------------- 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: 4.9990 chunk 31 optimal weight: 0.7980 chunk 17 optimal weight: 2.9990 chunk 10 optimal weight: 0.9990 chunk 20 optimal weight: 4.9990 chunk 16 optimal weight: 2.9990 chunk 32 optimal weight: 0.9990 chunk 12 optimal weight: 0.8980 chunk 19 optimal weight: 0.9990 chunk 23 optimal weight: 1.9990 chunk 37 optimal weight: 0.9990 overall best weight: 0.9386 ------------------------------------------------------------------------------- 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 ** both conformations clash, **PLEASE CHECK MANUALLY** A 388 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3541 r_free = 0.3541 target = 0.141655 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3048 r_free = 0.3048 target = 0.106552 restraints weight = 7714.946| |-----------------------------------------------------------------------------| r_work (start): 0.3024 rms_B_bonded: 2.59 r_work: 0.2889 rms_B_bonded: 2.94 restraints_weight: 0.5000 r_work: 0.2764 rms_B_bonded: 4.84 restraints_weight: 0.2500 r_work (final): 0.2764 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2777 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2777 r_free = 0.2777 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 = 0.2777 r_free = 0.2777 target_work(ls_wunit_k1) = 0.088 | | occupancies: max = 1.00 min = 0.44 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2777 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8596 moved from start: 0.1503 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= 0.166 Angle : 0.527 6.214 4583 Z= 0.270 Chirality : 0.043 0.125 498 Planarity : 0.006 0.063 583 Dihedral : 11.285 60.731 504 Min Nonbonded Distance : 2.526 Molprobity Statistics. All-atom Clashscore : 6.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.14 % Favored : 96.86 % Rotamer: Outliers : 2.06 % Allowed : 15.63 % 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: 1.36 (0.44), residues: 415 helix: 2.24 (0.37), residues: 211 sheet: 0.02 (0.72), residues: 63 loop : -0.74 (0.54), residues: 141 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 0.007 0.001 PHE A 57 TYR 0.014 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 70 residues out of total 338 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 64 time to evaluate : 0.346 Fit side-chains revert: symmetry clash REVERT: A 263 TRP cc_start: 0.7630 (t60) cc_final: 0.7424 (t60) REVERT: A 271 LYS cc_start: 0.7407 (OUTLIER) cc_final: 0.7158 (ptmt) outliers start: 6 outliers final: 2 residues processed: 67 average time/residue: 1.3360 time to fit residues: 92.0728 Evaluate side-chains 61 residues out of total 338 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 58 time to evaluate : 0.348 ------------------------------------------------------------------------------- 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 Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 41 random chunks: chunk 30 optimal weight: 7.9990 chunk 34 optimal weight: 0.5980 chunk 28 optimal weight: 7.9990 chunk 32 optimal weight: 5.9990 chunk 33 optimal weight: 1.9990 chunk 11 optimal weight: 0.8980 chunk 16 optimal weight: 0.0970 chunk 0 optimal weight: 10.0000 chunk 37 optimal weight: 0.9980 chunk 5 optimal weight: 7.9990 chunk 13 optimal weight: 2.9990 overall best weight: 0.9180 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3552 r_free = 0.3552 target = 0.141619 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3039 r_free = 0.3039 target = 0.105215 restraints weight = 10001.211| |-----------------------------------------------------------------------------| r_work (start): 0.2939 rms_B_bonded: 2.99 r_work: 0.2787 rms_B_bonded: 3.27 restraints_weight: 0.5000 r_work (final): 0.2787 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2841 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2841 r_free = 0.2841 target_work(ls_wunit_k1) = 0.093 | | occupancies: max = 1.00 min = 0.44 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2841 r_free = 0.2841 target_work(ls_wunit_k1) = 0.093 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2841 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8505 moved from start: 0.1781 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.023 3374 Z= 0.153 Angle : 0.501 6.129 4583 Z= 0.256 Chirality : 0.042 0.123 498 Planarity : 0.005 0.058 583 Dihedral : 9.145 54.444 494 Min Nonbonded Distance : 2.471 Molprobity Statistics. All-atom Clashscore : 5.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.14 % Favored : 96.86 % Rotamer: Outliers : 1.77 % Allowed : 17.11 % Favored : 81.12 % 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: 1.51 (0.44), residues: 415 helix: 2.35 (0.37), residues: 210 sheet: 0.09 (0.71), residues: 67 loop : -0.64 (0.54), residues: 138 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 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 408 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 to be fit. rotamer outliers: 5 poor density : 60 time to evaluate : 0.371 Fit side-chains REVERT: A 230 LEU cc_start: 0.8238 (mp) cc_final: 0.7654 (mp) REVERT: A 271 LYS cc_start: 0.7330 (OUTLIER) cc_final: 0.7071 (ptmt) outliers start: 5 outliers final: 3 residues processed: 64 average time/residue: 1.2333 time to fit residues: 81.3841 Evaluate side-chains 57 residues out of total 338 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 53 time to evaluate : 0.363 ------------------------------------------------------------------------------- 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 271 LYS Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 41 random chunks: chunk 34 optimal weight: 3.9990 chunk 21 optimal weight: 7.9990 chunk 23 optimal weight: 3.9990 chunk 22 optimal weight: 0.8980 chunk 9 optimal weight: 1.9990 chunk 19 optimal weight: 0.9990 chunk 36 optimal weight: 0.7980 chunk 38 optimal weight: 8.9990 chunk 40 optimal weight: 2.9990 chunk 11 optimal weight: 0.9980 chunk 3 optimal weight: 2.9990 overall best weight: 1.1384 ------------------------------------------------------------------------------- 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 337 GLN A 388 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3553 r_free = 0.3553 target = 0.142276 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3076 r_free = 0.3076 target = 0.108317 restraints weight = 4369.520| |-----------------------------------------------------------------------------| r_work (start): 0.3055 rms_B_bonded: 1.89 r_work: 0.2944 rms_B_bonded: 2.31 restraints_weight: 0.5000 r_work: 0.2831 rms_B_bonded: 3.85 restraints_weight: 0.2500 r_work (final): 0.2831 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2834 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2834 r_free = 0.2834 target_work(ls_wunit_k1) = 0.092 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2834 r_free = 0.2834 target_work(ls_wunit_k1) = 0.092 | | occupancies: max = 1.00 min = 0.45 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2834 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8575 moved from start: 0.1959 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= 0.162 Angle : 0.494 6.253 4583 Z= 0.250 Chirality : 0.042 0.125 498 Planarity : 0.005 0.054 583 Dihedral : 8.657 57.258 491 Min Nonbonded Distance : 2.469 Molprobity Statistics. All-atom Clashscore : 5.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.90 % Favored : 97.10 % Rotamer: Outliers : 1.47 % Allowed : 17.70 % Favored : 80.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.52 (0.44), residues: 415 helix: 2.40 (0.37), residues: 210 sheet: 0.01 (0.71), residues: 67 loop : -0.65 (0.55), residues: 138 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A 263 HIS 0.006 0.002 HIS A 394 PHE 0.008 0.001 PHE A 381 TYR 0.022 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 57 residues out of total 338 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 53 time to evaluate : 0.375 Fit side-chains REVERT: A 230 LEU cc_start: 0.8343 (mp) cc_final: 0.7714 (mp) outliers start: 4 outliers final: 4 residues processed: 57 average time/residue: 1.1717 time to fit residues: 68.9787 Evaluate side-chains 55 residues out of total 338 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 51 time to evaluate : 0.378 ------------------------------------------------------------------------------- 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 271 LYS Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 41 random chunks: chunk 3 optimal weight: 2.9990 chunk 34 optimal weight: 0.9990 chunk 25 optimal weight: 0.5980 chunk 14 optimal weight: 1.9990 chunk 22 optimal weight: 5.9990 chunk 36 optimal weight: 0.9980 chunk 23 optimal weight: 5.9990 chunk 2 optimal weight: 3.9990 chunk 30 optimal weight: 0.2980 chunk 32 optimal weight: 6.9990 chunk 20 optimal weight: 5.9990 overall best weight: 0.9784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 218 GLN ** A 267 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 388 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3560 r_free = 0.3560 target = 0.142533 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3061 r_free = 0.3061 target = 0.106820 restraints weight = 7817.934| |-----------------------------------------------------------------------------| r_work (start): 0.3042 rms_B_bonded: 2.57 r_work: 0.2907 rms_B_bonded: 2.93 restraints_weight: 0.5000 r_work: 0.2783 rms_B_bonded: 4.83 restraints_weight: 0.2500 r_work (final): 0.2783 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2782 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2782 r_free = 0.2782 target_work(ls_wunit_k1) = 0.089 | | occupancies: max = 1.00 min = 0.45 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2782 r_free = 0.2782 target_work(ls_wunit_k1) = 0.089 | | occupancies: max = 1.00 min = 0.47 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2782 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8597 moved from start: 0.2083 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= 0.148 Angle : 0.474 6.696 4583 Z= 0.240 Chirality : 0.042 0.124 498 Planarity : 0.005 0.050 583 Dihedral : 7.687 59.215 491 Min Nonbonded Distance : 2.477 Molprobity Statistics. All-atom Clashscore : 4.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.62 % Favored : 96.38 % 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: 1.58 (0.44), residues: 415 helix: 2.44 (0.37), residues: 210 sheet: 0.04 (0.71), residues: 67 loop : -0.64 (0.54), residues: 138 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 92 HIS 0.005 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 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 to be fit. rotamer outliers: 5 poor density : 57 time to evaluate : 0.384 Fit side-chains outliers start: 5 outliers final: 3 residues processed: 62 average time/residue: 1.2742 time to fit residues: 81.3162 Evaluate side-chains 55 residues out of total 338 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 52 time to evaluate : 0.331 ------------------------------------------------------------------------------- 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 Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 41 random chunks: chunk 21 optimal weight: 5.9990 chunk 1 optimal weight: 6.9990 chunk 3 optimal weight: 4.9990 chunk 35 optimal weight: 0.9990 chunk 39 optimal weight: 6.9990 chunk 6 optimal weight: 0.9980 chunk 33 optimal weight: 0.9990 chunk 24 optimal weight: 9.9990 chunk 38 optimal weight: 2.9990 chunk 36 optimal weight: 0.8980 chunk 26 optimal weight: 8.9990 overall best weight: 1.3786 ------------------------------------------------------------------------------- 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 234 GLN ** A 267 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 388 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3536 r_free = 0.3536 target = 0.140966 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3009 r_free = 0.3009 target = 0.104013 restraints weight = 11136.615| |-----------------------------------------------------------------------------| r_work (start): 0.2898 rms_B_bonded: 3.11 r_work: 0.2740 rms_B_bonded: 3.39 restraints_weight: 0.5000 r_work (final): 0.2740 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2828 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2828 r_free = 0.2828 target_work(ls_wunit_k1) = 0.092 | | occupancies: max = 1.00 min = 0.47 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2828 r_free = 0.2828 target_work(ls_wunit_k1) = 0.092 | | occupancies: max = 1.00 min = 0.47 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2828 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8521 moved from start: 0.2178 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= 0.172 Angle : 0.490 7.071 4583 Z= 0.248 Chirality : 0.042 0.126 498 Planarity : 0.005 0.049 583 Dihedral : 7.068 59.106 491 Min Nonbonded Distance : 2.499 Molprobity Statistics. All-atom Clashscore : 5.32 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: 1.57 (0.44), residues: 415 helix: 2.43 (0.37), residues: 210 sheet: 0.01 (0.71), residues: 67 loop : -0.61 (0.55), residues: 138 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 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 60 residues out of total 338 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 56 time to evaluate : 0.367 Fit side-chains REVERT: A 230 LEU cc_start: 0.8212 (mp) cc_final: 0.7646 (mp) outliers start: 4 outliers final: 3 residues processed: 59 average time/residue: 1.1476 time to fit residues: 69.9912 Evaluate side-chains 56 residues out of total 338 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 53 time to evaluate : 0.361 ------------------------------------------------------------------------------- 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 Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 41 random chunks: chunk 28 optimal weight: 8.9990 chunk 7 optimal weight: 4.9990 chunk 21 optimal weight: 7.9990 chunk 1 optimal weight: 5.9990 chunk 22 optimal weight: 3.9990 chunk 25 optimal weight: 0.9980 chunk 23 optimal weight: 7.9990 chunk 5 optimal weight: 6.9990 chunk 40 optimal weight: 0.7980 chunk 4 optimal weight: 0.9990 chunk 16 optimal weight: 0.0060 overall best weight: 1.3600 ------------------------------------------------------------------------------- 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 ** both conformations clash, **PLEASE CHECK MANUALLY** A 388 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3536 r_free = 0.3536 target = 0.140983 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 28)----------------| | r_work = 0.3035 r_free = 0.3035 target = 0.105761 restraints weight = 6208.604| |-----------------------------------------------------------------------------| r_work (start): 0.3028 rms_B_bonded: 2.28 r_work: 0.2903 rms_B_bonded: 2.69 restraints_weight: 0.5000 r_work: 0.2783 rms_B_bonded: 4.44 restraints_weight: 0.2500 r_work (final): 0.2783 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2794 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2794 r_free = 0.2794 target_work(ls_wunit_k1) = 0.090 | | occupancies: max = 1.00 min = 0.47 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2794 r_free = 0.2794 target_work(ls_wunit_k1) = 0.090 | | occupancies: max = 1.00 min = 0.47 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2794 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8614 moved from start: 0.2194 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= 0.175 Angle : 0.520 8.117 4583 Z= 0.264 Chirality : 0.043 0.167 498 Planarity : 0.005 0.048 583 Dihedral : 6.537 52.989 491 Min Nonbonded Distance : 2.423 Molprobity Statistics. All-atom Clashscore : 5.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.14 % Favored : 96.86 % Rotamer: Outliers : 1.47 % Allowed : 21.24 % Favored : 77.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.59 (0.44), residues: 415 helix: 2.43 (0.37), residues: 210 sheet: -0.03 (0.71), residues: 67 loop : -0.55 (0.55), residues: 138 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 263 HIS 0.006 0.001 HIS A 394 PHE 0.009 0.001 PHE A 381 TYR 0.007 0.001 TYR A 363 ARG 0.008 0.000 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 57 residues out of total 338 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 53 time to evaluate : 0.377 Fit side-chains REVERT: A 230 LEU cc_start: 0.8392 (mp) cc_final: 0.7793 (mp) REVERT: A 263 TRP cc_start: 0.6752 (t60) cc_final: 0.6455 (t60) REVERT: A 266 GLU cc_start: 0.8640 (tt0) cc_final: 0.8210 (pt0) REVERT: A 337 GLN cc_start: 0.8408 (OUTLIER) cc_final: 0.8136 (tt0) outliers start: 4 outliers final: 3 residues processed: 57 average time/residue: 1.2667 time to fit residues: 74.3593 Evaluate side-chains 53 residues out of total 338 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 49 time to evaluate : 0.347 ------------------------------------------------------------------------------- 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 337 GLN Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 41 random chunks: chunk 18 optimal weight: 0.4980 chunk 34 optimal weight: 0.5980 chunk 4 optimal weight: 4.9990 chunk 23 optimal weight: 9.9990 chunk 35 optimal weight: 0.9980 chunk 24 optimal weight: 7.9990 chunk 14 optimal weight: 1.9990 chunk 17 optimal weight: 5.9990 chunk 11 optimal weight: 0.9980 chunk 36 optimal weight: 3.9990 chunk 26 optimal weight: 3.9990 overall best weight: 1.0182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 267 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 388 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3559 r_free = 0.3559 target = 0.142630 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3050 r_free = 0.3050 target = 0.106417 restraints weight = 10782.503| |-----------------------------------------------------------------------------| r_work (start): 0.3022 rms_B_bonded: 3.02 r_work: 0.2876 rms_B_bonded: 3.29 restraints_weight: 0.5000 r_work (final): 0.2876 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2885 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2885 r_free = 0.2885 target_work(ls_wunit_k1) = 0.095 | | occupancies: max = 1.00 min = 0.47 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2885 r_free = 0.2885 target_work(ls_wunit_k1) = 0.095 | | occupancies: max = 1.00 min = 0.47 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2885 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8529 moved from start: 0.2254 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= 0.151 Angle : 0.503 7.833 4583 Z= 0.255 Chirality : 0.043 0.159 498 Planarity : 0.005 0.047 583 Dihedral : 6.172 48.706 491 Min Nonbonded Distance : 2.462 Molprobity Statistics. All-atom Clashscore : 5.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.90 % Favored : 97.10 % Rotamer: Outliers : 1.47 % Allowed : 21.53 % Favored : 76.99 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.62 (0.44), residues: 415 helix: 2.44 (0.36), residues: 210 sheet: -0.05 (0.71), residues: 67 loop : -0.49 (0.56), residues: 138 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 92 HIS 0.005 0.001 HIS A 394 PHE 0.009 0.001 PHE A 381 TYR 0.022 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 57 residues out of total 338 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 53 time to evaluate : 0.341 Fit side-chains REVERT: A 230 LEU cc_start: 0.8306 (mp) cc_final: 0.7715 (mp) REVERT: A 263 TRP cc_start: 0.6680 (t60) cc_final: 0.6357 (t60) REVERT: A 266 GLU cc_start: 0.8538 (tt0) cc_final: 0.8057 (pt0) outliers start: 4 outliers final: 3 residues processed: 57 average time/residue: 1.2048 time to fit residues: 70.8507 Evaluate side-chains 55 residues out of total 338 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 52 time to evaluate : 0.339 ------------------------------------------------------------------------------- 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 Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 41 random chunks: chunk 21 optimal weight: 0.0870 chunk 28 optimal weight: 9.9990 chunk 14 optimal weight: 0.9990 chunk 30 optimal weight: 1.9990 chunk 25 optimal weight: 6.9990 chunk 15 optimal weight: 0.9980 chunk 9 optimal weight: 0.9980 chunk 17 optimal weight: 1.9990 chunk 26 optimal weight: 5.9990 chunk 36 optimal weight: 2.9990 chunk 31 optimal weight: 5.9990 overall best weight: 1.0162 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 267 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 337 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 388 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3555 r_free = 0.3555 target = 0.142043 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3060 r_free = 0.3060 target = 0.107165 restraints weight = 6473.321| |-----------------------------------------------------------------------------| r_work (start): 0.2981 rms_B_bonded: 2.32 r_work: 0.2855 rms_B_bonded: 2.72 restraints_weight: 0.5000 r_work: 0.2736 rms_B_bonded: 4.47 restraints_weight: 0.2500 r_work (final): 0.2736 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2802 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2802 r_free = 0.2802 target_work(ls_wunit_k1) = 0.090 | | occupancies: max = 1.00 min = 0.47 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2802 r_free = 0.2802 target_work(ls_wunit_k1) = 0.090 | | occupancies: max = 1.00 min = 0.42 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2802 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8552 moved from start: 0.2290 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= 0.154 Angle : 0.502 7.458 4583 Z= 0.257 Chirality : 0.043 0.154 498 Planarity : 0.005 0.048 583 Dihedral : 6.050 46.860 491 Min Nonbonded Distance : 2.480 Molprobity Statistics. All-atom Clashscore : 5.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.38 % Favored : 96.62 % Rotamer: Outliers : 1.18 % Allowed : 21.53 % Favored : 77.29 % 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 (0.44), residues: 415 helix: 2.42 (0.36), residues: 210 sheet: -0.06 (0.71), residues: 67 loop : -0.53 (0.56), residues: 138 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 92 HIS 0.007 0.001 HIS A 394 PHE 0.009 0.001 PHE A 381 TYR 0.006 0.001 TYR A 363 ARG 0.009 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 56 residues out of total 338 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 53 time to evaluate : 0.354 Fit side-chains REVERT: A 230 LEU cc_start: 0.8310 (mp) cc_final: 0.7705 (mp) REVERT: A 263 TRP cc_start: 0.6645 (t60) cc_final: 0.6302 (t60) REVERT: A 266 GLU cc_start: 0.8525 (tt0) cc_final: 0.7983 (pt0) outliers start: 3 outliers final: 3 residues processed: 56 average time/residue: 1.2026 time to fit residues: 69.4340 Evaluate side-chains 54 residues out of total 338 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 51 time to evaluate : 0.351 ------------------------------------------------------------------------------- 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 Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 41 random chunks: chunk 20 optimal weight: 1.9990 chunk 36 optimal weight: 4.9990 chunk 39 optimal weight: 8.9990 chunk 14 optimal weight: 0.0570 chunk 29 optimal weight: 6.9990 chunk 30 optimal weight: 6.9990 chunk 24 optimal weight: 8.9990 chunk 21 optimal weight: 3.9990 chunk 40 optimal weight: 0.8980 chunk 31 optimal weight: 3.9990 chunk 6 optimal weight: 3.9990 overall best weight: 2.1904 ------------------------------------------------------------------------------- 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 ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 337 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 388 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3517 r_free = 0.3517 target = 0.138356 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3014 r_free = 0.3014 target = 0.103332 restraints weight = 6173.185| |-----------------------------------------------------------------------------| r_work (start): 0.2974 rms_B_bonded: 2.25 r_work: 0.2848 rms_B_bonded: 2.64 restraints_weight: 0.5000 r_work: 0.2729 rms_B_bonded: 4.36 restraints_weight: 0.2500 r_work (final): 0.2729 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2709 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2709 r_free = 0.2709 target_work(ls_wunit_k1) = 0.084 | | occupancies: max = 1.00 min = 0.42 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2709 r_free = 0.2709 target_work(ls_wunit_k1) = 0.084 | | occupancies: max = 1.00 min = 0.41 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2709 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8641 moved from start: 0.2332 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.026 3374 Z= 0.240 Angle : 0.539 7.303 4583 Z= 0.276 Chirality : 0.044 0.152 498 Planarity : 0.006 0.051 583 Dihedral : 6.133 45.983 491 Min Nonbonded Distance : 2.480 Molprobity Statistics. All-atom Clashscore : 6.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.90 % Favored : 97.10 % Rotamer: Outliers : 1.18 % Allowed : 21.83 % Favored : 76.99 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.55 (0.44), residues: 415 helix: 2.39 (0.37), residues: 210 sheet: -0.11 (0.69), residues: 67 loop : -0.52 (0.56), residues: 138 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 263 HIS 0.007 0.001 HIS A 394 PHE 0.009 0.001 PHE A 381 TYR 0.021 0.002 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 54 residues out of total 338 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 51 time to evaluate : 0.353 Fit side-chains REVERT: A 218 GLN cc_start: 0.9267 (tt0) cc_final: 0.9035 (tt0) REVERT: A 230 LEU cc_start: 0.8443 (mp) cc_final: 0.7860 (mp) REVERT: A 263 TRP cc_start: 0.6681 (t60) cc_final: 0.6342 (t60) REVERT: A 266 GLU cc_start: 0.8518 (tt0) cc_final: 0.7989 (pt0) REVERT: A 336 LEU cc_start: 0.9351 (tt) cc_final: 0.9133 (tp) outliers start: 3 outliers final: 2 residues processed: 54 average time/residue: 1.2281 time to fit residues: 68.4313 Evaluate side-chains 52 residues out of total 338 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 50 time to evaluate : 0.364 ------------------------------------------------------------------------------- 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 37 optimal weight: 0.8980 chunk 36 optimal weight: 4.9990 chunk 13 optimal weight: 0.0870 chunk 31 optimal weight: 5.9990 chunk 4 optimal weight: 3.9990 chunk 0 optimal weight: 10.0000 chunk 34 optimal weight: 1.9990 chunk 30 optimal weight: 0.6980 chunk 6 optimal weight: 0.0770 chunk 11 optimal weight: 2.9990 chunk 28 optimal weight: 5.9990 overall best weight: 0.7518 ------------------------------------------------------------------------------- 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 ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 337 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 388 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3553 r_free = 0.3553 target = 0.141243 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3056 r_free = 0.3056 target = 0.106278 restraints weight = 6134.318| |-----------------------------------------------------------------------------| r_work (start): 0.3012 rms_B_bonded: 2.29 r_work: 0.2885 rms_B_bonded: 2.70 restraints_weight: 0.5000 r_work: 0.2766 rms_B_bonded: 4.46 restraints_weight: 0.2500 r_work (final): 0.2766 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2729 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2729 r_free = 0.2729 target_work(ls_wunit_k1) = 0.086 | | occupancies: max = 1.00 min = 0.41 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2729 r_free = 0.2729 target_work(ls_wunit_k1) = 0.086 | | occupancies: max = 1.00 min = 0.39 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2729 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8589 moved from start: 0.2306 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.026 3374 Z= 0.140 Angle : 0.516 7.995 4583 Z= 0.259 Chirality : 0.043 0.148 498 Planarity : 0.005 0.052 583 Dihedral : 6.002 46.005 491 Min Nonbonded Distance : 2.497 Molprobity Statistics. All-atom Clashscore : 5.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.90 % Favored : 97.10 % Rotamer: Outliers : 0.88 % Allowed : 21.53 % 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: 1.60 (0.44), residues: 415 helix: 2.41 (0.36), residues: 210 sheet: -0.03 (0.70), residues: 67 loop : -0.47 (0.56), residues: 138 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 92 HIS 0.005 0.001 HIS A 394 PHE 0.009 0.001 PHE A 381 TYR 0.006 0.001 TYR A 250 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: 2925.08 seconds wall clock time: 52 minutes 23.94 seconds (3143.94 seconds total)