Starting phenix.real_space_refine on Sun Mar 10 22:56:23 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6up7_20836/03_2024/6up7_20836_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6up7_20836/03_2024/6up7_20836.map Found restraint, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6up7_20836/03_2024/6up7_20836_ligands.cif Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.2 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { restraint_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6up7_20836/03_2024/6up7_20836_ligands.cif" default_restraint = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6up7_20836/03_2024/6up7_20836_ligands.cif" real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6up7_20836/03_2024/6up7_20836.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6up7_20836/03_2024/6up7_20836.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6up7_20836/03_2024/6up7_20836_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6up7_20836/03_2024/6up7_20836_updated.pdb" } resolution = 4.2 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.002 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Anisotropic ADP refinement not supported. Converting 1653 atoms to isotropic. 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 4 5.16 5 C 2632 2.51 5 N 756 2.21 5 O 771 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "C ARG 9": "NH1" <-> "NH2" Residue "B ARG 65": "NH1" <-> "NH2" Residue "B ARG 236": "NH1" <-> "NH2" Residue "R ARG 182": "NH1" <-> "NH2" Residue "R ARG 323": "NH1" <-> "NH2" Residue "R ARG 372": "NH1" <-> "NH2" Time to flip residues: 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 4166 Number of models: 1 Model: "" Number of chains: 5 Chain: "C" Number of atoms: 48 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 48 Classifications: {'peptide': 6} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 1, 'TRANS': 4} Unresolved non-hydrogen bonds: 9 Unresolved non-hydrogen angles: 11 Unresolved non-hydrogen dihedrals: 7 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'ARG:plan': 1} Unresolved non-hydrogen planarities: 5 Chain: "B" Number of atoms: 2063 Number of conformers: 1 Conformer: "" Number of residues, atoms: 348, 2063 Classifications: {'peptide': 348} Incomplete info: {'truncation_to_alanine': 202} Link IDs: {'PTRANS': 24, 'TRANS': 323} Unresolved chain link angles: 5 Unresolved non-hydrogen bonds: 715 Unresolved non-hydrogen angles: 909 Unresolved non-hydrogen dihedrals: 569 Unresolved non-hydrogen chiralities: 72 Planarities with less than four sites: {'GLN:plan1': 5, 'ASP:plan': 21, 'TYR:plan': 7, 'ASN:plan1': 12, 'HIS:plan': 6, 'PHE:plan': 5, 'GLU:plan': 23, 'ARG:plan': 13} Unresolved non-hydrogen planarities: 385 Chain: "R" Number of atoms: 1970 Number of conformers: 1 Conformer: "" Number of residues, atoms: 322, 1970 Classifications: {'peptide': 322} Incomplete info: {'truncation_to_alanine': 183} Link IDs: {'PTRANS': 10, 'TRANS': 311} Chain breaks: 1 Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 599 Unresolved non-hydrogen angles: 771 Unresolved non-hydrogen dihedrals: 474 Unresolved non-hydrogen chiralities: 86 Planarities with less than four sites: {'GLN:plan1': 8, 'HIS:plan': 6, 'TYR:plan': 4, 'ASN:plan1': 9, 'TRP:plan': 1, 'ASP:plan': 8, 'PHE:plan': 7, 'GLU:plan': 6, 'ARG:plan': 10} Unresolved non-hydrogen planarities: 266 Chain: "V" Number of atoms: 45 Number of conformers: 1 Conformer: "" Number of residues, atoms: 9, 45 Classifications: {'peptide': 9} Incomplete info: {'truncation_to_alanine': 9} Link IDs: {'TRANS': 8} Unresolved non-hydrogen bonds: 18 Unresolved non-hydrogen angles: 27 Unresolved non-hydrogen dihedrals: 9 Planarities with less than four sites: {'UNK:plan-1': 9} Unresolved non-hydrogen planarities: 9 Chain: "R" Number of atoms: 40 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 40 Unusual residues: {'PIO': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 7 Unresolved non-hydrogen angles: 7 Unresolved non-hydrogen dihedrals: 7 Time building chain proxies: 3.06, per 1000 atoms: 0.73 Number of scatterers: 4166 At special positions: 0 Unit cell: (72.08, 87.98, 121.9, 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 4 16.00 P 3 15.00 O 771 8.00 N 756 7.00 C 2632 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=1, symmetry=0 Simple disulfide: pdb=" SG CYS R 141 " - pdb=" SG CYS R 224 " distance=2.02 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 1.74 Conformation dependent library (CDL) restraints added in 927.5 milliseconds 1336 Ramachandran restraints generated. 668 Oldfield, 0 Emsley, 668 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1310 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 12 helices and 4 sheets defined 37.0% alpha, 9.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.82 Creating SS restraints... Processing helix chain 'B' and resid 68 through 70 No H-bonds generated for 'chain 'B' and resid 68 through 70' Processing helix chain 'B' and resid 99 through 106 Processing helix chain 'R' and resid 52 through 54 No H-bonds generated for 'chain 'R' and resid 52 through 54' Processing helix chain 'R' and resid 60 through 92 Processing helix chain 'R' and resid 102 through 128 Proline residue: R 121 - end of helix removed outlier: 3.996A pdb=" N PHE R 127 " --> pdb=" O GLU R 123 " (cutoff:3.500A) Processing helix chain 'R' and resid 138 through 171 removed outlier: 3.769A pdb=" N ILE R 170 " --> pdb=" O ARG R 166 " (cutoff:3.500A) Processing helix chain 'R' and resid 175 through 179 Processing helix chain 'R' and resid 182 through 204 removed outlier: 3.795A pdb=" N ALA R 200 " --> pdb=" O SER R 196 " (cutoff:3.500A) removed outlier: 3.871A pdb=" N VAL R 201 " --> pdb=" O ALA R 197 " (cutoff:3.500A) Proline residue: R 202 - end of helix Processing helix chain 'R' and resid 230 through 269 removed outlier: 5.856A pdb=" N PHE R 247 " --> pdb=" O MET R 243 " (cutoff:3.500A) Proline residue: R 248 - end of helix Processing helix chain 'R' and resid 296 through 327 Proline residue: R 318 - end of helix Processing helix chain 'R' and resid 336 through 364 removed outlier: 3.948A pdb=" N ASN R 360 " --> pdb=" O SER R 356 " (cutoff:3.500A) Proline residue: R 361 - end of helix Processing helix chain 'R' and resid 370 through 382 Processing sheet with id= A, first strand: chain 'B' and resid 18 through 20 Processing sheet with id= B, first strand: chain 'B' and resid 52 through 60 Processing sheet with id= C, first strand: chain 'B' and resid 183 through 185 Processing sheet with id= D, first strand: chain 'B' and resid 249 through 252 removed outlier: 3.966A pdb=" N ALA B 239 " --> pdb=" O TYR B 249 " (cutoff:3.500A) removed outlier: 4.109A pdb=" N TYR B 321 " --> pdb=" O PHE B 349 " (cutoff:3.500A) removed outlier: 3.712A pdb=" N VAL B 345 " --> pdb=" O VAL B 325 " (cutoff:3.500A) 224 hydrogen bonds defined for protein. 651 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: 1.04 Time building geometry restraints manager: 1.87 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 1402 1.34 - 1.46: 815 1.46 - 1.57: 2021 1.57 - 1.69: 4 1.69 - 1.81: 4 Bond restraints: 4246 Sorted by residual: bond pdb=" C1B PIO R 400 " pdb=" O3C PIO R 400 " ideal model delta sigma weight residual 1.399 1.457 -0.058 2.00e-02 2.50e+03 8.27e+00 bond pdb=" C1A PIO R 400 " pdb=" O2C PIO R 400 " ideal model delta sigma weight residual 1.399 1.455 -0.056 2.00e-02 2.50e+03 7.95e+00 bond pdb=" C GLU R 291 " pdb=" N PRO R 292 " ideal model delta sigma weight residual 1.336 1.366 -0.030 1.25e-02 6.40e+03 5.91e+00 bond pdb=" CB GLN B 237 " pdb=" CG GLN B 237 " ideal model delta sigma weight residual 1.520 1.454 0.066 3.00e-02 1.11e+03 4.77e+00 bond pdb=" C MET R 120 " pdb=" N PRO R 121 " ideal model delta sigma weight residual 1.335 1.363 -0.028 1.30e-02 5.92e+03 4.65e+00 ... (remaining 4241 not shown) Histogram of bond angle deviations from ideal: 102.09 - 108.43: 320 108.43 - 114.77: 2244 114.77 - 121.12: 2060 121.12 - 127.46: 1222 127.46 - 133.81: 34 Bond angle restraints: 5880 Sorted by residual: angle pdb=" N GLN R 333 " pdb=" CA GLN R 333 " pdb=" C GLN R 333 " ideal model delta sigma weight residual 111.28 116.35 -5.07 1.09e+00 8.42e-01 2.16e+01 angle pdb=" N TRP R 334 " pdb=" CA TRP R 334 " pdb=" C TRP R 334 " ideal model delta sigma weight residual 109.07 115.86 -6.79 1.61e+00 3.86e-01 1.78e+01 angle pdb=" N ARG R 182 " pdb=" CA ARG R 182 " pdb=" C ARG R 182 " ideal model delta sigma weight residual 111.36 106.79 4.57 1.09e+00 8.42e-01 1.76e+01 angle pdb=" N LYS B 95 " pdb=" CA LYS B 95 " pdb=" C LYS B 95 " ideal model delta sigma weight residual 109.81 118.49 -8.68 2.21e+00 2.05e-01 1.54e+01 angle pdb=" N ASN R 360 " pdb=" CA ASN R 360 " pdb=" C ASN R 360 " ideal model delta sigma weight residual 109.81 117.99 -8.18 2.21e+00 2.05e-01 1.37e+01 ... (remaining 5875 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 14.99: 2334 14.99 - 29.99: 106 29.99 - 44.98: 19 44.98 - 59.97: 6 59.97 - 74.97: 2 Dihedral angle restraints: 2467 sinusoidal: 458 harmonic: 2009 Sorted by residual: dihedral pdb=" CA ILE B 241 " pdb=" C ILE B 241 " pdb=" N VAL B 242 " pdb=" CA VAL B 242 " ideal model delta harmonic sigma weight residual -180.00 -151.99 -28.01 0 5.00e+00 4.00e-02 3.14e+01 dihedral pdb=" CA LYS B 226 " pdb=" C LYS B 226 " pdb=" N THR B 227 " pdb=" CA THR B 227 " ideal model delta harmonic sigma weight residual 180.00 152.51 27.49 0 5.00e+00 4.00e-02 3.02e+01 dihedral pdb=" CA GLN R 95 " pdb=" C GLN R 95 " pdb=" N SER R 96 " pdb=" CA SER R 96 " ideal model delta harmonic sigma weight residual 180.00 153.88 26.12 0 5.00e+00 4.00e-02 2.73e+01 ... (remaining 2464 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.070: 588 0.070 - 0.141: 118 0.141 - 0.211: 21 0.211 - 0.282: 3 0.282 - 0.352: 2 Chirality restraints: 732 Sorted by residual: chirality pdb=" CB ILE B 317 " pdb=" CA ILE B 317 " pdb=" CG1 ILE B 317 " pdb=" CG2 ILE B 317 " both_signs ideal model delta sigma weight residual False 2.64 2.29 0.35 2.00e-01 2.50e+01 3.10e+00 chirality pdb=" CB ILE B 241 " pdb=" CA ILE B 241 " pdb=" CG1 ILE B 241 " pdb=" CG2 ILE B 241 " both_signs ideal model delta sigma weight residual False 2.64 2.30 0.35 2.00e-01 2.50e+01 3.03e+00 chirality pdb=" CA TRP R 316 " pdb=" N TRP R 316 " pdb=" C TRP R 316 " pdb=" CB TRP R 316 " both_signs ideal model delta sigma weight residual False 2.51 2.29 0.23 2.00e-01 2.50e+01 1.27e+00 ... (remaining 729 not shown) Planarity restraints: 786 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA TRP R 134 " 0.013 2.00e-02 2.50e+03 2.68e-02 7.18e+00 pdb=" C TRP R 134 " -0.046 2.00e-02 2.50e+03 pdb=" O TRP R 134 " 0.017 2.00e-02 2.50e+03 pdb=" N ALA R 135 " 0.016 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C PHE R 247 " 0.042 5.00e-02 4.00e+02 6.26e-02 6.28e+00 pdb=" N PRO R 248 " -0.108 5.00e-02 4.00e+02 pdb=" CA PRO R 248 " 0.030 5.00e-02 4.00e+02 pdb=" CD PRO R 248 " 0.036 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA PHE R 242 " -0.011 2.00e-02 2.50e+03 2.23e-02 4.98e+00 pdb=" C PHE R 242 " 0.039 2.00e-02 2.50e+03 pdb=" O PHE R 242 " -0.014 2.00e-02 2.50e+03 pdb=" N MET R 243 " -0.013 2.00e-02 2.50e+03 ... (remaining 783 not shown) Histogram of nonbonded interaction distances: 2.22 - 2.75: 710 2.75 - 3.29: 4229 3.29 - 3.83: 6881 3.83 - 4.36: 6692 4.36 - 4.90: 11822 Nonbonded interactions: 30334 Sorted by model distance: nonbonded pdb=" O PRO C 10 " pdb=" CE1 PHE R 326 " model vdw 2.216 3.340 nonbonded pdb=" O ALA B 301 " pdb=" OH TYR B 321 " model vdw 2.260 2.440 nonbonded pdb=" O VAL R 83 " pdb=" OG1 THR R 87 " model vdw 2.263 2.440 nonbonded pdb=" OG SER R 213 " pdb=" O ASP R 215 " model vdw 2.294 2.440 nonbonded pdb=" O LEU R 108 " pdb=" OG SER R 111 " model vdw 2.310 2.440 ... (remaining 30329 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue 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: 0.570 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.030 Construct map_model_manager: 0.010 Extract box with map and model: 2.320 Check model and map are aligned: 0.060 Set scattering table: 0.040 Process input model: 16.790 Find NCS groups from input model: 0.150 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:2.520 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 22.510 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8117 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 : 0.008 0.075 4246 Z= 0.559 Angle : 1.077 9.683 5880 Z= 0.592 Chirality : 0.061 0.352 732 Planarity : 0.008 0.063 786 Dihedral : 10.470 74.968 1154 Min Nonbonded Distance : 2.216 Molprobity Statistics. All-atom Clashscore : 9.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 13.17 % Favored : 86.83 % Rotamer: Outliers : 0.00 % Allowed : 7.32 % Favored : 92.68 % 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: -5.14 (0.26), residues: 668 helix: -1.80 (0.26), residues: 242 sheet: -4.64 (0.31), residues: 133 loop : -4.19 (0.30), residues: 293 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.006 TRP R 134 HIS 0.014 0.004 HIS R 320 PHE 0.020 0.003 PHE R 345 TYR 0.013 0.003 TYR B 272 ARG 0.006 0.002 ARG R 323 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1336 Ramachandran restraints generated. 668 Oldfield, 0 Emsley, 668 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1336 Ramachandran restraints generated. 668 Oldfield, 0 Emsley, 668 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 94 residues out of total 592 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 94 time to evaluate : 0.478 Fit side-chains REVERT: B 76 ARG cc_start: 0.9053 (ppp-140) cc_final: 0.8791 (ptm-80) REVERT: B 236 ARG cc_start: 0.8197 (mpp80) cc_final: 0.7601 (mtp85) REVERT: B 250 LYS cc_start: 0.8873 (ttpp) cc_final: 0.7841 (tttt) REVERT: R 88 LEU cc_start: 0.9423 (tt) cc_final: 0.8950 (tt) REVERT: R 102 HIS cc_start: 0.6600 (t-90) cc_final: 0.6119 (t-90) REVERT: R 104 HIS cc_start: 0.9020 (m90) cc_final: 0.8444 (m-70) REVERT: R 148 ARG cc_start: 0.8498 (ptp-110) cc_final: 0.8173 (ttp80) REVERT: R 190 SER cc_start: 0.9426 (m) cc_final: 0.9072 (p) REVERT: R 315 CYS cc_start: 0.8333 (p) cc_final: 0.7880 (p) REVERT: R 372 ARG cc_start: 0.8280 (ttp-170) cc_final: 0.7507 (tpt170) outliers start: 0 outliers final: 0 residues processed: 94 average time/residue: 0.2116 time to fit residues: 23.6597 Evaluate side-chains 77 residues out of total 592 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 77 time to evaluate : 0.481 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 67 random chunks: chunk 56 optimal weight: 6.9990 chunk 50 optimal weight: 10.0000 chunk 28 optimal weight: 0.7980 chunk 17 optimal weight: 0.8980 chunk 34 optimal weight: 4.9990 chunk 27 optimal weight: 10.0000 chunk 52 optimal weight: 8.9990 chunk 20 optimal weight: 3.9990 chunk 31 optimal weight: 5.9990 chunk 39 optimal weight: 0.0470 chunk 60 optimal weight: 0.7980 overall best weight: 1.3080 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 237 GLN R 104 HIS R 373 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8058 moved from start: 0.1923 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 4246 Z= 0.209 Angle : 0.640 6.304 5880 Z= 0.331 Chirality : 0.045 0.225 732 Planarity : 0.005 0.039 786 Dihedral : 7.108 73.442 731 Min Nonbonded Distance : 2.182 Molprobity Statistics. All-atom Clashscore : 9.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.33 % Favored : 89.67 % Rotamer: Outliers : 0.00 % Allowed : 4.88 % Favored : 95.12 % 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: -3.46 (0.30), residues: 668 helix: 0.38 (0.29), residues: 257 sheet: -4.33 (0.33), residues: 138 loop : -3.86 (0.32), residues: 273 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.002 TRP R 316 HIS 0.008 0.002 HIS R 373 PHE 0.007 0.001 PHE R 312 TYR 0.027 0.002 TYR R 153 ARG 0.007 0.001 ARG B 65 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1336 Ramachandran restraints generated. 668 Oldfield, 0 Emsley, 668 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1336 Ramachandran restraints generated. 668 Oldfield, 0 Emsley, 668 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 91 residues out of total 592 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 91 time to evaluate : 0.497 Fit side-chains REVERT: B 217 ASN cc_start: 0.9196 (t0) cc_final: 0.8977 (t0) REVERT: B 250 LYS cc_start: 0.9046 (ttpp) cc_final: 0.8738 (tttt) REVERT: R 88 LEU cc_start: 0.9327 (tt) cc_final: 0.8894 (tt) REVERT: R 98 GLN cc_start: 0.7688 (mt0) cc_final: 0.7445 (mt0) REVERT: R 102 HIS cc_start: 0.6547 (t-90) cc_final: 0.6075 (t-90) REVERT: R 144 TYR cc_start: 0.8379 (t80) cc_final: 0.7992 (t80) REVERT: R 190 SER cc_start: 0.9345 (m) cc_final: 0.8973 (p) REVERT: R 233 VAL cc_start: 0.9612 (m) cc_final: 0.9343 (p) REVERT: R 319 TYR cc_start: 0.8478 (t80) cc_final: 0.8268 (t80) REVERT: R 344 TYR cc_start: 0.8329 (m-80) cc_final: 0.7981 (m-80) outliers start: 0 outliers final: 0 residues processed: 91 average time/residue: 0.1968 time to fit residues: 21.8604 Evaluate side-chains 78 residues out of total 592 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 78 time to evaluate : 0.486 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 67 random chunks: chunk 33 optimal weight: 20.0000 chunk 18 optimal weight: 20.0000 chunk 50 optimal weight: 10.0000 chunk 41 optimal weight: 1.9990 chunk 16 optimal weight: 10.0000 chunk 60 optimal weight: 0.6980 chunk 65 optimal weight: 10.0000 chunk 54 optimal weight: 1.9990 chunk 20 optimal weight: 1.9990 chunk 48 optimal weight: 2.9990 chunk 45 optimal weight: 2.9990 overall best weight: 1.9388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 237 GLN R 104 HIS R 373 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8091 moved from start: 0.2369 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.031 4246 Z= 0.263 Angle : 0.635 8.318 5880 Z= 0.331 Chirality : 0.044 0.174 732 Planarity : 0.004 0.034 786 Dihedral : 6.975 84.674 731 Min Nonbonded Distance : 2.211 Molprobity Statistics. All-atom Clashscore : 11.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 11.98 % Favored : 88.02 % Rotamer: Outliers : 0.00 % Allowed : 4.39 % Favored : 95.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.73 (0.32), residues: 668 helix: 1.12 (0.31), residues: 260 sheet: -4.12 (0.34), residues: 139 loop : -3.53 (0.34), residues: 269 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP R 134 HIS 0.008 0.002 HIS R 373 PHE 0.011 0.002 PHE R 247 TYR 0.011 0.002 TYR B 63 ARG 0.002 0.001 ARG B 65 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1336 Ramachandran restraints generated. 668 Oldfield, 0 Emsley, 668 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1336 Ramachandran restraints generated. 668 Oldfield, 0 Emsley, 668 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 85 residues out of total 592 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 85 time to evaluate : 0.442 Fit side-chains REVERT: B 65 ARG cc_start: 0.7826 (tpp80) cc_final: 0.7601 (tpp80) REVERT: B 202 SER cc_start: 0.8792 (p) cc_final: 0.8388 (t) REVERT: B 217 ASN cc_start: 0.9231 (t0) cc_final: 0.8952 (p0) REVERT: B 218 VAL cc_start: 0.9289 (m) cc_final: 0.8998 (t) REVERT: R 88 LEU cc_start: 0.9370 (tt) cc_final: 0.8873 (tt) REVERT: R 102 HIS cc_start: 0.6637 (t-90) cc_final: 0.6164 (t-90) REVERT: R 190 SER cc_start: 0.9273 (m) cc_final: 0.8951 (p) REVERT: R 233 VAL cc_start: 0.9620 (m) cc_final: 0.9347 (p) REVERT: R 344 TYR cc_start: 0.8374 (m-80) cc_final: 0.7886 (m-80) outliers start: 0 outliers final: 0 residues processed: 85 average time/residue: 0.1687 time to fit residues: 17.7580 Evaluate side-chains 76 residues out of total 592 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 76 time to evaluate : 0.432 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 67 random chunks: chunk 31 optimal weight: 0.0070 chunk 6 optimal weight: 6.9990 chunk 29 optimal weight: 5.9990 chunk 40 optimal weight: 0.7980 chunk 61 optimal weight: 4.9990 chunk 64 optimal weight: 3.9990 chunk 57 optimal weight: 30.0000 chunk 17 optimal weight: 1.9990 chunk 53 optimal weight: 3.9990 chunk 36 optimal weight: 2.9990 chunk 0 optimal weight: 4.9990 overall best weight: 1.9604 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 237 GLN R 104 HIS R 373 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8089 moved from start: 0.2671 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 4246 Z= 0.269 Angle : 0.616 6.819 5880 Z= 0.322 Chirality : 0.044 0.162 732 Planarity : 0.004 0.037 786 Dihedral : 6.717 79.352 731 Min Nonbonded Distance : 2.160 Molprobity Statistics. All-atom Clashscore : 11.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 12.28 % Favored : 87.72 % Rotamer: Outliers : 0.00 % Allowed : 3.41 % Favored : 96.59 % 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: -2.41 (0.33), residues: 668 helix: 1.28 (0.32), residues: 260 sheet: -3.89 (0.36), residues: 139 loop : -3.28 (0.36), residues: 269 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.002 TRP R 134 HIS 0.008 0.002 HIS R 373 PHE 0.014 0.002 PHE B 244 TYR 0.010 0.002 TYR R 342 ARG 0.004 0.001 ARG R 323 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1336 Ramachandran restraints generated. 668 Oldfield, 0 Emsley, 668 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1336 Ramachandran restraints generated. 668 Oldfield, 0 Emsley, 668 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 87 residues out of total 592 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 87 time to evaluate : 0.482 Fit side-chains REVERT: B 63 TYR cc_start: 0.7890 (t80) cc_final: 0.7457 (t80) REVERT: B 202 SER cc_start: 0.8662 (p) cc_final: 0.8334 (t) REVERT: B 217 ASN cc_start: 0.9221 (t0) cc_final: 0.8944 (p0) REVERT: R 88 LEU cc_start: 0.9393 (tt) cc_final: 0.8928 (tt) REVERT: R 102 HIS cc_start: 0.6632 (t-90) cc_final: 0.6083 (t-90) REVERT: R 190 SER cc_start: 0.9274 (m) cc_final: 0.8943 (p) REVERT: R 233 VAL cc_start: 0.9651 (m) cc_final: 0.9384 (p) REVERT: R 344 TYR cc_start: 0.8331 (m-80) cc_final: 0.7861 (m-80) outliers start: 0 outliers final: 0 residues processed: 87 average time/residue: 0.1875 time to fit residues: 19.9533 Evaluate side-chains 77 residues out of total 592 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 77 time to evaluate : 0.462 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 67 random chunks: chunk 48 optimal weight: 5.9990 chunk 26 optimal weight: 0.9980 chunk 55 optimal weight: 7.9990 chunk 44 optimal weight: 2.9990 chunk 0 optimal weight: 4.9990 chunk 33 optimal weight: 20.0000 chunk 58 optimal weight: 0.2980 chunk 16 optimal weight: 9.9990 chunk 21 optimal weight: 10.0000 chunk 12 optimal weight: 4.9990 chunk 38 optimal weight: 4.9990 overall best weight: 2.8586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 237 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8140 moved from start: 0.2797 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.045 4246 Z= 0.364 Angle : 0.664 6.868 5880 Z= 0.354 Chirality : 0.046 0.183 732 Planarity : 0.004 0.028 786 Dihedral : 6.808 80.085 731 Min Nonbonded Distance : 2.169 Molprobity Statistics. All-atom Clashscore : 13.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 13.77 % Favored : 86.23 % Rotamer: Outliers : 0.49 % Allowed : 4.39 % Favored : 95.12 % 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: -2.53 (0.33), residues: 668 helix: 1.09 (0.32), residues: 256 sheet: -3.78 (0.37), residues: 140 loop : -3.28 (0.36), residues: 272 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP R 134 HIS 0.007 0.002 HIS R 102 PHE 0.013 0.002 PHE R 326 TYR 0.012 0.002 TYR B 321 ARG 0.005 0.001 ARG B 236 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1336 Ramachandran restraints generated. 668 Oldfield, 0 Emsley, 668 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1336 Ramachandran restraints generated. 668 Oldfield, 0 Emsley, 668 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 82 residues out of total 592 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 81 time to evaluate : 0.466 Fit side-chains REVERT: B 63 TYR cc_start: 0.7953 (t80) cc_final: 0.7561 (t80) REVERT: B 202 SER cc_start: 0.8644 (p) cc_final: 0.8313 (t) REVERT: B 217 ASN cc_start: 0.9237 (t0) cc_final: 0.8907 (p0) REVERT: R 88 LEU cc_start: 0.9402 (tt) cc_final: 0.8937 (tt) REVERT: R 102 HIS cc_start: 0.6706 (t-90) cc_final: 0.6158 (t-90) REVERT: R 190 SER cc_start: 0.9337 (m) cc_final: 0.9027 (p) REVERT: R 233 VAL cc_start: 0.9620 (m) cc_final: 0.9341 (p) outliers start: 1 outliers final: 1 residues processed: 82 average time/residue: 0.1754 time to fit residues: 17.8837 Evaluate side-chains 70 residues out of total 592 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 69 time to evaluate : 0.473 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 67 random chunks: chunk 15 optimal weight: 10.0000 chunk 64 optimal weight: 2.9990 chunk 53 optimal weight: 4.9990 chunk 30 optimal weight: 7.9990 chunk 5 optimal weight: 9.9990 chunk 21 optimal weight: 8.9990 chunk 34 optimal weight: 6.9990 chunk 62 optimal weight: 0.2980 chunk 7 optimal weight: 7.9990 chunk 36 optimal weight: 0.7980 chunk 47 optimal weight: 10.0000 overall best weight: 3.2186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 237 GLN R 104 HIS R 373 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8152 moved from start: 0.2897 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.051 4246 Z= 0.400 Angle : 0.701 9.057 5880 Z= 0.375 Chirality : 0.046 0.171 732 Planarity : 0.004 0.030 786 Dihedral : 7.236 87.922 731 Min Nonbonded Distance : 2.138 Molprobity Statistics. All-atom Clashscore : 15.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 13.62 % Favored : 86.38 % Rotamer: Outliers : 0.00 % Allowed : 4.39 % Favored : 95.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.56 (0.33), residues: 668 helix: 0.97 (0.32), residues: 256 sheet: -3.69 (0.37), residues: 138 loop : -3.26 (0.36), residues: 274 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.003 TRP R 316 HIS 0.011 0.003 HIS R 102 PHE 0.016 0.002 PHE R 326 TYR 0.016 0.002 TYR R 153 ARG 0.003 0.001 ARG B 236 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1336 Ramachandran restraints generated. 668 Oldfield, 0 Emsley, 668 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1336 Ramachandran restraints generated. 668 Oldfield, 0 Emsley, 668 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 82 residues out of total 592 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 82 time to evaluate : 0.514 Fit side-chains REVERT: B 202 SER cc_start: 0.8636 (p) cc_final: 0.8400 (t) REVERT: B 217 ASN cc_start: 0.9219 (t0) cc_final: 0.8915 (p0) REVERT: B 244 PHE cc_start: 0.7544 (t80) cc_final: 0.7245 (t80) REVERT: B 326 LYS cc_start: 0.8836 (mtpt) cc_final: 0.8616 (mttp) REVERT: R 88 LEU cc_start: 0.9419 (tt) cc_final: 0.8839 (tt) REVERT: R 102 HIS cc_start: 0.6775 (t-90) cc_final: 0.6192 (t-90) REVERT: R 190 SER cc_start: 0.9384 (m) cc_final: 0.9106 (p) REVERT: R 233 VAL cc_start: 0.9622 (m) cc_final: 0.9358 (p) REVERT: R 344 TYR cc_start: 0.8446 (m-80) cc_final: 0.8009 (m-80) outliers start: 0 outliers final: 0 residues processed: 82 average time/residue: 0.1768 time to fit residues: 18.0657 Evaluate side-chains 72 residues out of total 592 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 72 time to evaluate : 0.472 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 67 random chunks: chunk 36 optimal weight: 0.0870 chunk 54 optimal weight: 1.9990 chunk 64 optimal weight: 0.9990 chunk 40 optimal weight: 0.0980 chunk 39 optimal weight: 7.9990 chunk 29 optimal weight: 5.9990 chunk 25 optimal weight: 0.8980 chunk 38 optimal weight: 0.7980 chunk 19 optimal weight: 9.9990 chunk 12 optimal weight: 0.9990 chunk 41 optimal weight: 0.6980 overall best weight: 0.5158 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 237 GLN R 373 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8020 moved from start: 0.3450 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.025 4246 Z= 0.154 Angle : 0.585 7.273 5880 Z= 0.291 Chirality : 0.043 0.158 732 Planarity : 0.004 0.039 786 Dihedral : 6.656 87.014 731 Min Nonbonded Distance : 2.251 Molprobity Statistics. All-atom Clashscore : 8.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.53 % Favored : 91.47 % Rotamer: Outliers : 0.00 % Allowed : 1.46 % Favored : 98.54 % 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: -1.83 (0.34), residues: 668 helix: 1.79 (0.31), residues: 258 sheet: -3.46 (0.38), residues: 140 loop : -3.01 (0.37), residues: 270 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP R 316 HIS 0.007 0.002 HIS R 373 PHE 0.016 0.001 PHE R 247 TYR 0.018 0.001 TYR R 342 ARG 0.004 0.000 ARG R 323 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1336 Ramachandran restraints generated. 668 Oldfield, 0 Emsley, 668 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1336 Ramachandran restraints generated. 668 Oldfield, 0 Emsley, 668 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 88 residues out of total 592 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 88 time to evaluate : 0.442 Fit side-chains REVERT: B 217 ASN cc_start: 0.9266 (t0) cc_final: 0.8912 (p0) REVERT: B 326 LYS cc_start: 0.8715 (mtpt) cc_final: 0.8466 (mttm) REVERT: R 88 LEU cc_start: 0.9492 (tt) cc_final: 0.8737 (tt) REVERT: R 102 HIS cc_start: 0.6687 (t-90) cc_final: 0.5854 (t-90) REVERT: R 190 SER cc_start: 0.9241 (m) cc_final: 0.8902 (p) REVERT: R 233 VAL cc_start: 0.9577 (m) cc_final: 0.9337 (p) outliers start: 0 outliers final: 0 residues processed: 88 average time/residue: 0.1552 time to fit residues: 17.4125 Evaluate side-chains 73 residues out of total 592 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 73 time to evaluate : 0.465 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 67 random chunks: chunk 43 optimal weight: 6.9990 chunk 31 optimal weight: 9.9990 chunk 6 optimal weight: 5.9990 chunk 50 optimal weight: 9.9990 chunk 58 optimal weight: 6.9990 chunk 61 optimal weight: 5.9990 chunk 56 optimal weight: 10.0000 chunk 60 optimal weight: 0.0270 chunk 36 optimal weight: 5.9990 chunk 26 optimal weight: 0.0770 chunk 47 optimal weight: 6.9990 overall best weight: 3.6202 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 237 GLN B 248 GLN R 104 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8161 moved from start: 0.3149 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.057 4246 Z= 0.439 Angle : 0.709 6.927 5880 Z= 0.382 Chirality : 0.046 0.194 732 Planarity : 0.004 0.029 786 Dihedral : 6.936 86.798 731 Min Nonbonded Distance : 2.112 Molprobity Statistics. All-atom Clashscore : 17.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 14.37 % Favored : 85.63 % Rotamer: Outliers : 0.00 % Allowed : 1.95 % Favored : 98.05 % 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: -2.36 (0.33), residues: 668 helix: 1.06 (0.31), residues: 254 sheet: -3.54 (0.38), residues: 140 loop : -3.04 (0.37), residues: 274 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP R 134 HIS 0.008 0.002 HIS R 102 PHE 0.017 0.003 PHE R 326 TYR 0.018 0.002 TYR B 321 ARG 0.003 0.001 ARG R 148 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1336 Ramachandran restraints generated. 668 Oldfield, 0 Emsley, 668 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1336 Ramachandran restraints generated. 668 Oldfield, 0 Emsley, 668 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 79 residues out of total 592 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 79 time to evaluate : 0.460 Fit side-chains REVERT: R 88 LEU cc_start: 0.9582 (tt) cc_final: 0.8972 (tt) REVERT: R 102 HIS cc_start: 0.6925 (t-90) cc_final: 0.6214 (t-90) REVERT: R 144 TYR cc_start: 0.8527 (t80) cc_final: 0.8281 (t80) REVERT: R 190 SER cc_start: 0.9382 (m) cc_final: 0.9080 (p) REVERT: R 233 VAL cc_start: 0.9639 (m) cc_final: 0.9374 (p) REVERT: R 344 TYR cc_start: 0.8461 (m-80) cc_final: 0.8071 (m-80) outliers start: 0 outliers final: 0 residues processed: 79 average time/residue: 0.1523 time to fit residues: 15.8800 Evaluate side-chains 66 residues out of total 592 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 66 time to evaluate : 0.492 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 67 random chunks: chunk 18 optimal weight: 0.6980 chunk 54 optimal weight: 0.8980 chunk 56 optimal weight: 9.9990 chunk 59 optimal weight: 0.9990 chunk 39 optimal weight: 7.9990 chunk 63 optimal weight: 3.9990 chunk 38 optimal weight: 0.7980 chunk 30 optimal weight: 5.9990 chunk 44 optimal weight: 2.9990 chunk 66 optimal weight: 5.9990 chunk 61 optimal weight: 0.5980 overall best weight: 0.7982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 237 GLN R 373 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8042 moved from start: 0.3567 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.035 4246 Z= 0.173 Angle : 0.588 6.858 5880 Z= 0.297 Chirality : 0.043 0.148 732 Planarity : 0.004 0.033 786 Dihedral : 6.174 81.482 731 Min Nonbonded Distance : 2.179 Molprobity Statistics. All-atom Clashscore : 10.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.83 % Favored : 91.17 % Rotamer: Outliers : 0.00 % Allowed : 0.98 % Favored : 99.02 % 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: -1.81 (0.34), residues: 668 helix: 1.75 (0.31), residues: 257 sheet: -3.35 (0.37), residues: 145 loop : -2.95 (0.38), residues: 266 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP R 134 HIS 0.006 0.002 HIS R 102 PHE 0.032 0.001 PHE R 247 TYR 0.020 0.001 TYR R 342 ARG 0.002 0.000 ARG B 65 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1336 Ramachandran restraints generated. 668 Oldfield, 0 Emsley, 668 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1336 Ramachandran restraints generated. 668 Oldfield, 0 Emsley, 668 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 81 residues out of total 592 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 81 time to evaluate : 0.501 Fit side-chains REVERT: R 88 LEU cc_start: 0.9532 (tt) cc_final: 0.8725 (tt) REVERT: R 102 HIS cc_start: 0.6713 (t-90) cc_final: 0.5863 (t-90) REVERT: R 190 SER cc_start: 0.9257 (m) cc_final: 0.8926 (p) REVERT: R 233 VAL cc_start: 0.9587 (m) cc_final: 0.9358 (p) REVERT: R 344 TYR cc_start: 0.8354 (m-80) cc_final: 0.8104 (m-80) outliers start: 0 outliers final: 0 residues processed: 81 average time/residue: 0.1397 time to fit residues: 14.7430 Evaluate side-chains 71 residues out of total 592 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 71 time to evaluate : 0.487 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 67 random chunks: chunk 53 optimal weight: 5.9990 chunk 5 optimal weight: 0.0040 chunk 41 optimal weight: 4.9990 chunk 32 optimal weight: 0.6980 chunk 42 optimal weight: 0.6980 chunk 56 optimal weight: 9.9990 chunk 16 optimal weight: 0.0980 chunk 49 optimal weight: 3.9990 chunk 7 optimal weight: 10.0000 chunk 14 optimal weight: 6.9990 chunk 22 optimal weight: 10.0000 overall best weight: 1.0994 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 237 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** R 104 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8048 moved from start: 0.3648 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 4246 Z= 0.191 Angle : 0.578 7.065 5880 Z= 0.292 Chirality : 0.043 0.138 732 Planarity : 0.004 0.034 786 Dihedral : 6.071 81.785 731 Min Nonbonded Distance : 2.185 Molprobity Statistics. All-atom Clashscore : 12.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.33 % Favored : 89.67 % Rotamer: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.57 (0.34), residues: 668 helix: 1.83 (0.32), residues: 260 sheet: -3.14 (0.38), residues: 145 loop : -2.80 (0.39), residues: 263 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP R 134 HIS 0.006 0.002 HIS R 102 PHE 0.033 0.002 PHE R 247 TYR 0.023 0.001 TYR R 153 ARG 0.002 0.000 ARG B 65 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1336 Ramachandran restraints generated. 668 Oldfield, 0 Emsley, 668 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1336 Ramachandran restraints generated. 668 Oldfield, 0 Emsley, 668 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 80 residues out of total 592 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 80 time to evaluate : 0.554 Fit side-chains REVERT: R 88 LEU cc_start: 0.9556 (tt) cc_final: 0.8772 (tt) REVERT: R 102 HIS cc_start: 0.6884 (t-90) cc_final: 0.6008 (t-90) REVERT: R 190 SER cc_start: 0.9263 (m) cc_final: 0.8923 (p) REVERT: R 233 VAL cc_start: 0.9598 (m) cc_final: 0.9343 (p) REVERT: R 344 TYR cc_start: 0.8349 (m-80) cc_final: 0.8094 (m-80) outliers start: 0 outliers final: 0 residues processed: 80 average time/residue: 0.1351 time to fit residues: 14.2323 Evaluate side-chains 70 residues out of total 592 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 70 time to evaluate : 0.427 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 67 random chunks: chunk 54 optimal weight: 1.9990 chunk 6 optimal weight: 6.9990 chunk 9 optimal weight: 0.0000 chunk 46 optimal weight: 0.9980 chunk 3 optimal weight: 5.9990 chunk 38 optimal weight: 2.9990 chunk 60 optimal weight: 0.5980 chunk 35 optimal weight: 9.9990 chunk 45 optimal weight: 0.9980 chunk 1 optimal weight: 0.0270 chunk 42 optimal weight: 1.9990 overall best weight: 0.5242 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 237 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3424 r_free = 0.3424 target = 0.080698 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3119 r_free = 0.3119 target = 0.066960 restraints weight = 19708.937| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3148 r_free = 0.3148 target = 0.068190 restraints weight = 13944.067| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3166 r_free = 0.3166 target = 0.069008 restraints weight = 11005.227| |-----------------------------------------------------------------------------| r_work (final): 0.3163 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8030 moved from start: 0.4074 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.027 4246 Z= 0.146 Angle : 0.570 7.638 5880 Z= 0.282 Chirality : 0.042 0.134 732 Planarity : 0.003 0.026 786 Dihedral : 5.831 79.663 731 Min Nonbonded Distance : 2.186 Molprobity Statistics. All-atom Clashscore : 7.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.38 % Favored : 91.62 % Rotamer: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.28 (0.34), residues: 668 helix: 2.00 (0.32), residues: 263 sheet: -2.87 (0.40), residues: 141 loop : -2.71 (0.39), residues: 264 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP R 316 HIS 0.006 0.001 HIS B 219 PHE 0.040 0.002 PHE R 245 TYR 0.023 0.002 TYR R 342 ARG 0.004 0.000 ARG B 236 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1141.88 seconds wall clock time: 21 minutes 8.37 seconds (1268.37 seconds total)