Starting phenix.real_space_refine on Thu Dec 7 23:43:40 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6up7_20836/12_2023/6up7_20836_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6up7_20836/12_2023/6up7_20836.map Found restraint, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6up7_20836/12_2023/6up7_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_20836/12_2023/6up7_20836_ligands.cif" default_restraint = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6up7_20836/12_2023/6up7_20836_ligands.cif" real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6up7_20836/12_2023/6up7_20836.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6up7_20836/12_2023/6up7_20836.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6up7_20836/12_2023/6up7_20836_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6up7_20836/12_2023/6up7_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: 0.01s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/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: 2.83, per 1000 atoms: 0.68 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: 1.77 Conformation dependent library (CDL) restraints added in 936.5 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: 0.89 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: 1.03 Time building geometry restraints manager: 1.93 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: 0.540 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: 2.340 Check model and map are aligned: 0.060 Set scattering table: 0.040 Process input model: 16.570 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: 0.010 Load rotamer database and sin/cos tables:2.890 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 22.660 ------------------------------------------------------------------------------- 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 : 0.473 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 94 average time/residue: 0.2190 time to fit residues: 24.4768 Evaluate side-chains 74 residues out of total 592 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 74 time to evaluate : 0.501 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.6605 ------------------------------------------------------------------------------- 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: 2.9990 chunk 60 optimal weight: 0.9980 overall best weight: 1.9384 ------------------------------------------------------------------------------- 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: 0.8094 moved from start: 0.1940 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= 0.268 Angle : 0.683 11.476 5880 Z= 0.354 Chirality : 0.045 0.217 732 Planarity : 0.005 0.040 786 Dihedral : 7.181 75.122 731 Min Nonbonded Distance : 2.160 Molprobity Statistics. All-atom Clashscore : 11.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 12.43 % Favored : 87.57 % 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: 0.25 (0.29), residues: 258 sheet: -4.22 (0.34), residues: 133 loop : -3.82 (0.32), residues: 277 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.003 TRP R 316 HIS 0.008 0.002 HIS R 373 PHE 0.009 0.001 PHE R 312 TYR 0.025 0.002 TYR R 153 ARG 0.005 0.001 ARG B 236 *********************** 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 89 residues out of total 592 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 89 time to evaluate : 0.422 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 89 average time/residue: 0.1725 time to fit residues: 18.8824 Evaluate side-chains 72 residues out of total 592 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 72 time to evaluate : 0.417 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.5361 ------------------------------------------------------------------------------- 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: 0.9980 chunk 16 optimal weight: 10.0000 chunk 60 optimal weight: 0.0980 chunk 65 optimal weight: 6.9990 chunk 54 optimal weight: 1.9990 chunk 20 optimal weight: 7.9990 chunk 48 optimal weight: 0.7980 chunk 45 optimal weight: 1.9990 overall best weight: 1.1784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: R 104 HIS R 373 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8039 moved from start: 0.2433 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 4246 Z= 0.195 Angle : 0.608 7.551 5880 Z= 0.310 Chirality : 0.044 0.253 732 Planarity : 0.004 0.035 786 Dihedral : 6.643 77.770 731 Min Nonbonded Distance : 2.210 Molprobity Statistics. All-atom Clashscore : 9.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.18 % Favored : 89.82 % 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: -2.69 (0.32), residues: 668 helix: 1.11 (0.31), residues: 259 sheet: -4.00 (0.35), residues: 135 loop : -3.54 (0.33), residues: 274 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP R 316 HIS 0.008 0.001 HIS R 373 PHE 0.011 0.001 PHE R 247 TYR 0.008 0.001 TYR C 11 ARG 0.003 0.000 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 88 residues out of total 592 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 88 time to evaluate : 0.503 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 88 average time/residue: 0.1662 time to fit residues: 18.5763 Evaluate side-chains 73 residues out of total 592 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 73 time to evaluate : 0.479 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.6205 ------------------------------------------------------------------------------- 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: 4.9990 chunk 6 optimal weight: 6.9990 chunk 29 optimal weight: 7.9990 chunk 40 optimal weight: 5.9990 chunk 61 optimal weight: 5.9990 chunk 64 optimal weight: 2.9990 chunk 57 optimal weight: 30.0000 chunk 17 optimal weight: 1.9990 chunk 53 optimal weight: 3.9990 chunk 36 optimal weight: 0.9990 chunk 0 optimal weight: 4.9990 overall best weight: 2.9990 ------------------------------------------------------------------------------- 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: 0.8133 moved from start: 0.2670 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.049 4246 Z= 0.379 Angle : 0.695 9.204 5880 Z= 0.372 Chirality : 0.047 0.227 732 Planarity : 0.004 0.031 786 Dihedral : 7.240 82.157 731 Min Nonbonded Distance : 2.133 Molprobity Statistics. All-atom Clashscore : 15.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 13.47 % Favored : 86.53 % Rotamer: Outliers : 0.00 % Allowed : 5.37 % Favored : 94.63 % 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: -2.67 (0.32), residues: 668 helix: 0.94 (0.31), residues: 257 sheet: -3.87 (0.36), residues: 136 loop : -3.34 (0.35), residues: 275 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.003 TRP R 134 HIS 0.008 0.003 HIS R 373 PHE 0.016 0.002 PHE R 326 TYR 0.012 0.002 TYR C 11 ARG 0.003 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 79 residues out of total 592 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 79 time to evaluate : 0.478 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 79 average time/residue: 0.1596 time to fit residues: 16.0099 Evaluate side-chains 69 residues out of total 592 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 69 time to evaluate : 0.473 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.6000 ------------------------------------------------------------------------------- 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: 4.9990 chunk 26 optimal weight: 9.9990 chunk 55 optimal weight: 6.9990 chunk 44 optimal weight: 0.8980 chunk 0 optimal weight: 4.9990 chunk 33 optimal weight: 30.0000 chunk 58 optimal weight: 6.9990 chunk 16 optimal weight: 10.0000 chunk 21 optimal weight: 9.9990 chunk 12 optimal weight: 3.9990 chunk 38 optimal weight: 3.9990 overall best weight: 3.7788 ------------------------------------------------------------------------------- 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: 0.8160 moved from start: 0.2736 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.055 4246 Z= 0.459 Angle : 0.734 7.339 5880 Z= 0.400 Chirality : 0.048 0.243 732 Planarity : 0.004 0.029 786 Dihedral : 7.303 78.968 731 Min Nonbonded Distance : 2.161 Molprobity Statistics. All-atom Clashscore : 18.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 13.77 % Favored : 86.23 % 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: -2.81 (0.32), residues: 668 helix: 0.81 (0.31), residues: 251 sheet: -3.78 (0.37), residues: 127 loop : -3.45 (0.33), residues: 290 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.003 TRP R 134 HIS 0.009 0.003 HIS R 373 PHE 0.018 0.002 PHE R 326 TYR 0.011 0.002 TYR C 11 ARG 0.003 0.001 ARG B 65 *********************** 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 79 residues out of total 592 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 79 time to evaluate : 0.473 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 79 average time/residue: 0.1752 time to fit residues: 17.3840 Evaluate side-chains 66 residues out of total 592 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 66 time to evaluate : 0.483 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.6349 ------------------------------------------------------------------------------- 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: 0.9990 chunk 53 optimal weight: 3.9990 chunk 30 optimal weight: 4.9990 chunk 5 optimal weight: 9.9990 chunk 21 optimal weight: 9.9990 chunk 34 optimal weight: 2.9990 chunk 62 optimal weight: 7.9990 chunk 7 optimal weight: 5.9990 chunk 36 optimal weight: 0.4980 chunk 47 optimal weight: 5.9990 overall best weight: 2.6988 ------------------------------------------------------------------------------- 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: 0.8132 moved from start: 0.2930 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.039 4246 Z= 0.342 Angle : 0.679 9.515 5880 Z= 0.357 Chirality : 0.047 0.277 732 Planarity : 0.004 0.029 786 Dihedral : 7.335 86.019 731 Min Nonbonded Distance : 2.179 Molprobity Statistics. All-atom Clashscore : 16.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 13.92 % Favored : 86.08 % Rotamer: Outliers : 0.00 % Allowed : 2.44 % Favored : 97.56 % 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: -2.52 (0.32), residues: 668 helix: 1.03 (0.32), residues: 254 sheet: -3.61 (0.38), residues: 127 loop : -3.33 (0.34), residues: 287 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP R 316 HIS 0.008 0.002 HIS R 373 PHE 0.013 0.001 PHE R 247 TYR 0.014 0.002 TYR R 344 ARG 0.003 0.001 ARG B 65 *********************** 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 80 residues out of total 592 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 80 time to evaluate : 0.487 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 80 average time/residue: 0.1518 time to fit residues: 15.7383 Evaluate side-chains 69 residues out of total 592 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 69 time to evaluate : 0.493 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.6226 ------------------------------------------------------------------------------- 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: 0.0040 chunk 54 optimal weight: 3.9990 chunk 64 optimal weight: 0.5980 chunk 40 optimal weight: 4.9990 chunk 39 optimal weight: 6.9990 chunk 29 optimal weight: 0.0770 chunk 25 optimal weight: 0.9980 chunk 38 optimal weight: 0.8980 chunk 19 optimal weight: 0.0570 chunk 12 optimal weight: 2.9990 chunk 41 optimal weight: 0.8980 overall best weight: 0.3268 ------------------------------------------------------------------------------- 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: 0.7989 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 0.023 4246 Z= 0.140 Angle : 0.586 7.634 5880 Z= 0.292 Chirality : 0.043 0.166 732 Planarity : 0.003 0.031 786 Dihedral : 6.695 89.522 731 Min Nonbonded Distance : 2.282 Molprobity Statistics. All-atom Clashscore : 7.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.68 % Favored : 91.32 % 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: -1.77 (0.34), residues: 668 helix: 1.86 (0.32), residues: 257 sheet: -3.40 (0.39), residues: 138 loop : -3.03 (0.37), residues: 273 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP R 316 HIS 0.007 0.001 HIS R 373 PHE 0.020 0.001 PHE R 74 TYR 0.022 0.001 TYR R 153 ARG 0.003 0.001 ARG B 65 *********************** 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 89 residues out of total 592 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 89 time to evaluate : 0.484 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 89 average time/residue: 0.1584 time to fit residues: 18.1855 Evaluate side-chains 76 residues out of total 592 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 76 time to evaluate : 0.486 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.6143 ------------------------------------------------------------------------------- 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: 0.0370 chunk 6 optimal weight: 4.9990 chunk 50 optimal weight: 10.0000 chunk 58 optimal weight: 7.9990 chunk 61 optimal weight: 5.9990 chunk 56 optimal weight: 10.0000 chunk 60 optimal weight: 0.0980 chunk 36 optimal weight: 3.9990 chunk 26 optimal weight: 0.0370 chunk 47 optimal weight: 0.0670 overall best weight: 0.8476 ------------------------------------------------------------------------------- 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** B 248 GLN R 104 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8005 moved from start: 0.3786 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.052 4246 Z= 0.175 Angle : 0.589 12.634 5880 Z= 0.289 Chirality : 0.042 0.122 732 Planarity : 0.003 0.028 786 Dihedral : 6.575 89.210 731 Min Nonbonded Distance : 2.177 Molprobity Statistics. All-atom Clashscore : 10.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.13 % Favored : 90.87 % 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: -1.59 (0.34), residues: 668 helix: 2.01 (0.32), residues: 258 sheet: -3.26 (0.38), residues: 139 loop : -2.96 (0.36), residues: 271 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP R 316 HIS 0.011 0.001 HIS R 102 PHE 0.014 0.001 PHE R 247 TYR 0.023 0.002 TYR B 63 ARG 0.003 0.001 ARG B 65 *********************** 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 81 residues out of total 592 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 81 time to evaluate : 0.508 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 81 average time/residue: 0.1574 time to fit residues: 16.3263 Evaluate side-chains 72 residues out of total 592 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 72 time to evaluate : 0.434 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.5555 ------------------------------------------------------------------------------- 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: 0.0870 chunk 54 optimal weight: 0.1980 chunk 56 optimal weight: 9.9990 chunk 59 optimal weight: 4.9990 chunk 39 optimal weight: 7.9990 chunk 63 optimal weight: 5.9990 chunk 38 optimal weight: 1.9990 chunk 30 optimal weight: 9.9990 chunk 44 optimal weight: 3.9990 chunk 66 optimal weight: 2.9990 chunk 61 optimal weight: 5.9990 overall best weight: 1.8564 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8066 moved from start: 0.3685 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 4246 Z= 0.267 Angle : 0.615 7.618 5880 Z= 0.315 Chirality : 0.044 0.147 732 Planarity : 0.003 0.025 786 Dihedral : 6.565 89.808 731 Min Nonbonded Distance : 2.191 Molprobity Statistics. All-atom Clashscore : 13.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.78 % Favored : 89.22 % Rotamer: Outliers : 0.00 % Allowed : 0.49 % Favored : 99.51 % 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: -1.73 (0.34), residues: 668 helix: 1.69 (0.31), residues: 260 sheet: -3.14 (0.38), residues: 144 loop : -2.94 (0.38), residues: 264 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP R 134 HIS 0.005 0.001 HIS R 320 PHE 0.028 0.002 PHE R 245 TYR 0.016 0.002 TYR B 63 ARG 0.004 0.001 ARG B 236 *********************** 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 80 residues out of total 592 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 80 time to evaluate : 0.471 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 80 average time/residue: 0.1492 time to fit residues: 15.2920 Evaluate side-chains 72 residues out of total 592 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 72 time to evaluate : 0.465 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.5938 ------------------------------------------------------------------------------- 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: 2.9990 chunk 5 optimal weight: 10.0000 chunk 41 optimal weight: 3.9990 chunk 32 optimal weight: 0.9990 chunk 42 optimal weight: 4.9990 chunk 56 optimal weight: 9.9990 chunk 16 optimal weight: 9.9990 chunk 49 optimal weight: 4.9990 chunk 7 optimal weight: 8.9990 chunk 14 optimal weight: 7.9990 chunk 22 optimal weight: 0.1980 overall best weight: 2.6388 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8111 moved from start: 0.3625 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.050 4246 Z= 0.350 Angle : 0.656 7.075 5880 Z= 0.347 Chirality : 0.045 0.145 732 Planarity : 0.004 0.025 786 Dihedral : 6.667 86.130 731 Min Nonbonded Distance : 2.207 Molprobity Statistics. All-atom Clashscore : 14.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 11.83 % Favored : 88.17 % Rotamer: Outliers : 0.00 % Allowed : 0.49 % Favored : 99.51 % 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: -1.95 (0.33), residues: 668 helix: 1.38 (0.31), residues: 256 sheet: -3.14 (0.39), residues: 139 loop : -2.95 (0.37), residues: 273 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP R 134 HIS 0.002 0.001 HIS R 373 PHE 0.011 0.002 PHE R 127 TYR 0.021 0.002 TYR R 342 ARG 0.004 0.001 ARG B 236 ********************** 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 78 residues out of total 592 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 78 time to evaluate : 0.464 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 78 average time/residue: 0.1519 time to fit residues: 15.2841 Evaluate side-chains 67 residues out of total 592 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 67 time to evaluate : 0.489 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.5924 ------------------------------------------------------------------------------- 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: 2.9990 chunk 6 optimal weight: 1.9990 chunk 9 optimal weight: 0.6980 chunk 46 optimal weight: 2.9990 chunk 3 optimal weight: 6.9990 chunk 38 optimal weight: 1.9990 chunk 60 optimal weight: 0.9990 chunk 35 optimal weight: 9.9990 chunk 45 optimal weight: 0.6980 chunk 1 optimal weight: 1.9990 chunk 42 optimal weight: 0.8980 overall best weight: 1.0584 ------------------------------------------------------------------------------- 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 98 GLN R 373 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3380 r_free = 0.3380 target = 0.078527 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3062 r_free = 0.3062 target = 0.064497 restraints weight = 19830.185| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3089 r_free = 0.3089 target = 0.065660 restraints weight = 14357.193| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3109 r_free = 0.3109 target = 0.066509 restraints weight = 11415.450| |-----------------------------------------------------------------------------| r_work (final): 0.3105 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8085 moved from start: 0.3865 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 4246 Z= 0.195 Angle : 0.597 7.287 5880 Z= 0.301 Chirality : 0.043 0.139 732 Planarity : 0.003 0.025 786 Dihedral : 6.264 82.899 731 Min Nonbonded Distance : 2.228 Molprobity Statistics. All-atom Clashscore : 11.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.43 % Favored : 90.57 % 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: -1.71 (0.34), residues: 668 helix: 1.67 (0.31), residues: 259 sheet: -2.99 (0.39), residues: 144 loop : -2.96 (0.38), residues: 265 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.002 TRP R 134 HIS 0.007 0.002 HIS R 373 PHE 0.042 0.002 PHE R 245 TYR 0.013 0.001 TYR B 63 ARG 0.003 0.000 ARG B 236 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1096.09 seconds wall clock time: 20 minutes 27.55 seconds (1227.55 seconds total)