Starting phenix.real_space_refine (version: 1.20rc4) on Wed Dec 1 14:02:43 2021 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6vu5_21387/12_2021/6vu5_21387_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6vu5_21387/12_2021/6vu5_21387.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.5 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6vu5_21387/12_2021/6vu5_21387.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6vu5_21387/12_2021/6vu5_21387.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6vu5_21387/12_2021/6vu5_21387_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6vu5_21387/12_2021/6vu5_21387_updated.pdb" } resolution = 3.5 write_initial_geo_file = False refinement { macro_cycles = 10 } 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 ------------------------------------------------------------------------------- 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= 0.006 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Construct map_model_manager Extract box with map and model Check model and map are aligned Convert atoms to be neutral Process input model Symmetric amino acids flipped Residue "A ARG 4": "NH1" <-> "NH2" Residue "A GLU 20": "OE1" <-> "OE2" Residue "A ARG 23": "NH1" <-> "NH2" Residue "A ARG 27": "NH1" <-> "NH2" Residue "A GLU 55": "OE1" <-> "OE2" Residue "A ARG 63": "NH1" <-> "NH2" Residue "A ARG 75": "NH1" <-> "NH2" Residue "A ARG 77": "NH1" <-> "NH2" Residue "A ARG 139": "NH1" <-> "NH2" Residue "A GLU 159": "OE1" <-> "OE2" Residue "A ARG 166": "NH1" <-> "NH2" Residue "A ASP 177": "OD1" <-> "OD2" Residue "A ARG 179": "NH1" <-> "NH2" Residue "A ARG 190": "NH1" <-> "NH2" Residue "A GLU 206": "OE1" <-> "OE2" Residue "A ARG 237": "NH1" <-> "NH2" Residue "A ASP 240": "OD1" <-> "OD2" Residue "A ARG 319": "NH1" <-> "NH2" Residue "A ARG 342": "NH1" <-> "NH2" Residue "A ARG 345": "NH1" <-> "NH2" Residue "A ARG 348": "NH1" <-> "NH2" Residue "A ARG 363": "NH1" <-> "NH2" Residue "A ARG 378": "NH1" <-> "NH2" Residue "A ARG 389": "NH1" <-> "NH2" Residue "A ARG 405": "NH1" <-> "NH2" Residue "A ARG 422": "NH1" <-> "NH2" Residue "A ARG 429": "NH1" <-> "NH2" Residue "A ARG 446": "NH1" <-> "NH2" Residue "A GLU 447": "OE1" <-> "OE2" Residue "B PHE 220": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 228": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 338": "NH1" <-> "NH2" Time to flip residues: 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-1.20rc4-4434/modules/chem_data/mon_lib" Total number of atoms: 4657 Number of models: 1 Model: "" Number of chains: 2 Chain: "A" Number of atoms: 3589 Number of conformers: 1 Conformer: "" Number of residues, atoms: 468, 3589 Classifications: {'peptide': 468} Incomplete info: {'truncation_to_alanine': 42} Link IDs: {'PTRANS': 14, 'TRANS': 453} Chain breaks: 4 Unresolved non-hydrogen bonds: 111 Unresolved non-hydrogen angles: 152 Unresolved non-hydrogen dihedrals: 70 Planarities with less than four sites: {'GLN:plan1': 2, 'GLU:plan': 6, 'UNK:plan-1': 27, 'ARG:plan': 1, 'ASP:plan': 5} Unresolved non-hydrogen planarities: 79 Chain: "B" Number of atoms: 1068 Number of conformers: 1 Conformer: "" Number of residues, atoms: 135, 1068 Classifications: {'peptide': 135} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 13} Link IDs: {'PTRANS': 4, 'TRANS': 130} Chain breaks: 2 Unresolved non-hydrogen bonds: 54 Unresolved non-hydrogen angles: 68 Unresolved non-hydrogen dihedrals: 43 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'TYR:plan': 1, 'GLU:plan': 4, 'ARG:plan': 2, 'ASP:plan': 3} Unresolved non-hydrogen planarities: 42 Time building chain proxies: 3.05, per 1000 atoms: 0.65 Number of scatterers: 4657 At special positions: 0 Unit cell: (109.06, 58.22, 83.64, 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 25 16.00 P 2 15.00 O 854 8.00 N 815 7.00 C 2961 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amimo acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 2.05 Conformation dependent library (CDL) restraints added in 698.5 milliseconds 1112 Ramachandran restraints generated. 556 Oldfield, 0 Emsley, 556 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1168 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 30 helices and 1 sheets defined 49.0% alpha, 1.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 2.42 Creating SS restraints... Processing helix chain 'A' and resid 3 through 11 removed outlier: 3.771A pdb=" N ASP A 8 " --> pdb=" O ARG A 4 " (cutoff:3.500A) Processing helix chain 'A' and resid 20 through 28 removed outlier: 4.285A pdb=" N ARG A 27 " --> pdb=" O ARG A 23 " (cutoff:3.500A) removed outlier: 3.693A pdb=" N GLU A 28 " --> pdb=" O SER A 24 " (cutoff:3.500A) Processing helix chain 'A' and resid 37 through 56 removed outlier: 3.504A pdb=" N GLN A 40 " --> pdb=" O ASP A 37 " (cutoff:3.500A) removed outlier: 5.654A pdb=" N GLU A 41 " --> pdb=" O ALA A 38 " (cutoff:3.500A) removed outlier: 4.018A pdb=" N GLU A 55 " --> pdb=" O SER A 52 " (cutoff:3.500A) removed outlier: 3.541A pdb=" N GLN A 56 " --> pdb=" O VAL A 53 " (cutoff:3.500A) Processing helix chain 'A' and resid 65 through 75 removed outlier: 3.736A pdb=" N ARG A 75 " --> pdb=" O ARG A 71 " (cutoff:3.500A) Processing helix chain 'A' and resid 77 through 79 No H-bonds generated for 'chain 'A' and resid 77 through 79' Processing helix chain 'A' and resid 86 through 95 Processing helix chain 'A' and resid 112 through 126 Processing helix chain 'A' and resid 129 through 137 removed outlier: 3.727A pdb=" N MET A 133 " --> pdb=" O PRO A 129 " (cutoff:3.500A) removed outlier: 4.361A pdb=" N LEU A 134 " --> pdb=" O THR A 130 " (cutoff:3.500A) Processing helix chain 'A' and resid 141 through 149 removed outlier: 4.474A pdb=" N GLU A 146 " --> pdb=" O VAL A 142 " (cutoff:3.500A) removed outlier: 3.639A pdb=" N ARG A 147 " --> pdb=" O ARG A 143 " (cutoff:3.500A) Processing helix chain 'A' and resid 158 through 173 Processing helix chain 'A' and resid 188 through 199 removed outlier: 3.649A pdb=" N LEU A 198 " --> pdb=" O ASP A 194 " (cutoff:3.500A) Processing helix chain 'A' and resid 214 through 231 Processing helix chain 'A' and resid 243 through 259 removed outlier: 4.121A pdb=" N MET A 259 " --> pdb=" O ARG A 255 " (cutoff:3.500A) Processing helix chain 'A' and resid 265 through 279 removed outlier: 3.889A pdb=" N GLU A 268 " --> pdb=" O ASP A 265 " (cutoff:3.500A) removed outlier: 3.655A pdb=" N HIS A 271 " --> pdb=" O GLU A 268 " (cutoff:3.500A) Processing helix chain 'A' and resid 283 through 286 removed outlier: 3.676A pdb=" N LEU A 286 " --> pdb=" O LEU A 283 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 283 through 286' Processing helix chain 'A' and resid 314 through 319 Processing helix chain 'A' and resid 333 through 340 removed outlier: 4.586A pdb=" N THR A 338 " --> pdb=" O LEU A 334 " (cutoff:3.500A) Processing helix chain 'A' and resid 351 through 355 Processing helix chain 'A' and resid 372 through 381 removed outlier: 4.348A pdb=" N THR A 381 " --> pdb=" O VAL A 377 " (cutoff:3.500A) Processing helix chain 'A' and resid 385 through 388 No H-bonds generated for 'chain 'A' and resid 385 through 388' Processing helix chain 'A' and resid 390 through 397 removed outlier: 4.516A pdb=" N LEU A 395 " --> pdb=" O ALA A 391 " (cutoff:3.500A) Processing helix chain 'A' and resid 403 through 410 Processing helix chain 'A' and resid 414 through 416 No H-bonds generated for 'chain 'A' and resid 414 through 416' Processing helix chain 'A' and resid 475 through 482 Processing helix chain 'B' and resid 247 through 254 Processing helix chain 'B' and resid 256 through 259 No H-bonds generated for 'chain 'B' and resid 256 through 259' Processing helix chain 'B' and resid 276 through 278 No H-bonds generated for 'chain 'B' and resid 276 through 278' Processing helix chain 'B' and resid 288 through 290 No H-bonds generated for 'chain 'B' and resid 288 through 290' Processing helix chain 'B' and resid 303 through 314 Processing helix chain 'B' and resid 339 through 353 Processing sheet with id= A, first strand: chain 'B' and resid 269 through 272 removed outlier: 3.803A pdb=" N TYR B 325 " --> pdb=" O VAL B 269 " (cutoff:3.500A) removed outlier: 3.570A pdb=" N LEU B 271 " --> pdb=" O TYR B 325 " (cutoff:3.500A) 150 hydrogen bonds defined for protein. 381 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: 1.08 Time building geometry restraints manager: 2.19 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 1329 1.33 - 1.45: 735 1.45 - 1.57: 2621 1.57 - 1.69: 7 1.69 - 1.81: 39 Bond restraints: 4731 Sorted by residual: bond pdb=" CB VAL A 275 " pdb=" CG1 VAL A 275 " ideal model delta sigma weight residual 1.521 1.460 0.061 3.30e-02 9.18e+02 3.41e+00 bond pdb=" CG LEU A 224 " pdb=" CD2 LEU A 224 " ideal model delta sigma weight residual 1.521 1.470 0.051 3.30e-02 9.18e+02 2.42e+00 bond pdb=" CG LEU A 398 " pdb=" CD2 LEU A 398 " ideal model delta sigma weight residual 1.521 1.470 0.051 3.30e-02 9.18e+02 2.35e+00 bond pdb=" CB PRO A 332 " pdb=" CG PRO A 332 " ideal model delta sigma weight residual 1.492 1.417 0.075 5.00e-02 4.00e+02 2.25e+00 bond pdb=" C VAL A 403 " pdb=" N PRO A 404 " ideal model delta sigma weight residual 1.336 1.353 -0.018 1.23e-02 6.61e+03 2.10e+00 ... (remaining 4726 not shown) Histogram of bond angle deviations from ideal: 98.84 - 105.87: 81 105.87 - 112.89: 2555 112.89 - 119.92: 1685 119.92 - 126.95: 2052 126.95 - 133.98: 37 Bond angle restraints: 6410 Sorted by residual: angle pdb=" C VAL B 223 " pdb=" N THR B 224 " pdb=" CA THR B 224 " ideal model delta sigma weight residual 121.54 128.71 -7.17 1.91e+00 2.74e-01 1.41e+01 angle pdb=" CA LEU A 278 " pdb=" CB LEU A 278 " pdb=" CG LEU A 278 " ideal model delta sigma weight residual 116.30 126.28 -9.98 3.50e+00 8.16e-02 8.14e+00 angle pdb=" C ILE B 337 " pdb=" N ARG B 338 " pdb=" CA ARG B 338 " ideal model delta sigma weight residual 122.61 126.88 -4.27 1.56e+00 4.11e-01 7.51e+00 angle pdb=" C PHE A 228 " pdb=" N ASN A 229 " pdb=" CA ASN A 229 " ideal model delta sigma weight residual 122.65 118.39 4.26 1.60e+00 3.91e-01 7.10e+00 angle pdb=" CA PRO A 404 " pdb=" N PRO A 404 " pdb=" CD PRO A 404 " ideal model delta sigma weight residual 112.00 108.34 3.66 1.40e+00 5.10e-01 6.85e+00 ... (remaining 6405 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 18.37: 2566 18.37 - 36.74: 254 36.74 - 55.12: 49 55.12 - 73.49: 7 73.49 - 91.86: 4 Dihedral angle restraints: 2880 sinusoidal: 1102 harmonic: 1778 Sorted by residual: dihedral pdb=" CA PRO A 358 " pdb=" C PRO A 358 " pdb=" N LEU A 359 " pdb=" CA LEU A 359 " ideal model delta harmonic sigma weight residual 180.00 -150.71 -29.29 0 5.00e+00 4.00e-02 3.43e+01 dihedral pdb=" CA LEU A 395 " pdb=" C LEU A 395 " pdb=" N PHE A 396 " pdb=" CA PHE A 396 " ideal model delta harmonic sigma weight residual 180.00 154.40 25.60 0 5.00e+00 4.00e-02 2.62e+01 dihedral pdb=" CA LEU A 334 " pdb=" C LEU A 334 " pdb=" N SER A 335 " pdb=" CA SER A 335 " ideal model delta harmonic sigma weight residual 180.00 155.04 24.96 0 5.00e+00 4.00e-02 2.49e+01 ... (remaining 2877 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.100: 712 0.100 - 0.199: 47 0.199 - 0.299: 2 0.299 - 0.399: 0 0.399 - 0.499: 1 Chirality restraints: 762 Sorted by residual: chirality pdb=" CB ILE B 337 " pdb=" CA ILE B 337 " pdb=" CG1 ILE B 337 " pdb=" CG2 ILE B 337 " both_signs ideal model delta sigma weight residual False 2.64 2.15 0.50 2.00e-01 2.50e+01 6.22e+00 chirality pdb=" CB VAL A 288 " pdb=" CA VAL A 288 " pdb=" CG1 VAL A 288 " pdb=" CG2 VAL A 288 " both_signs ideal model delta sigma weight residual False -2.63 -2.39 -0.24 2.00e-01 2.50e+01 1.43e+00 chirality pdb=" CB VAL A 355 " pdb=" CA VAL A 355 " pdb=" CG1 VAL A 355 " pdb=" CG2 VAL A 355 " both_signs ideal model delta sigma weight residual False -2.63 -2.42 -0.21 2.00e-01 2.50e+01 1.11e+00 ... (remaining 759 not shown) Planarity restraints: 818 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C TYR B 261 " 0.048 5.00e-02 4.00e+02 7.33e-02 8.59e+00 pdb=" N PRO B 262 " -0.127 5.00e-02 4.00e+02 pdb=" CA PRO B 262 " 0.039 5.00e-02 4.00e+02 pdb=" CD PRO B 262 " 0.040 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C TYR A 156 " 0.038 5.00e-02 4.00e+02 5.78e-02 5.34e+00 pdb=" N PRO A 157 " -0.100 5.00e-02 4.00e+02 pdb=" CA PRO A 157 " 0.030 5.00e-02 4.00e+02 pdb=" CD PRO A 157 " 0.032 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ALA A 331 " -0.037 5.00e-02 4.00e+02 5.48e-02 4.81e+00 pdb=" N PRO A 332 " 0.095 5.00e-02 4.00e+02 pdb=" CA PRO A 332 " -0.027 5.00e-02 4.00e+02 pdb=" CD PRO A 332 " -0.031 5.00e-02 4.00e+02 ... (remaining 815 not shown) Histogram of nonbonded interaction distances: 2.23 - 2.76: 841 2.76 - 3.30: 4407 3.30 - 3.83: 7740 3.83 - 4.37: 8812 4.37 - 4.90: 14943 Nonbonded interactions: 36743 Sorted by model distance: nonbonded pdb=" O LEU A 168 " pdb=" OG1 THR A 172 " model vdw 2.230 2.440 nonbonded pdb=" O LEU A 227 " pdb=" OG1 THR A 231 " model vdw 2.241 2.440 nonbonded pdb=" O PRO A 213 " pdb=" OG1 THR A 217 " model vdw 2.328 2.440 nonbonded pdb=" O LEU A 281 " pdb=" NH2 ARG B 338 " model vdw 2.363 2.520 nonbonded pdb=" ND2 ASN B 266 " pdb=" O SER B 268 " model vdw 2.372 2.520 ... (remaining 36738 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 Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians P 2 5.49 5 S 25 5.16 5 C 2961 2.51 5 N 815 2.21 5 O 854 1.98 5 sf(0) = scattering factor at diffraction angle 0. 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 Write .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: 0.410 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Construct map_model_manager: 0.000 Extract box with map and model: 2.430 Check model and map are aligned: 0.070 Convert atoms to be neutral: 0.040 Process input model: 15.940 Find NCS groups from input model: 0.130 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Set scattering table: 0.010 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:2.510 Set ADP refinement strategy: 0.000 Write .geo file: 0.000 Internal consistency checks: 0.000 Total: 21.560 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7498 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 : 0.006 0.075 4731 Z= 0.406 Angle : 0.960 9.985 6410 Z= 0.498 Chirality : 0.056 0.499 762 Planarity : 0.007 0.073 818 Dihedral : 15.535 91.858 1712 Min Nonbonded Distance : 2.230 Molprobity Statistics. All-atom Clashscore : 8.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.99 % Favored : 91.01 % Rotamer Outliers : 0.00 % 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: -4.94 (0.26), residues: 556 helix: -3.14 (0.20), residues: 331 sheet: -1.07 (1.45), residues: 12 loop : -3.43 (0.34), residues: 213 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1112 Ramachandran restraints generated. 556 Oldfield, 0 Emsley, 556 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1112 Ramachandran restraints generated. 556 Oldfield, 0 Emsley, 556 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 122 residues out of total 504 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 122 time to evaluate : 0.551 Fit side-chains revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 122 average time/residue: 0.1552 time to fit residues: 24.2852 Evaluate side-chains 79 residues out of total 504 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 79 time to evaluate : 0.549 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.7581 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 59 random chunks: chunk 49 optimal weight: 0.0470 chunk 44 optimal weight: 10.0000 chunk 24 optimal weight: 1.9990 chunk 15 optimal weight: 0.0980 chunk 30 optimal weight: 1.9990 chunk 23 optimal weight: 0.9980 chunk 46 optimal weight: 2.9990 chunk 17 optimal weight: 2.9990 chunk 28 optimal weight: 0.9990 chunk 34 optimal weight: 0.0270 chunk 53 optimal weight: 3.9990 overall best weight: 0.4338 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 62 HIS A 184 GLN ** B 352 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7442 moved from start: 0.1688 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.042 4731 Z= 0.175 Angle : 0.672 12.682 6410 Z= 0.335 Chirality : 0.039 0.177 762 Planarity : 0.005 0.049 818 Dihedral : 7.400 85.115 657 Min Nonbonded Distance : 2.196 Molprobity Statistics. All-atom Clashscore : 12.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.01 % Favored : 92.99 % Rotamer Outliers : 2.94 % 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: -3.71 (0.30), residues: 556 helix: -2.08 (0.25), residues: 327 sheet: None (None), residues: 0 loop : -2.93 (0.34), residues: 229 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1112 Ramachandran restraints generated. 556 Oldfield, 0 Emsley, 556 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1112 Ramachandran restraints generated. 556 Oldfield, 0 Emsley, 556 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 106 residues out of total 504 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 92 time to evaluate : 0.558 Fit side-chains outliers start: 14 outliers final: 8 residues processed: 100 average time/residue: 0.1465 time to fit residues: 19.2733 Evaluate side-chains 89 residues out of total 504 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 81 time to evaluate : 0.556 Switching outliers to nearest non-outliers outliers start: 8 outliers final: 0 residues processed: 8 average time/residue: 0.0467 time to fit residues: 1.4444 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 59 random chunks: chunk 29 optimal weight: 0.9980 chunk 16 optimal weight: 1.9990 chunk 44 optimal weight: 10.0000 chunk 36 optimal weight: 1.9990 chunk 14 optimal weight: 0.0050 chunk 53 optimal weight: 7.9990 chunk 57 optimal weight: 6.9990 chunk 47 optimal weight: 0.1980 chunk 18 optimal weight: 0.4980 chunk 43 optimal weight: 9.9990 chunk 40 optimal weight: 2.9990 overall best weight: 0.7396 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 414 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 352 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7452 moved from start: 0.2032 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.084 4731 Z= 0.200 Angle : 0.607 8.661 6410 Z= 0.301 Chirality : 0.040 0.184 762 Planarity : 0.004 0.036 818 Dihedral : 7.078 82.547 657 Min Nonbonded Distance : 2.155 Molprobity Statistics. All-atom Clashscore : 13.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.55 % Favored : 92.45 % Rotamer Outliers : 3.57 % 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: -3.17 (0.32), residues: 556 helix: -1.67 (0.27), residues: 325 sheet: 0.02 (1.61), residues: 14 loop : -2.83 (0.37), residues: 217 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1112 Ramachandran restraints generated. 556 Oldfield, 0 Emsley, 556 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1112 Ramachandran restraints generated. 556 Oldfield, 0 Emsley, 556 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 105 residues out of total 504 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 88 time to evaluate : 0.455 Fit side-chains outliers start: 17 outliers final: 7 residues processed: 98 average time/residue: 0.1480 time to fit residues: 18.8157 Evaluate side-chains 83 residues out of total 504 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 76 time to evaluate : 0.415 Switching outliers to nearest non-outliers outliers start: 7 outliers final: 0 residues processed: 7 average time/residue: 0.0381 time to fit residues: 1.0512 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 59 random chunks: chunk 27 optimal weight: 3.9990 chunk 5 optimal weight: 2.9990 chunk 25 optimal weight: 2.9990 chunk 36 optimal weight: 0.6980 chunk 53 optimal weight: 3.9990 chunk 57 optimal weight: 8.9990 chunk 28 optimal weight: 0.0050 chunk 51 optimal weight: 4.9990 chunk 15 optimal weight: 4.9990 chunk 47 optimal weight: 0.5980 chunk 32 optimal weight: 0.3980 overall best weight: 0.9396 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 414 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7460 moved from start: 0.2308 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.055 4731 Z= 0.224 Angle : 0.652 9.762 6410 Z= 0.313 Chirality : 0.040 0.150 762 Planarity : 0.004 0.030 818 Dihedral : 6.894 81.952 657 Min Nonbonded Distance : 2.136 Molprobity Statistics. All-atom Clashscore : 14.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.73 % Favored : 92.27 % Rotamer Outliers : 2.31 % 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: -3.00 (0.33), residues: 556 helix: -1.52 (0.28), residues: 322 sheet: 0.03 (1.64), residues: 14 loop : -2.76 (0.37), residues: 220 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1112 Ramachandran restraints generated. 556 Oldfield, 0 Emsley, 556 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1112 Ramachandran restraints generated. 556 Oldfield, 0 Emsley, 556 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 94 residues out of total 504 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 83 time to evaluate : 0.557 Fit side-chains outliers start: 11 outliers final: 8 residues processed: 90 average time/residue: 0.1454 time to fit residues: 17.3945 Evaluate side-chains 85 residues out of total 504 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 77 time to evaluate : 0.558 Switching outliers to nearest non-outliers outliers start: 8 outliers final: 0 residues processed: 8 average time/residue: 0.0471 time to fit residues: 1.4169 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 59 random chunks: chunk 0 optimal weight: 10.0000 chunk 42 optimal weight: 2.9990 chunk 23 optimal weight: 0.9980 chunk 48 optimal weight: 7.9990 chunk 39 optimal weight: 0.9980 chunk 29 optimal weight: 0.8980 chunk 51 optimal weight: 3.9990 chunk 14 optimal weight: 2.9990 chunk 19 optimal weight: 0.6980 chunk 11 optimal weight: 0.9980 chunk 33 optimal weight: 3.9990 overall best weight: 0.9180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 414 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7456 moved from start: 0.2457 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.043 4731 Z= 0.220 Angle : 0.636 9.691 6410 Z= 0.306 Chirality : 0.040 0.205 762 Planarity : 0.004 0.065 818 Dihedral : 6.840 81.508 657 Min Nonbonded Distance : 2.128 Molprobity Statistics. All-atom Clashscore : 15.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.09 % Favored : 91.91 % Rotamer Outliers : 2.52 % 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: -3.02 (0.33), residues: 556 helix: -1.50 (0.28), residues: 328 sheet: -0.13 (1.60), residues: 14 loop : -2.83 (0.37), residues: 214 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1112 Ramachandran restraints generated. 556 Oldfield, 0 Emsley, 556 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1112 Ramachandran restraints generated. 556 Oldfield, 0 Emsley, 556 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 95 residues out of total 504 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 83 time to evaluate : 0.600 Fit side-chains outliers start: 12 outliers final: 10 residues processed: 86 average time/residue: 0.1537 time to fit residues: 17.7011 Evaluate side-chains 87 residues out of total 504 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 77 time to evaluate : 0.542 Switching outliers to nearest non-outliers outliers start: 10 outliers final: 0 residues processed: 10 average time/residue: 0.0475 time to fit residues: 1.6320 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 59 random chunks: chunk 14 optimal weight: 0.6980 chunk 57 optimal weight: 10.0000 chunk 47 optimal weight: 0.0370 chunk 26 optimal weight: 1.9990 chunk 4 optimal weight: 3.9990 chunk 18 optimal weight: 0.9980 chunk 29 optimal weight: 0.6980 chunk 55 optimal weight: 2.9990 chunk 6 optimal weight: 0.5980 chunk 32 optimal weight: 0.6980 chunk 41 optimal weight: 1.9990 overall best weight: 0.5458 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 414 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7403 moved from start: 0.2688 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.039 4731 Z= 0.179 Angle : 0.634 11.070 6410 Z= 0.300 Chirality : 0.039 0.181 762 Planarity : 0.004 0.034 818 Dihedral : 6.599 80.824 657 Min Nonbonded Distance : 2.152 Molprobity Statistics. All-atom Clashscore : 14.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.65 % Favored : 93.35 % Rotamer Outliers : 2.10 % 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: -2.72 (0.34), residues: 556 helix: -1.19 (0.29), residues: 315 sheet: -0.25 (1.56), residues: 14 loop : -2.74 (0.36), residues: 227 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1112 Ramachandran restraints generated. 556 Oldfield, 0 Emsley, 556 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1112 Ramachandran restraints generated. 556 Oldfield, 0 Emsley, 556 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 95 residues out of total 504 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 85 time to evaluate : 0.507 Fit side-chains outliers start: 10 outliers final: 5 residues processed: 90 average time/residue: 0.1465 time to fit residues: 17.7042 Evaluate side-chains 80 residues out of total 504 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 75 time to evaluate : 0.542 Switching outliers to nearest non-outliers outliers start: 5 outliers final: 0 residues processed: 5 average time/residue: 0.0476 time to fit residues: 1.2268 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 59 random chunks: chunk 32 optimal weight: 0.8980 chunk 48 optimal weight: 0.0770 chunk 31 optimal weight: 3.9990 chunk 56 optimal weight: 0.0270 chunk 35 optimal weight: 0.8980 chunk 34 optimal weight: 0.8980 chunk 26 optimal weight: 0.6980 chunk 22 optimal weight: 0.5980 chunk 33 optimal weight: 0.6980 chunk 17 optimal weight: 1.9990 chunk 11 optimal weight: 3.9990 overall best weight: 0.4196 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 229 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 271 HIS ** A 414 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 352 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7364 moved from start: 0.2866 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.038 4731 Z= 0.173 Angle : 0.639 11.183 6410 Z= 0.300 Chirality : 0.039 0.177 762 Planarity : 0.004 0.031 818 Dihedral : 6.474 80.203 657 Min Nonbonded Distance : 2.154 Molprobity Statistics. All-atom Clashscore : 14.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.47 % Favored : 93.53 % Rotamer Outliers : 1.05 % 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: -2.58 (0.34), residues: 556 helix: -1.07 (0.29), residues: 318 sheet: -0.24 (1.54), residues: 14 loop : -2.71 (0.38), residues: 224 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1112 Ramachandran restraints generated. 556 Oldfield, 0 Emsley, 556 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1112 Ramachandran restraints generated. 556 Oldfield, 0 Emsley, 556 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 92 residues out of total 504 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 87 time to evaluate : 0.594 Fit side-chains outliers start: 5 outliers final: 4 residues processed: 89 average time/residue: 0.1407 time to fit residues: 16.8789 Evaluate side-chains 87 residues out of total 504 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 83 time to evaluate : 0.585 Switching outliers to nearest non-outliers outliers start: 4 outliers final: 0 residues processed: 4 average time/residue: 0.0475 time to fit residues: 1.1108 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 59 random chunks: chunk 11 optimal weight: 2.9990 chunk 36 optimal weight: 1.9990 chunk 38 optimal weight: 1.9990 chunk 28 optimal weight: 1.9990 chunk 5 optimal weight: 0.8980 chunk 44 optimal weight: 10.0000 chunk 51 optimal weight: 2.9990 chunk 54 optimal weight: 0.9980 chunk 49 optimal weight: 1.9990 chunk 52 optimal weight: 7.9990 chunk 31 optimal weight: 1.9990 overall best weight: 1.5786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 414 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7502 moved from start: 0.2847 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.037 4731 Z= 0.310 Angle : 0.704 12.745 6410 Z= 0.334 Chirality : 0.043 0.172 762 Planarity : 0.004 0.031 818 Dihedral : 6.761 79.341 657 Min Nonbonded Distance : 2.101 Molprobity Statistics. All-atom Clashscore : 16.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.55 % Favored : 92.45 % Rotamer Outliers : 2.52 % 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: -2.72 (0.34), residues: 556 helix: -1.26 (0.28), residues: 319 sheet: -0.03 (1.65), residues: 14 loop : -2.67 (0.38), residues: 223 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1112 Ramachandran restraints generated. 556 Oldfield, 0 Emsley, 556 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1112 Ramachandran restraints generated. 556 Oldfield, 0 Emsley, 556 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 96 residues out of total 504 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 84 time to evaluate : 0.587 Fit side-chains outliers start: 12 outliers final: 8 residues processed: 89 average time/residue: 0.1516 time to fit residues: 17.8648 Evaluate side-chains 87 residues out of total 504 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 79 time to evaluate : 0.486 Switching outliers to nearest non-outliers outliers start: 8 outliers final: 0 residues processed: 8 average time/residue: 0.0446 time to fit residues: 1.3726 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 59 random chunks: chunk 23 optimal weight: 0.9990 chunk 41 optimal weight: 2.9990 chunk 16 optimal weight: 0.8980 chunk 47 optimal weight: 0.0980 chunk 50 optimal weight: 2.9990 chunk 52 optimal weight: 0.9990 chunk 34 optimal weight: 0.0060 chunk 56 optimal weight: 0.9990 chunk 26 optimal weight: 0.9990 chunk 38 optimal weight: 0.6980 chunk 58 optimal weight: 1.9990 overall best weight: 0.5398 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 229 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 414 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7401 moved from start: 0.3048 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.086 4731 Z= 0.233 Angle : 0.704 12.410 6410 Z= 0.331 Chirality : 0.040 0.225 762 Planarity : 0.005 0.105 818 Dihedral : 6.531 78.951 657 Min Nonbonded Distance : 2.127 Molprobity Statistics. All-atom Clashscore : 15.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.58 % Favored : 94.42 % Rotamer Outliers : 1.05 % 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: -2.48 (0.34), residues: 556 helix: -1.08 (0.29), residues: 318 sheet: -0.32 (1.54), residues: 14 loop : -2.51 (0.39), residues: 224 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1112 Ramachandran restraints generated. 556 Oldfield, 0 Emsley, 556 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1112 Ramachandran restraints generated. 556 Oldfield, 0 Emsley, 556 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 87 residues out of total 504 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 82 time to evaluate : 0.555 Fit side-chains outliers start: 5 outliers final: 3 residues processed: 85 average time/residue: 0.1474 time to fit residues: 16.6584 Evaluate side-chains 82 residues out of total 504 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 79 time to evaluate : 0.537 Switching outliers to nearest non-outliers outliers start: 3 outliers final: 0 residues processed: 3 average time/residue: 0.0476 time to fit residues: 0.9947 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 59 random chunks: chunk 54 optimal weight: 0.9980 chunk 46 optimal weight: 6.9990 chunk 4 optimal weight: 2.9990 chunk 36 optimal weight: 0.9990 chunk 28 optimal weight: 5.9990 chunk 37 optimal weight: 0.9990 chunk 49 optimal weight: 0.9980 chunk 14 optimal weight: 2.9990 chunk 43 optimal weight: 6.9990 chunk 6 optimal weight: 0.6980 chunk 13 optimal weight: 5.9990 overall best weight: 0.9384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 229 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7432 moved from start: 0.3153 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.067 4731 Z= 0.255 Angle : 0.715 12.795 6410 Z= 0.335 Chirality : 0.041 0.217 762 Planarity : 0.005 0.094 818 Dihedral : 6.580 78.513 657 Min Nonbonded Distance : 2.120 Molprobity Statistics. All-atom Clashscore : 15.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.83 % Favored : 93.17 % Rotamer Outliers : 1.26 % 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: -2.45 (0.34), residues: 556 helix: -1.07 (0.29), residues: 317 sheet: -0.31 (1.55), residues: 14 loop : -2.46 (0.39), residues: 225 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1112 Ramachandran restraints generated. 556 Oldfield, 0 Emsley, 556 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1112 Ramachandran restraints generated. 556 Oldfield, 0 Emsley, 556 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 84 residues out of total 504 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 78 time to evaluate : 0.553 Fit side-chains outliers start: 6 outliers final: 3 residues processed: 80 average time/residue: 0.1527 time to fit residues: 16.2430 Evaluate side-chains 81 residues out of total 504 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 78 time to evaluate : 0.555 Switching outliers to nearest non-outliers outliers start: 3 outliers final: 0 residues processed: 3 average time/residue: 0.0464 time to fit residues: 1.0069 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 59 random chunks: chunk 46 optimal weight: 0.4980 chunk 19 optimal weight: 0.7980 chunk 48 optimal weight: 20.0000 chunk 5 optimal weight: 0.0060 chunk 8 optimal weight: 4.9990 chunk 41 optimal weight: 0.0670 chunk 2 optimal weight: 2.9990 chunk 33 optimal weight: 0.9980 chunk 53 optimal weight: 8.9990 chunk 31 optimal weight: 0.0010 chunk 40 optimal weight: 0.8980 overall best weight: 0.2740 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 229 ASN ** 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 = 0.4230 r_free = 0.4230 target = 0.180428 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3894 r_free = 0.3894 target = 0.150764 restraints weight = 6793.512| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3943 r_free = 0.3943 target = 0.154899 restraints weight = 4044.767| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.3978 r_free = 0.3978 target = 0.157779 restraints weight = 2891.267| |-----------------------------------------------------------------------------| r_work (final): 0.3973 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7305 moved from start: 0.3397 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.060 4731 Z= 0.187 Angle : 0.679 12.489 6410 Z= 0.313 Chirality : 0.039 0.169 762 Planarity : 0.005 0.085 818 Dihedral : 6.315 77.581 657 Min Nonbonded Distance : 2.145 Molprobity Statistics. All-atom Clashscore : 15.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.04 % Favored : 94.96 % Rotamer Outliers : 0.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.32 (0.35), residues: 556 helix: -0.92 (0.29), residues: 316 sheet: -0.52 (1.51), residues: 14 loop : -2.45 (0.39), residues: 226 =============================================================================== Job complete usr+sys time: 1278.72 seconds wall clock time: 23 minutes 46.33 seconds (1426.33 seconds total)