Starting phenix.real_space_refine on Sun Mar 10 22:35:14 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7rxh_24731/03_2024/7rxh_24731_neut_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7rxh_24731/03_2024/7rxh_24731.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.3 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7rxh_24731/03_2024/7rxh_24731.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7rxh_24731/03_2024/7rxh_24731.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7rxh_24731/03_2024/7rxh_24731_neut_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7rxh_24731/03_2024/7rxh_24731_neut_updated.pdb" } resolution = 2.3 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= 0.001 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 7 Type Number sf(0) Gaussians Ca 2 9.91 5 P 15 5.49 5 S 18 5.16 5 C 3653 2.51 5 N 849 2.21 5 O 1046 1.98 5 H 48 0.53 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A GLU 37": "OE1" <-> "OE2" Residue "A GLU 57": "OE1" <-> "OE2" Residue "A GLU 94": "OE1" <-> "OE2" Residue "A GLU 154": "OE1" <-> "OE2" Residue "A ARG 168": "NH1" <-> "NH2" Residue "A ARG 229": "NH1" <-> "NH2" Residue "A GLU 248": "OE1" <-> "OE2" Residue "A GLU 258": "OE1" <-> "OE2" Residue "A ARG 276": "NH1" <-> "NH2" Residue "A ARG 496": "NH1" <-> "NH2" Residue "A ARG 498": "NH1" <-> "NH2" Residue "A GLU 543": "OE1" <-> "OE2" Residue "A ARG 545": "NH1" <-> "NH2" Residue "A ARG 557": "NH1" <-> "NH2" Residue "A GLU 596": "OE1" <-> "OE2" Residue "A ARG 606": "NH1" <-> "NH2" Residue "A ARG 625": "NH1" <-> "NH2" Residue "A ARG 629": "NH1" <-> "NH2" Residue "A ARG 642": "NH1" <-> "NH2" Residue "A ARG 647": "NH1" <-> "NH2" Residue "A ARG 651": "NH1" <-> "NH2" Time to flip residues: 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 5631 Number of models: 1 Model: "" Number of chains: 1 Chain: "A" Number of atoms: 5631 Number of conformers: 1 Conformer: "" Number of residues, atoms: 668, 5631 Unusual residues: {' CA': 2, 'PGW': 16} Classifications: {'peptide': 626, 'undetermined': 18, 'water': 24} Incomplete info: {'truncation_to_alanine': 17} Link IDs: {'PTRANS': 30, 'TRANS': 595, None: 42} Not linked: pdbres="SER A 660 " pdbres=" CA A 801 " Not linked: pdbres=" CA A 801 " pdbres=" CA A 802 " Not linked: pdbres=" CA A 802 " pdbres="PGW A 803 " Not linked: pdbres="PGW A 803 " pdbres="PGW A 804 " Not linked: pdbres="PGW A 804 " pdbres="PGW A 805 " ... (remaining 37 not shown) Chain breaks: 1 Unresolved non-hydrogen bonds: 396 Unresolved non-hydrogen angles: 428 Unresolved non-hydrogen dihedrals: 422 Unresolved non-hydrogen chiralities: 13 Planarities with less than four sites: {'HIS:plan': 1, 'TYR:plan': 1, 'ASP:plan': 1, 'PGW:plan-2': 1, 'PGW:plan-3': 10, 'GLU:plan': 8, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 89 Time building chain proxies: 3.70, per 1000 atoms: 0.66 Number of scatterers: 5631 At special positions: 0 Unit cell: (72.7901, 85.5107, 98.938, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 7 Type Number sf(0) Ca 2 19.99 S 18 16.00 P 15 15.00 O 1046 8.00 N 849 7.00 C 3653 6.00 H 48 1.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 2.19 Conformation dependent library (CDL) restraints added in 1.1 seconds 1244 Ramachandran restraints generated. 622 Oldfield, 0 Emsley, 622 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1200 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 23 helices and 1 sheets defined 66.9% alpha, 3.8% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.12 Creating SS restraints... Processing helix chain 'A' and resid 29 through 45 Processing helix chain 'A' and resid 69 through 85 Processing helix chain 'A' and resid 96 through 98 No H-bonds generated for 'chain 'A' and resid 96 through 98' Processing helix chain 'A' and resid 104 through 116 Processing helix chain 'A' and resid 119 through 121 No H-bonds generated for 'chain 'A' and resid 119 through 121' Processing helix chain 'A' and resid 145 through 157 removed outlier: 4.179A pdb=" N LYS A 157 " --> pdb=" O ARG A 153 " (cutoff:3.500A) Processing helix chain 'A' and resid 163 through 173 Processing helix chain 'A' and resid 175 through 204 removed outlier: 3.696A pdb=" N MET A 192 " --> pdb=" O PHE A 188 " (cutoff:3.500A) removed outlier: 4.677A pdb=" N PHE A 193 " --> pdb=" O ARG A 189 " (cutoff:3.500A) Proline residue: A 194 - end of helix Processing helix chain 'A' and resid 210 through 237 Processing helix chain 'A' and resid 243 through 246 Processing helix chain 'A' and resid 273 through 310 removed outlier: 4.355A pdb=" N LEU A 282 " --> pdb=" O TYR A 278 " (cutoff:3.500A) removed outlier: 4.853A pdb=" N GLN A 283 " --> pdb=" O ARG A 279 " (cutoff:3.500A) removed outlier: 4.802A pdb=" N VAL A 284 " --> pdb=" O GLN A 280 " (cutoff:3.500A) Proline residue: A 285 - end of helix Processing helix chain 'A' and resid 318 through 349 removed outlier: 4.462A pdb=" N ILE A 323 " --> pdb=" O TYR A 319 " (cutoff:3.500A) Proline residue: A 324 - end of helix Proline residue: A 333 - end of helix Processing helix chain 'A' and resid 355 through 383 removed outlier: 3.980A pdb=" N VAL A 368 " --> pdb=" O GLN A 364 " (cutoff:3.500A) removed outlier: 4.234A pdb=" N VAL A 369 " --> pdb=" O LYS A 365 " (cutoff:3.500A) Proline residue: A 377 - end of helix Processing helix chain 'A' and resid 393 through 404 removed outlier: 4.124A pdb=" N ASP A 397 " --> pdb=" O PRO A 394 " (cutoff:3.500A) removed outlier: 4.244A pdb=" N VAL A 398 " --> pdb=" O TYR A 395 " (cutoff:3.500A) removed outlier: 3.905A pdb=" N LEU A 401 " --> pdb=" O VAL A 398 " (cutoff:3.500A) Processing helix chain 'A' and resid 409 through 413 Processing helix chain 'A' and resid 425 through 434 Processing helix chain 'A' and resid 436 through 462 removed outlier: 4.735A pdb=" N VAL A 448 " --> pdb=" O LEU A 444 " (cutoff:3.500A) Proline residue: A 449 - end of helix Processing helix chain 'A' and resid 491 through 502 removed outlier: 3.656A pdb=" N GLU A 502 " --> pdb=" O ARG A 498 " (cutoff:3.500A) Processing helix chain 'A' and resid 508 through 528 Proline residue: A 527 - end of helix Processing helix chain 'A' and resid 532 through 553 removed outlier: 3.787A pdb=" N ARG A 545 " --> pdb=" O TRP A 541 " (cutoff:3.500A) Processing helix chain 'A' and resid 567 through 590 removed outlier: 4.376A pdb=" N SER A 584 " --> pdb=" O SER A 581 " (cutoff:3.500A) Processing helix chain 'A' and resid 607 through 634 removed outlier: 3.528A pdb=" N LYS A 634 " --> pdb=" O SER A 630 " (cutoff:3.500A) Processing helix chain 'A' and resid 638 through 657 Processing sheet with id= A, first strand: chain 'A' and resid 136 through 140 removed outlier: 6.593A pdb=" N ARG A 21 " --> pdb=" O ASP A 137 " (cutoff:3.500A) removed outlier: 4.097A pdb=" N ILE A 139 " --> pdb=" O VAL A 19 " (cutoff:3.500A) removed outlier: 6.235A pdb=" N VAL A 19 " --> pdb=" O ILE A 139 " (cutoff:3.500A) removed outlier: 3.732A pdb=" N SER A 59 " --> pdb=" O ASP A 56 " (cutoff:3.500A) removed outlier: 5.287A pdb=" N PHE A 61 " --> pdb=" O GLN A 54 " (cutoff:3.500A) removed outlier: 5.353A pdb=" N GLN A 54 " --> pdb=" O PHE A 61 " (cutoff:3.500A) removed outlier: 6.862A pdb=" N PHE A 63 " --> pdb=" O VAL A 52 " (cutoff:3.500A) removed outlier: 5.524A pdb=" N VAL A 52 " --> pdb=" O PHE A 63 " (cutoff:3.500A) removed outlier: 7.095A pdb=" N ARG A 65 " --> pdb=" O THR A 50 " (cutoff:3.500A) removed outlier: 5.209A pdb=" N THR A 50 " --> pdb=" O ARG A 65 " (cutoff:3.500A) 303 hydrogen bonds defined for protein. 825 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: 1.55 Time building geometry restraints manager: 2.33 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.83 - 1.03: 48 1.03 - 1.22: 33 1.22 - 1.42: 2317 1.42 - 1.61: 3274 1.61 - 1.81: 52 Bond restraints: 5724 Sorted by residual: bond pdb=" C1 PGW A 810 " pdb=" O01 PGW A 810 " ideal model delta sigma weight residual 1.332 1.426 -0.094 2.00e-02 2.50e+03 2.22e+01 bond pdb=" C1 PGW A 807 " pdb=" O01 PGW A 807 " ideal model delta sigma weight residual 1.332 1.422 -0.090 2.00e-02 2.50e+03 2.02e+01 bond pdb=" C1 PGW A 809 " pdb=" O01 PGW A 809 " ideal model delta sigma weight residual 1.332 1.422 -0.090 2.00e-02 2.50e+03 2.02e+01 bond pdb=" C1 PGW A 817 " pdb=" O01 PGW A 817 " ideal model delta sigma weight residual 1.332 1.421 -0.089 2.00e-02 2.50e+03 1.96e+01 bond pdb=" C1 PGW A 814 " pdb=" O01 PGW A 814 " ideal model delta sigma weight residual 1.332 1.420 -0.088 2.00e-02 2.50e+03 1.93e+01 ... (remaining 5719 not shown) Histogram of bond angle deviations from ideal: 99.95 - 106.76: 167 106.76 - 113.58: 3244 113.58 - 120.40: 2262 120.40 - 127.21: 1916 127.21 - 134.03: 63 Bond angle restraints: 7652 Sorted by residual: angle pdb=" N ARG A 404 " pdb=" CA ARG A 404 " pdb=" C ARG A 404 " ideal model delta sigma weight residual 113.16 119.81 -6.65 1.42e+00 4.96e-01 2.19e+01 angle pdb=" N GLU A 418 " pdb=" CA GLU A 418 " pdb=" C GLU A 418 " ideal model delta sigma weight residual 109.96 103.92 6.04 1.50e+00 4.44e-01 1.62e+01 angle pdb=" C ARG A 404 " pdb=" N PRO A 405 " pdb=" CA PRO A 405 " ideal model delta sigma weight residual 119.84 114.93 4.91 1.25e+00 6.40e-01 1.54e+01 angle pdb=" O11 PGW A 807 " pdb=" P PGW A 807 " pdb=" O12 PGW A 807 " ideal model delta sigma weight residual 98.90 110.35 -11.45 3.00e+00 1.11e-01 1.46e+01 angle pdb=" N ILE A 421 " pdb=" CA ILE A 421 " pdb=" C ILE A 421 " ideal model delta sigma weight residual 109.51 114.97 -5.46 1.43e+00 4.89e-01 1.46e+01 ... (remaining 7647 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 34.98: 3238 34.98 - 69.95: 182 69.95 - 104.93: 35 104.93 - 139.90: 8 139.90 - 174.87: 11 Dihedral angle restraints: 3474 sinusoidal: 1624 harmonic: 1850 Sorted by residual: dihedral pdb=" CA ALA A 389 " pdb=" C ALA A 389 " pdb=" N SER A 390 " pdb=" CA SER A 390 " ideal model delta harmonic sigma weight residual 180.00 153.91 26.09 0 5.00e+00 4.00e-02 2.72e+01 dihedral pdb=" O01 PGW A 810 " pdb=" C01 PGW A 810 " pdb=" C02 PGW A 810 " pdb=" O03 PGW A 810 " ideal model delta sinusoidal sigma weight residual 59.30 -115.57 174.87 1 3.00e+01 1.11e-03 2.13e+01 dihedral pdb=" C03 PGW A 810 " pdb=" C01 PGW A 810 " pdb=" C02 PGW A 810 " pdb=" O03 PGW A 810 " ideal model delta sinusoidal sigma weight residual 295.35 121.86 173.49 1 3.00e+01 1.11e-03 2.13e+01 ... (remaining 3471 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.068: 707 0.068 - 0.136: 88 0.136 - 0.203: 16 0.203 - 0.271: 0 0.271 - 0.339: 1 Chirality restraints: 812 Sorted by residual: chirality pdb=" CA ARG A 404 " pdb=" N ARG A 404 " pdb=" C ARG A 404 " pdb=" CB ARG A 404 " both_signs ideal model delta sigma weight residual False 2.51 2.17 0.34 2.00e-01 2.50e+01 2.87e+00 chirality pdb=" CA ILE A 421 " pdb=" N ILE A 421 " pdb=" C ILE A 421 " pdb=" CB ILE A 421 " both_signs ideal model delta sigma weight residual False 2.43 2.25 0.19 2.00e-01 2.50e+01 8.65e-01 chirality pdb=" C02 PGW A 813 " pdb=" C01 PGW A 813 " pdb=" C03 PGW A 813 " pdb=" O01 PGW A 813 " both_signs ideal model delta sigma weight residual False 2.36 2.54 -0.18 2.00e-01 2.50e+01 8.11e-01 ... (remaining 809 not shown) Planarity restraints: 930 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA TYR A 352 " -0.010 2.00e-02 2.50e+03 1.92e-02 3.70e+00 pdb=" C TYR A 352 " 0.033 2.00e-02 2.50e+03 pdb=" O TYR A 352 " -0.013 2.00e-02 2.50e+03 pdb=" N GLU A 353 " -0.011 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C VAL A 393 " 0.030 5.00e-02 4.00e+02 4.52e-02 3.26e+00 pdb=" N PRO A 394 " -0.078 5.00e-02 4.00e+02 pdb=" CA PRO A 394 " 0.022 5.00e-02 4.00e+02 pdb=" CD PRO A 394 " 0.026 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C SER A 526 " 0.029 5.00e-02 4.00e+02 4.32e-02 2.98e+00 pdb=" N PRO A 527 " -0.075 5.00e-02 4.00e+02 pdb=" CA PRO A 527 " 0.022 5.00e-02 4.00e+02 pdb=" CD PRO A 527 " 0.024 5.00e-02 4.00e+02 ... (remaining 927 not shown) Histogram of nonbonded interaction distances: 1.72 - 2.30: 30 2.30 - 2.87: 2038 2.87 - 3.45: 6658 3.45 - 4.02: 11584 4.02 - 4.60: 16859 Nonbonded interactions: 37169 Sorted by model distance: nonbonded pdb=" OG SER A 546 " pdb=" H1 HOH A2702 " model vdw 1.723 1.850 nonbonded pdb=" O LYS A 556 " pdb=" H1 HOH A2709 " model vdw 1.739 1.850 nonbonded pdb=" OH TYR A 621 " pdb=" H1 HOH A2704 " model vdw 1.740 1.850 nonbonded pdb=" OG1 THR A 116 " pdb=" H1 HOH A2705 " model vdw 1.769 1.850 nonbonded pdb=" OD2 ASP A 233 " pdb=" H1 HOH A2703 " model vdw 1.778 1.850 ... (remaining 37164 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 individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 2.490 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.140 Extract box with map and model: 11.740 Check model and map are aligned: 0.080 Set scattering table: 0.050 Process input model: 19.510 Find NCS groups from input model: 0.150 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:12.440 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 46.620 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7459 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 : 0.009 0.094 5676 Z= 0.540 Angle : 1.403 11.447 7628 Z= 0.571 Chirality : 0.050 0.339 812 Planarity : 0.005 0.045 930 Dihedral : 24.726 174.875 2274 Min Nonbonded Distance : 2.211 Molprobity Statistics. All-atom Clashscore : 13.92 Ramachandran Plot: Outliers : 0.16 % Allowed : 2.73 % Favored : 97.11 % Rotamer: Outliers : 0.56 % Allowed : 2.22 % Favored : 97.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.87 (0.31), residues: 622 helix: 0.09 (0.22), residues: 424 sheet: -0.80 (0.80), residues: 27 loop : -2.04 (0.45), residues: 171 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.028 0.003 TRP A 155 HIS 0.008 0.002 HIS A 619 PHE 0.018 0.002 PHE A 388 TYR 0.013 0.002 TYR A 352 ARG 0.005 0.001 ARG A 496 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1244 Ramachandran restraints generated. 622 Oldfield, 0 Emsley, 622 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1244 Ramachandran restraints generated. 622 Oldfield, 0 Emsley, 622 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 94 residues out of total 557 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 91 time to evaluate : 0.634 Fit side-chains outliers start: 3 outliers final: 1 residues processed: 92 average time/residue: 1.2235 time to fit residues: 117.5845 Evaluate side-chains 51 residues out of total 557 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 50 time to evaluate : 0.653 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 421 ILE Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 66 random chunks: chunk 55 optimal weight: 0.5980 chunk 50 optimal weight: 0.9990 chunk 27 optimal weight: 2.9990 chunk 17 optimal weight: 0.5980 chunk 33 optimal weight: 0.7980 chunk 26 optimal weight: 0.9990 chunk 51 optimal weight: 0.6980 chunk 20 optimal weight: 0.6980 chunk 31 optimal weight: 0.9980 chunk 38 optimal weight: 0.6980 chunk 59 optimal weight: 0.5980 overall best weight: 0.6380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 23 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 78 GLN A 102 GLN A 135 ASN A 148 ASN A 171 ASN A 283 GLN A 370 ASN A 438 GLN A 453 GLN A 539 ASN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8000 moved from start: 0.3207 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.024 5676 Z= 0.189 Angle : 0.551 6.396 7628 Z= 0.271 Chirality : 0.038 0.166 812 Planarity : 0.004 0.034 930 Dihedral : 24.668 170.449 1100 Min Nonbonded Distance : 2.070 Molprobity Statistics. All-atom Clashscore : 17.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.25 % Favored : 97.75 % Rotamer: Outliers : 1.48 % Allowed : 10.56 % Favored : 87.96 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.90 (0.34), residues: 622 helix: 1.51 (0.25), residues: 425 sheet: -0.24 (0.93), residues: 24 loop : -1.61 (0.47), residues: 173 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.033 0.002 TRP A 155 HIS 0.002 0.001 HIS A 400 PHE 0.011 0.001 PHE A 456 TYR 0.015 0.001 TYR A 180 ARG 0.004 0.000 ARG A 454 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1244 Ramachandran restraints generated. 622 Oldfield, 0 Emsley, 622 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1244 Ramachandran restraints generated. 622 Oldfield, 0 Emsley, 622 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 56 residues out of total 557 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 48 time to evaluate : 0.559 Fit side-chains outliers start: 8 outliers final: 4 residues processed: 51 average time/residue: 1.1730 time to fit residues: 63.0780 Evaluate side-chains 44 residues out of total 557 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 40 time to evaluate : 0.622 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 288 LEU Chi-restraints excluded: chain A residue 353 GLU Chi-restraints excluded: chain A residue 421 ILE Chi-restraints excluded: chain A residue 592 SER Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 66 random chunks: chunk 33 optimal weight: 4.9990 chunk 18 optimal weight: 2.9990 chunk 49 optimal weight: 0.0980 chunk 40 optimal weight: 10.0000 chunk 16 optimal weight: 3.9990 chunk 60 optimal weight: 0.0060 chunk 64 optimal weight: 20.0000 chunk 53 optimal weight: 0.6980 chunk 59 optimal weight: 0.3980 chunk 20 optimal weight: 0.5980 chunk 48 optimal weight: 0.6980 overall best weight: 0.3596 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 23 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 78 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8072 moved from start: 0.3929 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.028 5676 Z= 0.120 Angle : 0.416 4.697 7628 Z= 0.214 Chirality : 0.036 0.132 812 Planarity : 0.003 0.031 930 Dihedral : 20.614 170.400 1100 Min Nonbonded Distance : 2.039 Molprobity Statistics. All-atom Clashscore : 16.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.41 % Favored : 97.59 % Rotamer: Outliers : 1.85 % Allowed : 11.30 % Favored : 86.85 % 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: 1.70 (0.35), residues: 622 helix: 2.10 (0.26), residues: 425 sheet: 0.24 (0.93), residues: 24 loop : -1.28 (0.47), residues: 173 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.028 0.002 TRP A 155 HIS 0.003 0.000 HIS A 619 PHE 0.007 0.001 PHE A 575 TYR 0.009 0.001 TYR A 187 ARG 0.005 0.000 ARG A 642 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1244 Ramachandran restraints generated. 622 Oldfield, 0 Emsley, 622 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1244 Ramachandran restraints generated. 622 Oldfield, 0 Emsley, 622 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 57 residues out of total 557 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 47 time to evaluate : 0.614 Fit side-chains outliers start: 10 outliers final: 6 residues processed: 52 average time/residue: 1.1482 time to fit residues: 63.0775 Evaluate side-chains 40 residues out of total 557 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 34 time to evaluate : 0.624 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 33 ILE Chi-restraints excluded: chain A residue 41 LEU Chi-restraints excluded: chain A residue 288 LEU Chi-restraints excluded: chain A residue 454 ARG Chi-restraints excluded: chain A residue 592 SER Chi-restraints excluded: chain A residue 658 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 66 random chunks: chunk 59 optimal weight: 2.9990 chunk 45 optimal weight: 4.9990 chunk 31 optimal weight: 2.9990 chunk 6 optimal weight: 2.9990 chunk 28 optimal weight: 2.9990 chunk 40 optimal weight: 9.9990 chunk 60 optimal weight: 3.9990 chunk 63 optimal weight: 10.0000 chunk 57 optimal weight: 3.9990 chunk 17 optimal weight: 2.9990 chunk 53 optimal weight: 2.9990 overall best weight: 2.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 23 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8345 moved from start: 0.5629 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.009 0.056 5676 Z= 0.578 Angle : 0.610 5.747 7628 Z= 0.329 Chirality : 0.045 0.193 812 Planarity : 0.004 0.033 930 Dihedral : 20.927 173.261 1098 Min Nonbonded Distance : 1.982 Molprobity Statistics. All-atom Clashscore : 14.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.54 % Favored : 96.46 % Rotamer: Outliers : 2.22 % Allowed : 10.56 % Favored : 87.22 % 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: 1.33 (0.34), residues: 622 helix: 1.69 (0.25), residues: 423 sheet: 0.17 (0.93), residues: 24 loop : -1.03 (0.47), residues: 175 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.033 0.002 TRP A 155 HIS 0.010 0.001 HIS A 619 PHE 0.018 0.002 PHE A 193 TYR 0.019 0.002 TYR A 212 ARG 0.003 0.001 ARG A 425 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1244 Ramachandran restraints generated. 622 Oldfield, 0 Emsley, 622 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1244 Ramachandran restraints generated. 622 Oldfield, 0 Emsley, 622 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 48 residues out of total 557 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 36 time to evaluate : 0.635 Fit side-chains outliers start: 12 outliers final: 4 residues processed: 44 average time/residue: 1.1750 time to fit residues: 54.6034 Evaluate side-chains 38 residues out of total 557 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 34 time to evaluate : 0.595 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 454 ARG Chi-restraints excluded: chain A residue 611 LEU Chi-restraints excluded: chain A residue 658 VAL Chi-restraints excluded: chain A residue 659 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 66 random chunks: chunk 36 optimal weight: 0.4980 chunk 0 optimal weight: 0.5980 chunk 47 optimal weight: 0.8980 chunk 26 optimal weight: 0.9990 chunk 54 optimal weight: 0.5980 chunk 44 optimal weight: 4.9990 chunk 32 optimal weight: 1.9990 chunk 57 optimal weight: 2.9990 chunk 16 optimal weight: 0.5980 chunk 21 optimal weight: 0.7980 chunk 12 optimal weight: 1.9990 overall best weight: 0.6180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 23 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 113 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8260 moved from start: 0.5734 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.026 5676 Z= 0.152 Angle : 0.407 3.977 7628 Z= 0.221 Chirality : 0.037 0.140 812 Planarity : 0.003 0.029 930 Dihedral : 18.988 175.413 1098 Min Nonbonded Distance : 2.047 Molprobity Statistics. All-atom Clashscore : 14.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.05 % Favored : 96.95 % Rotamer: Outliers : 1.67 % Allowed : 11.11 % Favored : 87.22 % 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: 1.82 (0.35), residues: 622 helix: 2.09 (0.26), residues: 422 sheet: 0.28 (0.97), residues: 24 loop : -0.87 (0.49), residues: 176 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.002 TRP A 155 HIS 0.003 0.001 HIS A 619 PHE 0.006 0.001 PHE A 615 TYR 0.008 0.001 TYR A 180 ARG 0.003 0.000 ARG A 268 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1244 Ramachandran restraints generated. 622 Oldfield, 0 Emsley, 622 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1244 Ramachandran restraints generated. 622 Oldfield, 0 Emsley, 622 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 45 residues out of total 557 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 36 time to evaluate : 0.633 Fit side-chains REVERT: A 454 ARG cc_start: 0.7432 (OUTLIER) cc_final: 0.7137 (tpt170) outliers start: 9 outliers final: 3 residues processed: 42 average time/residue: 1.4564 time to fit residues: 64.0611 Evaluate side-chains 38 residues out of total 557 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 34 time to evaluate : 0.620 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 288 LEU Chi-restraints excluded: chain A residue 353 GLU Chi-restraints excluded: chain A residue 454 ARG Chi-restraints excluded: chain A residue 611 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 66 random chunks: chunk 37 optimal weight: 4.9990 chunk 15 optimal weight: 3.9990 chunk 63 optimal weight: 10.0000 chunk 53 optimal weight: 1.9990 chunk 29 optimal weight: 2.9990 chunk 5 optimal weight: 2.9990 chunk 21 optimal weight: 1.9990 chunk 33 optimal weight: 4.9990 chunk 61 optimal weight: 2.9990 chunk 7 optimal weight: 0.4980 chunk 36 optimal weight: 2.9990 overall best weight: 2.0988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 23 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8332 moved from start: 0.5926 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.047 5676 Z= 0.409 Angle : 0.511 4.575 7628 Z= 0.278 Chirality : 0.042 0.175 812 Planarity : 0.004 0.033 930 Dihedral : 18.865 173.690 1098 Min Nonbonded Distance : 2.035 Molprobity Statistics. All-atom Clashscore : 14.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.70 % Favored : 96.30 % Rotamer: Outliers : 2.41 % Allowed : 10.00 % Favored : 87.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.69 (0.35), residues: 622 helix: 1.96 (0.26), residues: 423 sheet: 0.24 (0.96), residues: 24 loop : -0.85 (0.50), residues: 175 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.002 TRP A 155 HIS 0.008 0.001 HIS A 619 PHE 0.015 0.002 PHE A 193 TYR 0.015 0.002 TYR A 212 ARG 0.002 0.000 ARG A 642 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1244 Ramachandran restraints generated. 622 Oldfield, 0 Emsley, 622 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1244 Ramachandran restraints generated. 622 Oldfield, 0 Emsley, 622 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 50 residues out of total 557 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 37 time to evaluate : 0.576 Fit side-chains REVERT: A 454 ARG cc_start: 0.7498 (OUTLIER) cc_final: 0.7232 (tpt170) outliers start: 13 outliers final: 3 residues processed: 46 average time/residue: 1.3641 time to fit residues: 65.7863 Evaluate side-chains 40 residues out of total 557 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 36 time to evaluate : 0.610 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 41 LEU Chi-restraints excluded: chain A residue 353 GLU Chi-restraints excluded: chain A residue 454 ARG Chi-restraints excluded: chain A residue 611 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 66 random chunks: chunk 46 optimal weight: 3.9990 chunk 36 optimal weight: 0.9980 chunk 53 optimal weight: 0.7980 chunk 35 optimal weight: 0.5980 chunk 63 optimal weight: 9.9990 chunk 39 optimal weight: 0.0970 chunk 38 optimal weight: 0.7980 chunk 29 optimal weight: 0.7980 chunk 25 optimal weight: 8.9990 chunk 37 optimal weight: 0.6980 chunk 19 optimal weight: 0.8980 overall best weight: 0.5978 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 23 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 185 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8258 moved from start: 0.6002 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.026 5676 Z= 0.148 Angle : 0.397 3.880 7628 Z= 0.215 Chirality : 0.036 0.137 812 Planarity : 0.003 0.032 930 Dihedral : 17.356 176.109 1098 Min Nonbonded Distance : 2.007 Molprobity Statistics. All-atom Clashscore : 15.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.38 % Favored : 96.62 % Rotamer: Outliers : 1.67 % Allowed : 11.85 % Favored : 86.48 % 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: 2.02 (0.36), residues: 622 helix: 2.20 (0.26), residues: 423 sheet: 0.35 (0.96), residues: 24 loop : -0.70 (0.50), residues: 175 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP A 155 HIS 0.003 0.001 HIS A 619 PHE 0.007 0.001 PHE A 419 TYR 0.008 0.001 TYR A 180 ARG 0.004 0.000 ARG A 642 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1244 Ramachandran restraints generated. 622 Oldfield, 0 Emsley, 622 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1244 Ramachandran restraints generated. 622 Oldfield, 0 Emsley, 622 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 46 residues out of total 557 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 37 time to evaluate : 0.605 Fit side-chains REVERT: A 454 ARG cc_start: 0.7467 (OUTLIER) cc_final: 0.7163 (mmt-90) outliers start: 9 outliers final: 4 residues processed: 43 average time/residue: 1.3839 time to fit residues: 62.3884 Evaluate side-chains 41 residues out of total 557 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 36 time to evaluate : 0.627 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 41 LEU Chi-restraints excluded: chain A residue 421 ILE Chi-restraints excluded: chain A residue 454 ARG Chi-restraints excluded: chain A residue 526 SER Chi-restraints excluded: chain A residue 611 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 66 random chunks: chunk 12 optimal weight: 4.9990 chunk 40 optimal weight: 0.0040 chunk 43 optimal weight: 4.9990 chunk 31 optimal weight: 0.9990 chunk 5 optimal weight: 3.9990 chunk 50 optimal weight: 0.5980 chunk 57 optimal weight: 2.9990 chunk 60 optimal weight: 0.9990 chunk 55 optimal weight: 0.8980 chunk 59 optimal weight: 0.6980 chunk 35 optimal weight: 3.9990 overall best weight: 0.6394 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 23 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 185 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8259 moved from start: 0.6086 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.027 5676 Z= 0.159 Angle : 0.397 3.931 7628 Z= 0.215 Chirality : 0.037 0.139 812 Planarity : 0.003 0.031 930 Dihedral : 16.262 177.485 1098 Min Nonbonded Distance : 1.991 Molprobity Statistics. All-atom Clashscore : 15.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.22 % Favored : 96.78 % Rotamer: Outliers : 1.11 % Allowed : 12.78 % Favored : 86.11 % 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: 2.21 (0.36), residues: 622 helix: 2.38 (0.26), residues: 420 sheet: 0.54 (0.98), residues: 24 loop : -0.67 (0.50), residues: 178 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.001 TRP A 155 HIS 0.004 0.001 HIS A 619 PHE 0.007 0.001 PHE A 181 TYR 0.009 0.001 TYR A 212 ARG 0.004 0.000 ARG A 642 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1244 Ramachandran restraints generated. 622 Oldfield, 0 Emsley, 622 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1244 Ramachandran restraints generated. 622 Oldfield, 0 Emsley, 622 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 43 residues out of total 557 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 37 time to evaluate : 0.581 Fit side-chains REVERT: A 454 ARG cc_start: 0.7506 (OUTLIER) cc_final: 0.7280 (tpt170) outliers start: 6 outliers final: 3 residues processed: 40 average time/residue: 1.3734 time to fit residues: 57.6897 Evaluate side-chains 40 residues out of total 557 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 36 time to evaluate : 0.649 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 41 LEU Chi-restraints excluded: chain A residue 454 ARG Chi-restraints excluded: chain A residue 526 SER Chi-restraints excluded: chain A residue 611 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 66 random chunks: chunk 25 optimal weight: 0.0170 chunk 46 optimal weight: 4.9990 chunk 18 optimal weight: 0.3980 chunk 53 optimal weight: 0.8980 chunk 56 optimal weight: 0.9990 chunk 59 optimal weight: 2.9990 chunk 38 optimal weight: 1.9990 chunk 62 optimal weight: 4.9990 chunk 29 optimal weight: 0.6980 chunk 43 optimal weight: 4.9990 chunk 65 optimal weight: 50.0000 overall best weight: 0.6020 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 23 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 185 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8242 moved from start: 0.6174 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.026 5676 Z= 0.145 Angle : 0.381 3.859 7628 Z= 0.206 Chirality : 0.036 0.133 812 Planarity : 0.003 0.033 930 Dihedral : 15.348 179.655 1098 Min Nonbonded Distance : 1.965 Molprobity Statistics. All-atom Clashscore : 15.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.05 % Favored : 96.95 % Rotamer: Outliers : 1.11 % Allowed : 12.96 % Favored : 85.93 % 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: 2.34 (0.36), residues: 622 helix: 2.44 (0.26), residues: 422 sheet: 0.74 (0.99), residues: 24 loop : -0.58 (0.50), residues: 176 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP A 155 HIS 0.004 0.001 HIS A 619 PHE 0.008 0.001 PHE A 419 TYR 0.008 0.001 TYR A 212 ARG 0.003 0.000 ARG A 642 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1244 Ramachandran restraints generated. 622 Oldfield, 0 Emsley, 622 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1244 Ramachandran restraints generated. 622 Oldfield, 0 Emsley, 622 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 47 residues out of total 557 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 41 time to evaluate : 0.613 Fit side-chains outliers start: 6 outliers final: 3 residues processed: 45 average time/residue: 1.3425 time to fit residues: 63.4844 Evaluate side-chains 40 residues out of total 557 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 37 time to evaluate : 0.617 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 41 LEU Chi-restraints excluded: chain A residue 421 ILE Chi-restraints excluded: chain A residue 611 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 66 random chunks: chunk 60 optimal weight: 0.9990 chunk 52 optimal weight: 3.9990 chunk 5 optimal weight: 2.9990 chunk 40 optimal weight: 3.9990 chunk 32 optimal weight: 3.9990 chunk 41 optimal weight: 1.9990 chunk 55 optimal weight: 1.9990 chunk 16 optimal weight: 1.9990 chunk 48 optimal weight: 2.9990 chunk 7 optimal weight: 3.9990 chunk 14 optimal weight: 2.9990 overall best weight: 1.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 23 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 185 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8326 moved from start: 0.6197 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.045 5676 Z= 0.380 Angle : 0.502 4.487 7628 Z= 0.272 Chirality : 0.041 0.164 812 Planarity : 0.004 0.032 930 Dihedral : 15.992 178.493 1098 Min Nonbonded Distance : 1.947 Molprobity Statistics. All-atom Clashscore : 14.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.70 % Favored : 96.30 % Rotamer: Outliers : 1.11 % Allowed : 13.15 % Favored : 85.74 % 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: 1.96 (0.35), residues: 622 helix: 2.17 (0.26), residues: 420 sheet: 0.59 (0.98), residues: 24 loop : -0.74 (0.50), residues: 178 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.002 TRP A 155 HIS 0.008 0.001 HIS A 619 PHE 0.014 0.002 PHE A 193 TYR 0.015 0.001 TYR A 212 ARG 0.003 0.000 ARG A 642 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1244 Ramachandran restraints generated. 622 Oldfield, 0 Emsley, 622 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1244 Ramachandran restraints generated. 622 Oldfield, 0 Emsley, 622 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 44 residues out of total 557 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 38 time to evaluate : 0.611 Fit side-chains outliers start: 6 outliers final: 4 residues processed: 42 average time/residue: 1.4637 time to fit residues: 64.3962 Evaluate side-chains 41 residues out of total 557 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 37 time to evaluate : 0.546 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 41 LEU Chi-restraints excluded: chain A residue 46 VAL Chi-restraints excluded: chain A residue 526 SER Chi-restraints excluded: chain A residue 611 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 66 random chunks: chunk 52 optimal weight: 0.8980 chunk 21 optimal weight: 0.7980 chunk 53 optimal weight: 0.7980 chunk 6 optimal weight: 1.9990 chunk 9 optimal weight: 0.6980 chunk 46 optimal weight: 2.9990 chunk 2 optimal weight: 0.7980 chunk 37 optimal weight: 0.5980 chunk 60 optimal weight: 0.9990 chunk 35 optimal weight: 0.9980 chunk 44 optimal weight: 5.9990 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 23 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 185 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3299 r_free = 0.3299 target = 0.095914 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.2800 r_free = 0.2800 target = 0.067350 restraints weight = 8075.003| |-----------------------------------------------------------------------------| r_work (start): 0.2762 rms_B_bonded: 2.01 r_work: 0.2593 rms_B_bonded: 3.17 restraints_weight: 0.5000 r_work: 0.2450 rms_B_bonded: 4.86 restraints_weight: 0.2500 r_work (final): 0.2450 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8765 moved from start: 0.6233 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.025 5676 Z= 0.166 Angle : 0.401 3.798 7628 Z= 0.218 Chirality : 0.037 0.141 812 Planarity : 0.003 0.032 930 Dihedral : 15.297 178.893 1098 Min Nonbonded Distance : 1.955 Molprobity Statistics. All-atom Clashscore : 15.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.22 % Favored : 96.78 % Rotamer: Outliers : 0.74 % Allowed : 13.52 % Favored : 85.74 % 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: 2.21 (0.36), residues: 622 helix: 2.33 (0.26), residues: 420 sheet: 0.53 (0.96), residues: 24 loop : -0.55 (0.51), residues: 178 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP A 155 HIS 0.004 0.001 HIS A 619 PHE 0.007 0.001 PHE A 399 TYR 0.008 0.001 TYR A 212 ARG 0.004 0.000 ARG A 642 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2186.34 seconds wall clock time: 39 minutes 29.86 seconds (2369.86 seconds total)