Starting phenix.real_space_refine on Thu Dec 7 23:22:02 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7rxh_24731/12_2023/7rxh_24731_neut_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7rxh_24731/12_2023/7rxh_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_24731/12_2023/7rxh_24731.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7rxh_24731/12_2023/7rxh_24731.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7rxh_24731/12_2023/7rxh_24731_neut_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7rxh_24731/12_2023/7rxh_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: 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/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: 3.52, per 1000 atoms: 0.63 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: 2.23 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: 1.34 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: 1.39 Time building geometry restraints manager: 2.41 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: 2.890 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: 11.900 Check model and map are aligned: 0.070 Set scattering table: 0.070 Process input model: 18.970 Find NCS groups from input model: 0.140 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:11.020 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 45.220 ------------------------------------------------------------------------------- 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 : 0.577 Fit side-chains outliers start: 3 outliers final: 1 residues processed: 92 average time/residue: 1.2074 time to fit residues: 116.1638 Evaluate side-chains 51 residues out of total 557 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 50 time to evaluate : 0.584 Switching outliers to nearest non-outliers outliers start: 1 outliers final: 0 residues processed: 1 average time/residue: 0.0930 time to fit residues: 0.8973 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 176 HIS A 216 ASN A 283 GLN A 370 ASN A 438 GLN A 453 GLN A 539 ASN ** A 619 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8052 moved from start: 0.3837 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 5676 Z= 0.194 Angle : 0.617 7.084 7628 Z= 0.291 Chirality : 0.038 0.177 812 Planarity : 0.004 0.034 930 Dihedral : 23.912 172.854 1098 Min Nonbonded Distance : 2.013 Molprobity Statistics. All-atom Clashscore : 19.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.41 % Favored : 97.59 % Rotamer: Outliers : 1.85 % Allowed : 10.37 % Favored : 87.78 % 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: 0.95 (0.34), residues: 622 helix: 1.51 (0.25), residues: 425 sheet: -0.10 (0.94), residues: 24 loop : -1.49 (0.47), residues: 173 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.032 0.002 TRP A 155 HIS 0.002 0.001 HIS A 400 PHE 0.013 0.002 PHE A 456 TYR 0.017 0.001 TYR A 180 ARG 0.003 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 61 residues out of total 557 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 51 time to evaluate : 0.612 Fit side-chains outliers start: 10 outliers final: 4 residues processed: 56 average time/residue: 1.1719 time to fit residues: 69.1274 Evaluate side-chains 44 residues out of total 557 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 40 time to evaluate : 0.618 Switching outliers to nearest non-outliers outliers start: 4 outliers final: 2 residues processed: 2 average time/residue: 0.8404 time to fit residues: 2.5750 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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: 1.9990 chunk 49 optimal weight: 0.0010 chunk 40 optimal weight: 7.9990 chunk 16 optimal weight: 3.9990 chunk 60 optimal weight: 0.0020 chunk 64 optimal weight: 20.0000 chunk 53 optimal weight: 0.9980 chunk 59 optimal weight: 0.7980 chunk 20 optimal weight: 0.9980 chunk 48 optimal weight: 1.9990 overall best weight: 0.5594 ------------------------------------------------------------------------------- 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: 0.8157 moved from start: 0.4419 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.057 5676 Z= 0.164 Angle : 0.443 5.673 7628 Z= 0.231 Chirality : 0.037 0.138 812 Planarity : 0.003 0.034 930 Dihedral : 20.511 169.748 1098 Min Nonbonded Distance : 2.099 Molprobity Statistics. All-atom Clashscore : 15.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.41 % Favored : 97.59 % Rotamer: Outliers : 2.04 % Allowed : 11.85 % 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: 1.65 (0.35), residues: 622 helix: 2.05 (0.26), residues: 425 sheet: 0.30 (0.94), residues: 24 loop : -1.27 (0.47), residues: 173 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.027 0.002 TRP A 155 HIS 0.005 0.001 HIS A 619 PHE 0.009 0.001 PHE A 575 TYR 0.010 0.001 TYR A 212 ARG 0.006 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 56 residues out of total 557 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 45 time to evaluate : 0.628 Fit side-chains outliers start: 11 outliers final: 3 residues processed: 52 average time/residue: 1.2181 time to fit residues: 66.7234 Evaluate side-chains 41 residues out of total 557 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 38 time to evaluate : 0.591 Switching outliers to nearest non-outliers outliers start: 3 outliers final: 2 residues processed: 1 average time/residue: 0.0908 time to fit residues: 0.9405 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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: 0.9990 chunk 6 optimal weight: 2.9990 chunk 28 optimal weight: 5.9990 chunk 40 optimal weight: 10.0000 chunk 60 optimal weight: 2.9990 chunk 63 optimal weight: 10.0000 chunk 57 optimal weight: 2.9990 chunk 17 optimal weight: 2.9990 chunk 53 optimal weight: 0.7980 overall best weight: 2.1588 ------------------------------------------------------------------------------- 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: 0.8312 moved from start: 0.5470 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.039 5676 Z= 0.413 Angle : 0.524 5.554 7628 Z= 0.283 Chirality : 0.042 0.180 812 Planarity : 0.004 0.035 930 Dihedral : 20.087 172.441 1098 Min Nonbonded Distance : 1.954 Molprobity Statistics. All-atom Clashscore : 13.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.38 % Favored : 96.62 % Rotamer: Outliers : 2.41 % Allowed : 9.63 % 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: 1.51 (0.34), residues: 622 helix: 1.85 (0.25), residues: 423 sheet: 0.30 (0.96), residues: 24 loop : -1.01 (0.48), residues: 175 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.032 0.002 TRP A 155 HIS 0.009 0.001 HIS A 619 PHE 0.016 0.002 PHE A 193 TYR 0.015 0.002 TYR A 589 ARG 0.003 0.000 ARG A 268 *********************** 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 50 residues out of total 557 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 37 time to evaluate : 0.606 Fit side-chains outliers start: 13 outliers final: 3 residues processed: 47 average time/residue: 1.2043 time to fit residues: 59.7136 Evaluate side-chains 37 residues out of total 557 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 34 time to evaluate : 0.611 Switching outliers to nearest non-outliers outliers start: 3 outliers final: 2 residues processed: 1 average time/residue: 2.1206 time to fit residues: 2.9890 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 66 random chunks: chunk 36 optimal weight: 0.2980 chunk 0 optimal weight: 2.9990 chunk 47 optimal weight: 0.7980 chunk 26 optimal weight: 0.9980 chunk 54 optimal weight: 0.8980 chunk 44 optimal weight: 5.9990 chunk 32 optimal weight: 2.9990 chunk 57 optimal weight: 2.9990 chunk 16 optimal weight: 2.9990 chunk 21 optimal weight: 0.6980 chunk 12 optimal weight: 0.5980 overall best weight: 0.6580 ------------------------------------------------------------------------------- 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: 0.8249 moved from start: 0.5628 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.025 5676 Z= 0.156 Angle : 0.399 3.928 7628 Z= 0.216 Chirality : 0.036 0.142 812 Planarity : 0.003 0.030 930 Dihedral : 18.175 173.617 1098 Min Nonbonded Distance : 2.003 Molprobity Statistics. All-atom Clashscore : 14.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.89 % Favored : 97.11 % Rotamer: Outliers : 1.30 % Allowed : 11.67 % Favored : 87.04 % 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: 1.87 (0.35), residues: 622 helix: 2.12 (0.26), residues: 424 sheet: 0.47 (0.97), residues: 24 loop : -0.90 (0.49), residues: 174 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.002 TRP A 155 HIS 0.004 0.001 HIS A 619 PHE 0.006 0.001 PHE A 181 TYR 0.008 0.001 TYR A 212 ARG 0.003 0.000 ARG A 642 *********************** 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 42 residues out of total 557 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 35 time to evaluate : 0.623 Fit side-chains outliers start: 7 outliers final: 2 residues processed: 40 average time/residue: 1.3780 time to fit residues: 58.0265 Evaluate side-chains 38 residues out of total 557 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 36 time to evaluate : 0.615 Switching outliers to nearest non-outliers outliers start: 2 outliers final: 1 residues processed: 1 average time/residue: 0.0993 time to fit residues: 0.9556 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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: 9.9990 chunk 53 optimal weight: 0.7980 chunk 29 optimal weight: 1.9990 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: 2.9990 chunk 36 optimal weight: 0.9980 overall best weight: 1.7586 ------------------------------------------------------------------------------- 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: 0.8317 moved from start: 0.5821 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.042 5676 Z= 0.342 Angle : 0.487 4.981 7628 Z= 0.265 Chirality : 0.040 0.169 812 Planarity : 0.004 0.034 930 Dihedral : 18.086 172.358 1098 Min Nonbonded Distance : 2.034 Molprobity Statistics. All-atom Clashscore : 13.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.86 % Favored : 96.14 % Rotamer: Outliers : 1.85 % Allowed : 10.74 % Favored : 87.41 % 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: 1.79 (0.35), residues: 622 helix: 2.05 (0.26), residues: 423 sheet: 0.39 (0.96), residues: 24 loop : -0.86 (0.49), residues: 175 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.029 0.002 TRP A 155 HIS 0.008 0.001 HIS A 619 PHE 0.014 0.002 PHE A 193 TYR 0.015 0.002 TYR A 212 ARG 0.004 0.000 ARG A 268 *********************** 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 49 residues out of total 557 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 39 time to evaluate : 0.609 Fit side-chains outliers start: 10 outliers final: 2 residues processed: 47 average time/residue: 1.4269 time to fit residues: 70.1623 Evaluate side-chains 39 residues out of total 557 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 37 time to evaluate : 0.592 Switching outliers to nearest non-outliers outliers start: 2 outliers final: 2 residues processed: 0 time to fit residues: 0.7537 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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: 0.6980 chunk 53 optimal weight: 0.9980 chunk 35 optimal weight: 0.5980 chunk 63 optimal weight: 9.9990 chunk 39 optimal weight: 3.9990 chunk 38 optimal weight: 2.9990 chunk 29 optimal weight: 0.8980 chunk 25 optimal weight: 10.0000 chunk 37 optimal weight: 0.7980 chunk 19 optimal weight: 0.4980 overall best weight: 0.6980 ------------------------------------------------------------------------------- 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: 0.8264 moved from start: 0.5922 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.024 5676 Z= 0.159 Angle : 0.400 3.856 7628 Z= 0.217 Chirality : 0.037 0.143 812 Planarity : 0.003 0.030 930 Dihedral : 17.001 173.779 1098 Min Nonbonded Distance : 2.002 Molprobity Statistics. All-atom Clashscore : 15.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.38 % Favored : 96.62 % Rotamer: Outliers : 1.11 % Allowed : 11.30 % 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: 2.07 (0.36), residues: 622 helix: 2.25 (0.26), residues: 423 sheet: 0.48 (0.96), residues: 24 loop : -0.72 (0.50), residues: 175 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.002 TRP A 155 HIS 0.003 0.001 HIS A 619 PHE 0.005 0.001 PHE A 615 TYR 0.008 0.001 TYR A 212 ARG 0.004 0.000 ARG A 268 *********************** 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 45 residues out of total 557 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 39 time to evaluate : 0.614 Fit side-chains outliers start: 6 outliers final: 2 residues processed: 43 average time/residue: 1.3484 time to fit residues: 60.9136 Evaluate side-chains 40 residues out of total 557 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 38 time to evaluate : 0.598 Switching outliers to nearest non-outliers outliers start: 2 outliers final: 1 residues processed: 1 average time/residue: 0.0988 time to fit residues: 0.9270 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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: 0.0770 chunk 43 optimal weight: 4.9990 chunk 31 optimal weight: 0.6980 chunk 5 optimal weight: 2.9990 chunk 50 optimal weight: 0.6980 chunk 57 optimal weight: 2.9990 chunk 60 optimal weight: 3.9990 chunk 55 optimal weight: 0.6980 chunk 59 optimal weight: 2.9990 chunk 35 optimal weight: 3.9990 overall best weight: 1.0340 ------------------------------------------------------------------------------- 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: 0.8287 moved from start: 0.6023 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 5676 Z= 0.213 Angle : 0.429 4.204 7628 Z= 0.234 Chirality : 0.038 0.145 812 Planarity : 0.003 0.033 930 Dihedral : 16.354 174.312 1098 Min Nonbonded Distance : 1.970 Molprobity Statistics. All-atom Clashscore : 14.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.54 % Favored : 96.46 % Rotamer: Outliers : 0.56 % Allowed : 12.22 % 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: 2.10 (0.36), residues: 622 helix: 2.29 (0.26), residues: 420 sheet: 0.55 (0.96), residues: 24 loop : -0.73 (0.50), residues: 178 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.026 0.002 TRP A 155 HIS 0.005 0.001 HIS A 619 PHE 0.010 0.001 PHE A 193 TYR 0.012 0.001 TYR A 212 ARG 0.003 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 44 residues out of total 557 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 41 time to evaluate : 0.614 Fit side-chains outliers start: 3 outliers final: 1 residues processed: 44 average time/residue: 1.2886 time to fit residues: 59.5941 Evaluate side-chains 41 residues out of total 557 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 40 time to evaluate : 0.565 Switching outliers to nearest non-outliers outliers start: 1 outliers final: 1 residues processed: 0 time to fit residues: 0.8062 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 66 random chunks: chunk 25 optimal weight: 0.9980 chunk 46 optimal weight: 3.9990 chunk 18 optimal weight: 0.6980 chunk 53 optimal weight: 0.7980 chunk 56 optimal weight: 2.9990 chunk 59 optimal weight: 2.9990 chunk 38 optimal weight: 0.7980 chunk 62 optimal weight: 4.9990 chunk 29 optimal weight: 0.6980 chunk 43 optimal weight: 0.9980 chunk 65 optimal weight: 50.0000 overall best weight: 0.7980 ------------------------------------------------------------------------------- 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: 0.8267 moved from start: 0.6089 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= 0.172 Angle : 0.400 3.887 7628 Z= 0.217 Chirality : 0.037 0.141 812 Planarity : 0.003 0.030 930 Dihedral : 15.760 175.259 1098 Min Nonbonded Distance : 1.970 Molprobity Statistics. All-atom Clashscore : 15.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.38 % Favored : 96.62 % Rotamer: Outliers : 1.11 % Allowed : 11.85 % Favored : 87.04 % 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: 2.18 (0.36), residues: 622 helix: 2.36 (0.26), residues: 420 sheet: 0.57 (0.95), residues: 24 loop : -0.69 (0.50), residues: 178 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.002 TRP A 155 HIS 0.004 0.001 HIS A 619 PHE 0.007 0.001 PHE A 193 TYR 0.009 0.001 TYR A 212 ARG 0.003 0.000 ARG A 268 *********************** 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 45 residues out of total 557 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 39 time to evaluate : 0.589 Fit side-chains outliers start: 6 outliers final: 5 residues processed: 42 average time/residue: 1.3379 time to fit residues: 59.0474 Evaluate side-chains 45 residues out of total 557 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 40 time to evaluate : 0.671 Switching outliers to nearest non-outliers outliers start: 5 outliers final: 1 residues processed: 4 average time/residue: 0.4554 time to fit residues: 2.8215 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 66 random chunks: chunk 60 optimal weight: 0.3980 chunk 52 optimal weight: 0.8980 chunk 5 optimal weight: 3.9990 chunk 40 optimal weight: 2.9990 chunk 32 optimal weight: 3.9990 chunk 41 optimal weight: 0.9980 chunk 55 optimal weight: 3.9990 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: 1.4584 ------------------------------------------------------------------------------- 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: 0.8306 moved from start: 0.6143 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 5676 Z= 0.287 Angle : 0.454 4.362 7628 Z= 0.247 Chirality : 0.039 0.156 812 Planarity : 0.003 0.032 930 Dihedral : 15.813 174.818 1098 Min Nonbonded Distance : 1.995 Molprobity Statistics. All-atom Clashscore : 13.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.86 % Favored : 96.14 % Rotamer: Outliers : 0.74 % Allowed : 12.22 % Favored : 87.04 % 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: 2.05 (0.36), residues: 622 helix: 2.26 (0.26), residues: 420 sheet: 0.57 (0.97), residues: 24 loop : -0.77 (0.50), residues: 178 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.026 0.002 TRP A 155 HIS 0.006 0.001 HIS A 619 PHE 0.011 0.001 PHE A 193 TYR 0.013 0.001 TYR A 212 ARG 0.004 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 42 residues out of total 557 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 38 time to evaluate : 0.632 Fit side-chains outliers start: 4 outliers final: 1 residues processed: 41 average time/residue: 1.4304 time to fit residues: 61.9171 Evaluate side-chains 39 residues out of total 557 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 38 time to evaluate : 0.649 Switching outliers to nearest non-outliers outliers start: 1 outliers final: 1 residues processed: 0 time to fit residues: 0.8669 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 66 random chunks: chunk 52 optimal weight: 0.9980 chunk 21 optimal weight: 0.7980 chunk 53 optimal weight: 0.8980 chunk 6 optimal weight: 2.9990 chunk 9 optimal weight: 1.9990 chunk 46 optimal weight: 0.8980 chunk 2 optimal weight: 0.9980 chunk 37 optimal weight: 0.0870 chunk 60 optimal weight: 0.3980 chunk 35 optimal weight: 1.9990 chunk 44 optimal weight: 3.9990 overall best weight: 0.6158 ------------------------------------------------------------------------------- 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 = 0.3307 r_free = 0.3307 target = 0.096592 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.2813 r_free = 0.2813 target = 0.068000 restraints weight = 8058.382| |-----------------------------------------------------------------------------| r_work (start): 0.2769 rms_B_bonded: 2.01 r_work: 0.2596 rms_B_bonded: 3.21 restraints_weight: 0.5000 r_work: 0.2449 rms_B_bonded: 4.92 restraints_weight: 0.2500 r_work (final): 0.2449 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8756 moved from start: 0.6178 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= 0.151 Angle : 0.394 3.832 7628 Z= 0.214 Chirality : 0.036 0.139 812 Planarity : 0.003 0.029 930 Dihedral : 15.200 176.057 1098 Min Nonbonded Distance : 2.011 Molprobity Statistics. All-atom Clashscore : 15.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.22 % Favored : 96.78 % Rotamer: Outliers : 0.37 % Allowed : 12.59 % Favored : 87.04 % 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: 2.24 (0.36), residues: 622 helix: 2.38 (0.26), residues: 420 sheet: 0.67 (0.97), residues: 24 loop : -0.62 (0.51), residues: 178 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.002 TRP A 155 HIS 0.004 0.001 HIS A 619 PHE 0.006 0.001 PHE A 399 TYR 0.009 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: 2177.27 seconds wall clock time: 39 minutes 32.20 seconds (2372.20 seconds total)