Starting phenix.real_space_refine (version: 1.21rc1) on Thu Apr 20 05:36:58 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7rxh_24731/04_2023/7rxh_24731_neut_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7rxh_24731/04_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_24731/04_2023/7rxh_24731.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7rxh_24731/04_2023/7rxh_24731.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7rxh_24731/04_2023/7rxh_24731_neut_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7rxh_24731/04_2023/7rxh_24731_neut_updated.pdb" } resolution = 2.3 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 sd= 0.001 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-1.21rc1-4938/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: 331 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: 3.42, per 1000 atoms: 0.61 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: 2.15 Conformation dependent library (CDL) restraints added in 704.6 milliseconds 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: 0.56 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: 1.52 Time building geometry restraints manager: 2.35 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 - 32.34: 3165 32.34 - 64.67: 167 64.67 - 97.01: 20 97.01 - 129.35: 2 129.35 - 161.68: 3 Dihedral angle restraints: 3357 sinusoidal: 1507 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=" C01 PGW A 811 " pdb=" C19 PGW A 811 " pdb=" O03 PGW A 811 " pdb=" O04 PGW A 811 " ideal model delta sinusoidal sigma weight residual 9.00 -152.68 161.68 1 3.00e+01 1.11e-03 2.08e+01 dihedral pdb=" C08 PGW A 813 " pdb=" C06 PGW A 813 " pdb=" C07 PGW A 813 " pdb=" C10 PGW A 813 " ideal model delta sinusoidal sigma weight residual 178.64 -20.24 -161.12 1 3.00e+01 1.11e-03 2.08e+01 ... (remaining 3354 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: 3.080 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 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: 17.840 Find NCS groups from input model: 0.160 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:12.190 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 45.310 ------------------------------------------------------------------------------- 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 : 19.483 161.685 2157 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 % 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 *********************** 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 : 0.668 Fit side-chains outliers start: 3 outliers final: 1 residues processed: 92 average time/residue: 1.2377 time to fit residues: 119.2021 Evaluate side-chains 51 residues out of total 557 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 50 time to evaluate : 0.643 Switching outliers to nearest non-outliers outliers start: 1 outliers final: 0 residues processed: 1 average time/residue: 0.1147 time to fit residues: 1.0386 ------------------------------------------------------------------------------- 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 ** both conformations clash, **PLEASE CHECK MANUALLY** A 148 ASN A 171 ASN A 176 HIS 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: 10 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8038 moved from start: 0.3542 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.036 5676 Z= 0.188 Angle : 0.545 6.270 7628 Z= 0.268 Chirality : 0.037 0.160 812 Planarity : 0.004 0.033 930 Dihedral : 17.200 156.246 981 Min Nonbonded Distance : 2.017 Molprobity Statistics. All-atom Clashscore : 18.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.25 % Favored : 97.75 % Rotamer Outliers : 1.67 % 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: 1.54 (0.25), residues: 425 sheet: -0.26 (0.93), residues: 24 loop : -1.53 (0.47), residues: 173 *********************** 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 60 residues out of total 557 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 51 time to evaluate : 0.647 Fit side-chains outliers start: 9 outliers final: 3 residues processed: 55 average time/residue: 1.2233 time to fit residues: 70.9676 Evaluate side-chains 42 residues out of total 557 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 39 time to evaluate : 0.642 Switching outliers to nearest non-outliers outliers start: 3 outliers final: 1 residues processed: 2 average time/residue: 0.9501 time to fit residues: 2.8844 ------------------------------------------------------------------------------- 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: 2.9990 chunk 49 optimal weight: 0.8980 chunk 40 optimal weight: 10.0000 chunk 16 optimal weight: 3.9990 chunk 60 optimal weight: 2.9990 chunk 64 optimal weight: 20.0000 chunk 53 optimal weight: 0.9980 chunk 59 optimal weight: 2.9990 chunk 20 optimal weight: 0.9980 chunk 48 optimal weight: 0.5980 overall best weight: 1.2982 ------------------------------------------------------------------------------- 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: 0.8284 moved from start: 0.5254 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.044 5676 Z= 0.273 Angle : 0.514 5.257 7628 Z= 0.277 Chirality : 0.039 0.161 812 Planarity : 0.004 0.040 930 Dihedral : 15.770 154.200 981 Min Nonbonded Distance : 1.976 Molprobity Statistics. All-atom Clashscore : 13.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.54 % Favored : 96.46 % Rotamer Outliers : 2.04 % 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: 1.33 (0.34), residues: 622 helix: 1.74 (0.25), residues: 424 sheet: 0.11 (0.91), residues: 24 loop : -1.15 (0.47), residues: 174 *********************** 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 50 residues out of total 557 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 39 time to evaluate : 0.603 Fit side-chains outliers start: 11 outliers final: 3 residues processed: 46 average time/residue: 1.2079 time to fit residues: 58.6809 Evaluate side-chains 38 residues out of total 557 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 35 time to evaluate : 0.614 Switching outliers to nearest non-outliers outliers start: 3 outliers final: 2 residues processed: 1 average time/residue: 2.0920 time to fit residues: 2.9949 ------------------------------------------------------------------------------- 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: 3.9990 chunk 31 optimal weight: 0.9990 chunk 6 optimal weight: 2.9990 chunk 28 optimal weight: 4.9990 chunk 40 optimal weight: 10.0000 chunk 60 optimal weight: 0.7980 chunk 63 optimal weight: 9.9990 chunk 57 optimal weight: 2.9990 chunk 17 optimal weight: 2.9990 chunk 53 optimal weight: 0.0980 overall best weight: 1.5786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 23 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8303 moved from start: 0.5675 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.031 5676 Z= 0.301 Angle : 0.466 5.343 7628 Z= 0.254 Chirality : 0.039 0.167 812 Planarity : 0.004 0.036 930 Dihedral : 14.876 152.790 981 Min Nonbonded Distance : 2.045 Molprobity Statistics. All-atom Clashscore : 13.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.86 % Favored : 96.14 % Rotamer Outliers : 2.41 % 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: 1.58 (0.35), residues: 622 helix: 1.91 (0.26), residues: 424 sheet: 0.20 (0.95), residues: 24 loop : -1.00 (0.49), residues: 174 *********************** 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 51 residues out of total 557 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 38 time to evaluate : 0.667 Fit side-chains outliers start: 13 outliers final: 5 residues processed: 48 average time/residue: 1.2897 time to fit residues: 65.2362 Evaluate side-chains 38 residues out of total 557 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 33 time to evaluate : 0.657 Switching outliers to nearest non-outliers outliers start: 5 outliers final: 2 residues processed: 3 average time/residue: 0.0837 time to fit residues: 1.2501 ------------------------------------------------------------------------------- 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: 1.9990 chunk 0 optimal weight: 3.9990 chunk 47 optimal weight: 2.9990 chunk 26 optimal weight: 0.3980 chunk 54 optimal weight: 2.9990 chunk 44 optimal weight: 2.9990 chunk 32 optimal weight: 3.9990 chunk 57 optimal weight: 3.9990 chunk 16 optimal weight: 2.9990 chunk 21 optimal weight: 1.9990 chunk 12 optimal weight: 0.7980 overall best weight: 1.6386 ------------------------------------------------------------------------------- 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: 0.8322 moved from start: 0.5872 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.037 5676 Z= 0.316 Angle : 0.477 4.578 7628 Z= 0.262 Chirality : 0.040 0.167 812 Planarity : 0.004 0.037 930 Dihedral : 14.155 131.248 981 Min Nonbonded Distance : 2.036 Molprobity Statistics. All-atom Clashscore : 12.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.18 % Favored : 95.82 % Rotamer Outliers : 1.85 % 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: 1.67 (0.35), residues: 622 helix: 1.95 (0.26), residues: 423 sheet: 0.36 (0.98), residues: 24 loop : -0.87 (0.49), residues: 175 *********************** 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: 10 poor density : 35 time to evaluate : 0.599 Fit side-chains outliers start: 10 outliers final: 3 residues processed: 43 average time/residue: 1.5464 time to fit residues: 69.6223 Evaluate side-chains 37 residues out of total 557 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 34 time to evaluate : 0.649 Switching outliers to nearest non-outliers outliers start: 3 outliers final: 2 residues processed: 1 average time/residue: 1.7769 time to fit residues: 2.6896 ------------------------------------------------------------------------------- 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: 0.7980 chunk 15 optimal weight: 2.9990 chunk 63 optimal weight: 9.9990 chunk 53 optimal weight: 0.9990 chunk 29 optimal weight: 1.9990 chunk 5 optimal weight: 1.9990 chunk 21 optimal weight: 1.9990 chunk 33 optimal weight: 3.9990 chunk 61 optimal weight: 2.9990 chunk 7 optimal weight: 0.0870 chunk 36 optimal weight: 0.7980 overall best weight: 0.9362 ------------------------------------------------------------------------------- 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 A 185 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8285 moved from start: 0.5966 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.027 5676 Z= 0.197 Angle : 0.404 3.992 7628 Z= 0.222 Chirality : 0.037 0.148 812 Planarity : 0.003 0.033 930 Dihedral : 13.115 101.344 981 Min Nonbonded Distance : 2.041 Molprobity Statistics. All-atom Clashscore : 13.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.54 % Favored : 96.46 % Rotamer Outliers : 1.85 % 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: 1.93 (0.35), residues: 622 helix: 2.18 (0.26), residues: 423 sheet: 0.39 (0.97), residues: 24 loop : -0.87 (0.49), residues: 175 *********************** 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 : 0.680 Fit side-chains outliers start: 10 outliers final: 4 residues processed: 46 average time/residue: 1.4029 time to fit residues: 67.8058 Evaluate side-chains 38 residues out of total 557 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 34 time to evaluate : 0.670 Switching outliers to nearest non-outliers outliers start: 4 outliers final: 4 residues processed: 0 time to fit residues: 0.8583 ------------------------------------------------------------------------------- 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: 0.7980 chunk 35 optimal weight: 1.9990 chunk 63 optimal weight: 9.9990 chunk 39 optimal weight: 6.9990 chunk 38 optimal weight: 0.9990 chunk 29 optimal weight: 0.6980 chunk 25 optimal weight: 9.9990 chunk 37 optimal weight: 0.9990 chunk 19 optimal weight: 3.9990 overall best weight: 0.8384 ------------------------------------------------------------------------------- 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: 0.8281 moved from start: 0.6015 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.026 5676 Z= 0.182 Angle : 0.399 3.969 7628 Z= 0.219 Chirality : 0.037 0.150 812 Planarity : 0.003 0.033 930 Dihedral : 12.554 84.792 981 Min Nonbonded Distance : 2.038 Molprobity Statistics. All-atom Clashscore : 14.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.70 % Favored : 96.30 % Rotamer Outliers : 1.48 % 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: 2.00 (0.36), residues: 622 helix: 2.28 (0.26), residues: 419 sheet: 0.48 (0.97), residues: 24 loop : -0.92 (0.49), residues: 179 *********************** 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 43 residues out of total 557 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 35 time to evaluate : 0.681 Fit side-chains outliers start: 8 outliers final: 4 residues processed: 42 average time/residue: 1.4527 time to fit residues: 64.0932 Evaluate side-chains 37 residues out of total 557 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 33 time to evaluate : 0.640 Switching outliers to nearest non-outliers outliers start: 4 outliers final: 3 residues processed: 1 average time/residue: 0.0973 time to fit residues: 0.9916 ------------------------------------------------------------------------------- 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: 2.9990 chunk 40 optimal weight: 0.0980 chunk 43 optimal weight: 4.9990 chunk 31 optimal weight: 1.9990 chunk 5 optimal weight: 3.9990 chunk 50 optimal weight: 0.8980 chunk 57 optimal weight: 3.9990 chunk 60 optimal weight: 0.8980 chunk 55 optimal weight: 1.9990 chunk 59 optimal weight: 2.9990 chunk 35 optimal weight: 3.9990 overall best weight: 1.1784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 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: 0.8301 moved from start: 0.6065 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.033 5676 Z= 0.238 Angle : 0.425 4.133 7628 Z= 0.233 Chirality : 0.038 0.153 812 Planarity : 0.003 0.033 930 Dihedral : 12.367 83.676 981 Min Nonbonded Distance : 2.031 Molprobity Statistics. All-atom Clashscore : 13.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.70 % Favored : 96.30 % Rotamer Outliers : 1.48 % 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: 2.00 (0.35), residues: 622 helix: 2.26 (0.26), residues: 420 sheet: 0.47 (0.97), residues: 24 loop : -0.87 (0.49), residues: 178 *********************** 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 42 residues out of total 557 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 34 time to evaluate : 0.667 Fit side-chains outliers start: 8 outliers final: 5 residues processed: 40 average time/residue: 1.5503 time to fit residues: 65.0127 Evaluate side-chains 41 residues out of total 557 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 36 time to evaluate : 0.652 Switching outliers to nearest non-outliers outliers start: 5 outliers final: 2 residues processed: 3 average time/residue: 0.6288 time to fit residues: 2.8821 ------------------------------------------------------------------------------- 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: 0.0870 chunk 46 optimal weight: 3.9990 chunk 18 optimal weight: 0.6980 chunk 53 optimal weight: 0.9990 chunk 56 optimal weight: 1.9990 chunk 59 optimal weight: 0.5980 chunk 38 optimal weight: 0.6980 chunk 62 optimal weight: 3.9990 chunk 29 optimal weight: 0.9980 chunk 43 optimal weight: 3.9990 chunk 65 optimal weight: 40.0000 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8266 moved from start: 0.6107 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= 0.150 Angle : 0.381 3.872 7628 Z= 0.208 Chirality : 0.036 0.140 812 Planarity : 0.003 0.030 930 Dihedral : 11.836 83.079 981 Min Nonbonded Distance : 2.018 Molprobity Statistics. All-atom Clashscore : 14.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.22 % Favored : 96.78 % Rotamer Outliers : 0.74 % 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: 2.17 (0.36), residues: 622 helix: 2.38 (0.26), residues: 421 sheet: 0.53 (0.96), residues: 24 loop : -0.79 (0.50), residues: 177 *********************** 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 43 residues out of total 557 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 39 time to evaluate : 0.632 Fit side-chains outliers start: 4 outliers final: 2 residues processed: 42 average time/residue: 1.4849 time to fit residues: 65.4090 Evaluate side-chains 38 residues out of total 557 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 36 time to evaluate : 0.670 Switching outliers to nearest non-outliers outliers start: 2 outliers final: 2 residues processed: 0 time to fit residues: 0.7760 ------------------------------------------------------------------------------- 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: 0.2980 chunk 52 optimal weight: 3.9990 chunk 5 optimal weight: 3.9990 chunk 40 optimal weight: 0.7980 chunk 32 optimal weight: 3.9990 chunk 41 optimal weight: 1.9990 chunk 55 optimal weight: 0.9980 chunk 16 optimal weight: 0.5980 chunk 48 optimal weight: 2.9990 chunk 7 optimal weight: 3.9990 chunk 14 optimal weight: 2.9990 overall best weight: 0.9382 ------------------------------------------------------------------------------- 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: 0.8285 moved from start: 0.6144 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.029 5676 Z= 0.199 Angle : 0.402 3.979 7628 Z= 0.221 Chirality : 0.037 0.147 812 Planarity : 0.003 0.032 930 Dihedral : 11.684 82.136 981 Min Nonbonded Distance : 2.023 Molprobity Statistics. All-atom Clashscore : 14.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.22 % Favored : 96.78 % Rotamer Outliers : 0.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.20 (0.36), residues: 622 helix: 2.39 (0.26), residues: 420 sheet: 0.56 (0.96), residues: 24 loop : -0.75 (0.50), residues: 178 ********************** 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 39 residues out of total 557 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 36 time to evaluate : 0.619 Fit side-chains outliers start: 3 outliers final: 2 residues processed: 39 average time/residue: 1.5090 time to fit residues: 61.7261 Evaluate side-chains 38 residues out of total 557 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 36 time to evaluate : 0.654 Switching outliers to nearest non-outliers outliers start: 2 outliers final: 2 residues processed: 0 time to fit residues: 0.8694 ------------------------------------------------------------------------------- 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: 1.9990 chunk 21 optimal weight: 1.9990 chunk 53 optimal weight: 0.8980 chunk 6 optimal weight: 1.9990 chunk 9 optimal weight: 0.9990 chunk 46 optimal weight: 2.9990 chunk 2 optimal weight: 1.9990 chunk 37 optimal weight: 3.9990 chunk 60 optimal weight: 0.9990 chunk 35 optimal weight: 3.9990 chunk 44 optimal weight: 5.9990 overall best weight: 1.3788 ------------------------------------------------------------------------------- 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 = 0.3258 r_free = 0.3258 target = 0.093266 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.2750 r_free = 0.2750 target = 0.064751 restraints weight = 8096.376| |-----------------------------------------------------------------------------| r_work (start): 0.2718 rms_B_bonded: 1.99 r_work: 0.2543 rms_B_bonded: 3.16 restraints_weight: 0.5000 r_work: 0.2398 rms_B_bonded: 4.82 restraints_weight: 0.2500 r_work (final): 0.2398 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8803 moved from start: 0.6172 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.035 5676 Z= 0.271 Angle : 0.439 4.275 7628 Z= 0.241 Chirality : 0.039 0.158 812 Planarity : 0.003 0.033 930 Dihedral : 11.832 80.728 981 Min Nonbonded Distance : 2.016 Molprobity Statistics. All-atom Clashscore : 13.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.70 % Favored : 96.30 % Rotamer Outliers : 1.30 % 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: 2.12 (0.36), residues: 622 helix: 2.31 (0.26), residues: 420 sheet: 0.44 (0.96), residues: 24 loop : -0.71 (0.50), residues: 178 =============================================================================== Job complete usr+sys time: 2130.21 seconds wall clock time: 38 minutes 30.42 seconds (2310.42 seconds total)