Starting phenix.real_space_refine on Sun Mar 10 21:26:49 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8jpd_36476/03_2024/8jpd_36476_neut_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8jpd_36476/03_2024/8jpd_36476.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.81 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8jpd_36476/03_2024/8jpd_36476.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8jpd_36476/03_2024/8jpd_36476.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8jpd_36476/03_2024/8jpd_36476_neut_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8jpd_36476/03_2024/8jpd_36476_neut_updated.pdb" } resolution = 2.81 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= 0.001 sd= 0.064 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: 4 Type Number sf(0) Gaussians S 37 5.16 5 C 3330 2.51 5 N 891 2.21 5 O 940 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "G GLU 52": "OE1" <-> "OE2" Residue "G GLU 87": "OE1" <-> "OE2" Residue "G GLU 88": "OE1" <-> "OE2" Residue "G GLU 116": "OE1" <-> "OE2" Residue "G ASP 169": "OD1" <-> "OD2" Residue "G GLU 204": "OE1" <-> "OE2" Residue "G ASP 212": "OD1" <-> "OD2" Residue "G PHE 253": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G PHE 261": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G ASP 272": "OD1" <-> "OD2" Residue "G ASP 278": "OD1" <-> "OD2" Residue "G GLU 300": "OE1" <-> "OE2" Residue "G PHE 342": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G ASP 403": "OD1" <-> "OD2" Residue "G ASP 455": "OD1" <-> "OD2" Residue "G ASP 481": "OD1" <-> "OD2" Residue "G GLU 523": "OE1" <-> "OE2" Residue "G GLU 537": "OE1" <-> "OE2" Residue "G GLU 604": "OE1" <-> "OE2" Residue "G PHE 630": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G GLU 639": "OE1" <-> "OE2" Residue "G GLU 653": "OE1" <-> "OE2" Time to flip residues: 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 5198 Number of models: 1 Model: "" Number of chains: 2 Chain: "G" Number of atoms: 5163 Number of conformers: 1 Conformer: "" Number of residues, atoms: 658, 5163 Classifications: {'peptide': 658} Incomplete info: {'truncation_to_alanine': 50} Link IDs: {'PTRANS': 28, 'TRANS': 629} Unresolved non-hydrogen bonds: 197 Unresolved non-hydrogen angles: 240 Unresolved non-hydrogen dihedrals: 161 Unresolved non-hydrogen chiralities: 7 Planarities with less than four sites: {'GLN:plan1': 4, 'ASP:plan': 8, 'TYR:plan': 1, 'ASN:plan1': 1, 'HIS:plan': 2, 'GLU:plan': 12, 'ARG:plan': 4} Unresolved non-hydrogen planarities: 128 Chain: "G" Number of atoms: 35 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 35 Unusual residues: {'STU': 1} Classifications: {'undetermined': 1} Time building chain proxies: 3.46, per 1000 atoms: 0.67 Number of scatterers: 5198 At special positions: 0 Unit cell: (81.576, 104.648, 88.992, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 37 16.00 O 940 8.00 N 891 7.00 C 3330 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 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 954.2 milliseconds 1312 Ramachandran restraints generated. 656 Oldfield, 0 Emsley, 656 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1240 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 32 helices and 5 sheets defined 48.5% alpha, 12.5% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.26 Creating SS restraints... Processing helix chain 'G' and resid 4 through 18 Processing helix chain 'G' and resid 24 through 27 Processing helix chain 'G' and resid 37 through 50 removed outlier: 3.594A pdb=" N ARG G 40 " --> pdb=" O PRO G 37 " (cutoff:3.500A) removed outlier: 3.519A pdb=" N MET G 43 " --> pdb=" O ARG G 40 " (cutoff:3.500A) removed outlier: 4.512A pdb=" N GLN G 44 " --> pdb=" O SER G 41 " (cutoff:3.500A) removed outlier: 3.668A pdb=" N ASP G 49 " --> pdb=" O TYR G 46 " (cutoff:3.500A) Processing helix chain 'G' and resid 55 through 59 Processing helix chain 'G' and resid 62 through 75 Processing helix chain 'G' and resid 77 through 94 Proline residue: G 81 - end of helix removed outlier: 3.687A pdb=" N LYS G 94 " --> pdb=" O LYS G 90 " (cutoff:3.500A) Processing helix chain 'G' and resid 98 through 112 removed outlier: 4.148A pdb=" N VAL G 103 " --> pdb=" O GLU G 99 " (cutoff:3.500A) Processing helix chain 'G' and resid 114 through 119 Processing helix chain 'G' and resid 126 through 137 Processing helix chain 'G' and resid 147 through 157 Processing helix chain 'G' and resid 160 through 167 Processing helix chain 'G' and resid 169 through 182 Processing helix chain 'G' and resid 188 through 190 No H-bonds generated for 'chain 'G' and resid 188 through 190' Processing helix chain 'G' and resid 224 through 229 Processing helix chain 'G' and resid 233 through 247 Processing helix chain 'G' and resid 279 through 286 Processing helix chain 'G' and resid 291 through 311 removed outlier: 4.156A pdb=" N PHE G 296 " --> pdb=" O PRO G 292 " (cutoff:3.500A) removed outlier: 3.901A pdb=" N TYR G 297 " --> pdb=" O ASP G 293 " (cutoff:3.500A) removed outlier: 3.661A pdb=" N ARG G 311 " --> pdb=" O HIS G 307 " (cutoff:3.500A) Processing helix chain 'G' and resid 320 through 322 No H-bonds generated for 'chain 'G' and resid 320 through 322' Processing helix chain 'G' and resid 359 through 362 No H-bonds generated for 'chain 'G' and resid 359 through 362' Processing helix chain 'G' and resid 370 through 386 removed outlier: 3.520A pdb=" N SER G 376 " --> pdb=" O ASP G 373 " (cutoff:3.500A) Processing helix chain 'G' and resid 399 through 407 removed outlier: 4.781A pdb=" N MET G 405 " --> pdb=" O GLU G 401 " (cutoff:3.500A) removed outlier: 5.375A pdb=" N THR G 406 " --> pdb=" O ILE G 402 " (cutoff:3.500A) removed outlier: 4.925A pdb=" N LEU G 407 " --> pdb=" O ASP G 403 " (cutoff:3.500A) Processing helix chain 'G' and resid 419 through 428 Processing helix chain 'G' and resid 444 through 448 Processing helix chain 'G' and resid 451 through 453 No H-bonds generated for 'chain 'G' and resid 451 through 453' Processing helix chain 'G' and resid 458 through 463 Processing helix chain 'G' and resid 482 through 485 No H-bonds generated for 'chain 'G' and resid 482 through 485' Processing helix chain 'G' and resid 490 through 493 Processing helix chain 'G' and resid 500 through 506 removed outlier: 4.038A pdb=" N LEU G 505 " --> pdb=" O SER G 501 " (cutoff:3.500A) removed outlier: 4.184A pdb=" N TYR G 506 " --> pdb=" O ASP G 502 " (cutoff:3.500A) Processing helix chain 'G' and resid 514 through 524 Processing helix chain 'G' and resid 526 through 547 Processing helix chain 'G' and resid 603 through 605 No H-bonds generated for 'chain 'G' and resid 603 through 605' Processing helix chain 'G' and resid 637 through 658 Processing sheet with id= A, first strand: chain 'G' and resid 191 through 193 removed outlier: 3.771A pdb=" N TYR G 259 " --> pdb=" O ILE G 270 " (cutoff:3.500A) removed outlier: 7.056A pdb=" N ASP G 272 " --> pdb=" O MET G 257 " (cutoff:3.500A) removed outlier: 7.779A pdb=" N MET G 257 " --> pdb=" O ASP G 272 " (cutoff:3.500A) Processing sheet with id= B, first strand: chain 'G' and resid 323 through 325 Processing sheet with id= C, first strand: chain 'G' and resid 559 through 568 removed outlier: 6.707A pdb=" N LEU G 583 " --> pdb=" O ILE G 560 " (cutoff:3.500A) removed outlier: 4.389A pdb=" N HIS G 562 " --> pdb=" O PHE G 581 " (cutoff:3.500A) removed outlier: 6.669A pdb=" N PHE G 581 " --> pdb=" O HIS G 562 " (cutoff:3.500A) removed outlier: 4.530A pdb=" N TYR G 564 " --> pdb=" O ARG G 579 " (cutoff:3.500A) removed outlier: 6.729A pdb=" N ARG G 579 " --> pdb=" O TYR G 564 " (cutoff:3.500A) removed outlier: 4.835A pdb=" N SER G 566 " --> pdb=" O GLN G 577 " (cutoff:3.500A) removed outlier: 5.471A pdb=" N GLN G 577 " --> pdb=" O SER G 566 " (cutoff:3.500A) removed outlier: 3.555A pdb=" N TYR G 580 " --> pdb=" O ARG G 591 " (cutoff:3.500A) removed outlier: 3.634A pdb=" N TYR G 582 " --> pdb=" O GLU G 589 " (cutoff:3.500A) removed outlier: 5.554A pdb=" N TRP G 590 " --> pdb=" O SER G 599 " (cutoff:3.500A) removed outlier: 4.740A pdb=" N SER G 599 " --> pdb=" O TRP G 590 " (cutoff:3.500A) Processing sheet with id= D, first strand: chain 'G' and resid 629 through 632 Processing sheet with id= E, first strand: chain 'G' and resid 196 through 200 removed outlier: 6.732A pdb=" N VAL G 205 " --> pdb=" O ILE G 197 " (cutoff:3.500A) removed outlier: 5.069A pdb=" N ARG G 199 " --> pdb=" O GLY G 203 " (cutoff:3.500A) removed outlier: 7.373A pdb=" N GLY G 203 " --> pdb=" O ARG G 199 " (cutoff:3.500A) 220 hydrogen bonds defined for protein. 588 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: 1.67 Time building geometry restraints manager: 2.20 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.17 - 1.30: 860 1.30 - 1.42: 1385 1.42 - 1.55: 3016 1.55 - 1.68: 2 1.68 - 1.81: 59 Bond restraints: 5322 Sorted by residual: bond pdb=" C ASP G 637 " pdb=" O ASP G 637 " ideal model delta sigma weight residual 1.243 1.179 0.063 9.90e-03 1.02e+04 4.11e+01 bond pdb=" C ILE G 529 " pdb=" O ILE G 529 " ideal model delta sigma weight residual 1.237 1.167 0.070 1.13e-02 7.83e+03 3.81e+01 bond pdb=" C TRP G 590 " pdb=" O TRP G 590 " ideal model delta sigma weight residual 1.235 1.169 0.066 1.25e-02 6.40e+03 2.79e+01 bond pdb=" C GLN G 598 " pdb=" O GLN G 598 " ideal model delta sigma weight residual 1.234 1.179 0.055 1.22e-02 6.72e+03 2.05e+01 bond pdb=" C HIS G 282 " pdb=" O HIS G 282 " ideal model delta sigma weight residual 1.236 1.190 0.046 1.26e-02 6.30e+03 1.34e+01 ... (remaining 5317 not shown) Histogram of bond angle deviations from ideal: 99.59 - 106.60: 167 106.60 - 113.61: 2867 113.61 - 120.62: 2316 120.62 - 127.63: 1777 127.63 - 134.63: 71 Bond angle restraints: 7198 Sorted by residual: angle pdb=" N ILE G 529 " pdb=" CA ILE G 529 " pdb=" C ILE G 529 " ideal model delta sigma weight residual 110.42 104.79 5.63 9.60e-01 1.09e+00 3.44e+01 angle pdb=" N SER G 636 " pdb=" CA SER G 636 " pdb=" C SER G 636 " ideal model delta sigma weight residual 109.50 102.43 7.07 1.58e+00 4.01e-01 2.00e+01 angle pdb=" CA ILE G 529 " pdb=" C ILE G 529 " pdb=" N ASN G 530 " ideal model delta sigma weight residual 116.89 121.57 -4.68 1.11e+00 8.12e-01 1.78e+01 angle pdb=" CA ILE G 529 " pdb=" C ILE G 529 " pdb=" O ILE G 529 " ideal model delta sigma weight residual 121.17 116.71 4.46 1.06e+00 8.90e-01 1.77e+01 angle pdb=" N THR G 533 " pdb=" CA THR G 533 " pdb=" C THR G 533 " ideal model delta sigma weight residual 111.07 107.23 3.84 1.07e+00 8.73e-01 1.29e+01 ... (remaining 7193 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.84: 2881 17.84 - 35.69: 264 35.69 - 53.53: 42 53.53 - 71.37: 9 71.37 - 89.21: 6 Dihedral angle restraints: 3202 sinusoidal: 1284 harmonic: 1918 Sorted by residual: dihedral pdb=" CA LYS G 567 " pdb=" C LYS G 567 " pdb=" N MET G 568 " pdb=" CA MET G 568 " ideal model delta harmonic sigma weight residual 180.00 -159.52 -20.48 0 5.00e+00 4.00e-02 1.68e+01 dihedral pdb=" C23 STU G 701 " pdb=" C21 STU G 701 " pdb=" C22 STU G 701 " pdb=" N2 STU G 701 " ideal model delta sinusoidal sigma weight residual 76.33 141.41 -65.08 1 2.00e+01 2.50e-03 1.39e+01 dihedral pdb=" CA THR G 524 " pdb=" C THR G 524 " pdb=" N VAL G 525 " pdb=" CA VAL G 525 " ideal model delta harmonic sigma weight residual -180.00 -162.87 -17.13 0 5.00e+00 4.00e-02 1.17e+01 ... (remaining 3199 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.028: 482 0.028 - 0.056: 199 0.056 - 0.084: 56 0.084 - 0.112: 28 0.112 - 0.141: 14 Chirality restraints: 779 Sorted by residual: chirality pdb=" CA TRP G 590 " pdb=" N TRP G 590 " pdb=" C TRP G 590 " pdb=" CB TRP G 590 " both_signs ideal model delta sigma weight residual False 2.51 2.65 -0.14 2.00e-01 2.50e+01 4.94e-01 chirality pdb=" CA ILE G 323 " pdb=" N ILE G 323 " pdb=" C ILE G 323 " pdb=" CB ILE G 323 " both_signs ideal model delta sigma weight residual False 2.43 2.56 -0.13 2.00e-01 2.50e+01 4.23e-01 chirality pdb=" CA ILE G 471 " pdb=" N ILE G 471 " pdb=" C ILE G 471 " pdb=" CB ILE G 471 " both_signs ideal model delta sigma weight residual False 2.43 2.56 -0.13 2.00e-01 2.50e+01 4.05e-01 ... (remaining 776 not shown) Planarity restraints: 924 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA TRP G 590 " 0.017 2.00e-02 2.50e+03 3.50e-02 1.23e+01 pdb=" C TRP G 590 " -0.061 2.00e-02 2.50e+03 pdb=" O TRP G 590 " 0.023 2.00e-02 2.50e+03 pdb=" N ARG G 591 " 0.021 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ASP G 635 " -0.017 2.00e-02 2.50e+03 3.42e-02 1.17e+01 pdb=" C ASP G 635 " 0.059 2.00e-02 2.50e+03 pdb=" O ASP G 635 " -0.022 2.00e-02 2.50e+03 pdb=" N SER G 636 " -0.020 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C ASP G 637 " 0.044 5.00e-02 4.00e+02 6.75e-02 7.30e+00 pdb=" N PRO G 638 " -0.117 5.00e-02 4.00e+02 pdb=" CA PRO G 638 " 0.034 5.00e-02 4.00e+02 pdb=" CD PRO G 638 " 0.039 5.00e-02 4.00e+02 ... (remaining 921 not shown) Histogram of nonbonded interaction distances: 2.28 - 2.81: 1418 2.81 - 3.33: 5047 3.33 - 3.85: 8516 3.85 - 4.38: 10220 4.38 - 4.90: 17645 Nonbonded interactions: 42846 Sorted by model distance: nonbonded pdb=" O THR G 406 " pdb=" NH2 ARG G 431 " model vdw 2.283 2.520 nonbonded pdb=" OD1 ASP G 326 " pdb=" N HIS G 330 " model vdw 2.303 2.520 nonbonded pdb=" O PHE G 417 " pdb=" NH1 ARG G 422 " model vdw 2.321 2.520 nonbonded pdb=" O ASP G 455 " pdb=" OD1 ASP G 455 " model vdw 2.332 3.040 nonbonded pdb=" O SER G 350 " pdb=" OG SER G 350 " model vdw 2.349 2.440 ... (remaining 42841 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: 2.740 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: 0.010 Extract box with map and model: 7.220 Check model and map are aligned: 0.080 Set scattering table: 0.050 Process input model: 19.540 Find NCS groups from input model: 0.150 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:15.580 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 45.390 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7541 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 : 0.004 0.070 5322 Z= 0.255 Angle : 0.613 7.073 7198 Z= 0.365 Chirality : 0.038 0.141 779 Planarity : 0.005 0.068 924 Dihedral : 14.353 89.213 1962 Min Nonbonded Distance : 2.283 Molprobity Statistics. All-atom Clashscore : 4.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.74 % Favored : 97.26 % Rotamer: Outliers : 0.37 % Allowed : 6.92 % Favored : 92.71 % 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: 0.83 (0.33), residues: 656 helix: 1.14 (0.30), residues: 308 sheet: 0.50 (0.65), residues: 66 loop : 0.03 (0.39), residues: 282 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.026 0.002 TRP G 590 HIS 0.009 0.001 HIS G 282 PHE 0.016 0.001 PHE G 296 TYR 0.025 0.001 TYR G 651 ARG 0.010 0.001 ARG G 516 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1312 Ramachandran restraints generated. 656 Oldfield, 0 Emsley, 656 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1312 Ramachandran restraints generated. 656 Oldfield, 0 Emsley, 656 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 148 residues out of total 585 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 146 time to evaluate : 0.520 Fit side-chains revert: symmetry clash REVERT: G 92 TYR cc_start: 0.7487 (t80) cc_final: 0.7242 (t80) REVERT: G 106 ARG cc_start: 0.6852 (ttt-90) cc_final: 0.5785 (tpt170) REVERT: G 568 MET cc_start: 0.5623 (tpt) cc_final: 0.5361 (mmp) outliers start: 2 outliers final: 2 residues processed: 146 average time/residue: 1.2724 time to fit residues: 192.6976 Evaluate side-chains 88 residues out of total 585 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 86 time to evaluate : 0.607 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 245 LEU Chi-restraints excluded: chain G residue 636 SER Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 65 random chunks: chunk 54 optimal weight: 4.9990 chunk 49 optimal weight: 1.9990 chunk 27 optimal weight: 1.9990 chunk 16 optimal weight: 0.7980 chunk 33 optimal weight: 0.9980 chunk 26 optimal weight: 0.9990 chunk 50 optimal weight: 0.9990 chunk 19 optimal weight: 0.5980 chunk 30 optimal weight: 3.9990 chunk 37 optimal weight: 0.8980 chunk 59 optimal weight: 0.3980 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** G 140 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 155 GLN G 194 HIS G 434 ASN G 508 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7777 moved from start: 0.2670 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 5322 Z= 0.233 Angle : 0.582 5.937 7198 Z= 0.297 Chirality : 0.042 0.136 779 Planarity : 0.004 0.045 924 Dihedral : 5.443 64.472 725 Min Nonbonded Distance : 2.119 Molprobity Statistics. All-atom Clashscore : 6.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.29 % Favored : 97.71 % Rotamer: Outliers : 4.49 % Allowed : 14.21 % Favored : 81.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.10 (0.34), residues: 656 helix: 1.36 (0.30), residues: 318 sheet: 0.46 (0.64), residues: 67 loop : 0.18 (0.39), residues: 271 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.002 TRP G 590 HIS 0.004 0.001 HIS G 131 PHE 0.014 0.001 PHE G 391 TYR 0.016 0.002 TYR G 651 ARG 0.003 0.000 ARG G 69 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1312 Ramachandran restraints generated. 656 Oldfield, 0 Emsley, 656 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1312 Ramachandran restraints generated. 656 Oldfield, 0 Emsley, 656 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 119 residues out of total 585 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 95 time to evaluate : 0.595 Fit side-chains REVERT: G 106 ARG cc_start: 0.7018 (ttt-90) cc_final: 0.5802 (tpt170) REVERT: G 380 MET cc_start: 0.7980 (OUTLIER) cc_final: 0.7124 (ttt) outliers start: 24 outliers final: 6 residues processed: 109 average time/residue: 1.3667 time to fit residues: 155.0716 Evaluate side-chains 78 residues out of total 585 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 71 time to evaluate : 0.918 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 102 LEU Chi-restraints excluded: chain G residue 150 ILE Chi-restraints excluded: chain G residue 228 LYS Chi-restraints excluded: chain G residue 380 MET Chi-restraints excluded: chain G residue 426 GLU Chi-restraints excluded: chain G residue 512 THR Chi-restraints excluded: chain G residue 567 LYS Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 65 random chunks: chunk 32 optimal weight: 1.9990 chunk 18 optimal weight: 0.6980 chunk 49 optimal weight: 4.9990 chunk 40 optimal weight: 2.9990 chunk 16 optimal weight: 2.9990 chunk 59 optimal weight: 3.9990 chunk 63 optimal weight: 1.9990 chunk 52 optimal weight: 0.5980 chunk 58 optimal weight: 1.9990 chunk 20 optimal weight: 1.9990 chunk 47 optimal weight: 7.9990 overall best weight: 1.4586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: G 135 HIS ** G 140 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 155 GLN G 285 GLN G 445 GLN G 459 GLN G 508 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7903 moved from start: 0.3658 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.041 5322 Z= 0.375 Angle : 0.642 6.514 7198 Z= 0.328 Chirality : 0.044 0.156 779 Planarity : 0.005 0.046 924 Dihedral : 5.777 68.913 722 Min Nonbonded Distance : 2.127 Molprobity Statistics. All-atom Clashscore : 6.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.90 % Favored : 97.10 % Rotamer: Outliers : 5.23 % Allowed : 16.45 % Favored : 78.32 % 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: 0.67 (0.34), residues: 656 helix: 1.10 (0.30), residues: 318 sheet: -0.45 (0.56), residues: 76 loop : 0.08 (0.40), residues: 262 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.002 TRP G 590 HIS 0.006 0.001 HIS G 194 PHE 0.030 0.002 PHE G 572 TYR 0.011 0.002 TYR G 281 ARG 0.004 0.001 ARG G 431 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1312 Ramachandran restraints generated. 656 Oldfield, 0 Emsley, 656 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1312 Ramachandran restraints generated. 656 Oldfield, 0 Emsley, 656 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 105 residues out of total 585 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 77 time to evaluate : 0.591 Fit side-chains revert: symmetry clash REVERT: G 69 ARG cc_start: 0.8007 (OUTLIER) cc_final: 0.7692 (ttt-90) REVERT: G 363 GLN cc_start: 0.8195 (mt0) cc_final: 0.7954 (mt0) REVERT: G 380 MET cc_start: 0.8158 (OUTLIER) cc_final: 0.7452 (ttt) REVERT: G 504 GLU cc_start: 0.7298 (OUTLIER) cc_final: 0.6823 (tm-30) REVERT: G 630 PHE cc_start: 0.7649 (m-80) cc_final: 0.7366 (m-80) outliers start: 28 outliers final: 8 residues processed: 94 average time/residue: 1.3647 time to fit residues: 133.1646 Evaluate side-chains 82 residues out of total 585 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 71 time to evaluate : 0.517 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 69 ARG Chi-restraints excluded: chain G residue 150 ILE Chi-restraints excluded: chain G residue 192 SER Chi-restraints excluded: chain G residue 228 LYS Chi-restraints excluded: chain G residue 380 MET Chi-restraints excluded: chain G residue 385 LEU Chi-restraints excluded: chain G residue 426 GLU Chi-restraints excluded: chain G residue 431 ARG Chi-restraints excluded: chain G residue 463 LEU Chi-restraints excluded: chain G residue 504 GLU Chi-restraints excluded: chain G residue 512 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 65 random chunks: chunk 58 optimal weight: 2.9990 chunk 44 optimal weight: 1.9990 chunk 30 optimal weight: 0.6980 chunk 6 optimal weight: 0.9980 chunk 28 optimal weight: 1.9990 chunk 39 optimal weight: 4.9990 chunk 59 optimal weight: 0.2980 chunk 62 optimal weight: 0.9990 chunk 31 optimal weight: 0.7980 chunk 56 optimal weight: 1.9990 chunk 16 optimal weight: 0.8980 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** G 140 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 459 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7872 moved from start: 0.3880 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 5322 Z= 0.220 Angle : 0.542 6.285 7198 Z= 0.276 Chirality : 0.040 0.131 779 Planarity : 0.004 0.046 924 Dihedral : 5.449 65.219 722 Min Nonbonded Distance : 2.149 Molprobity Statistics. All-atom Clashscore : 6.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.44 % Favored : 97.56 % Rotamer: Outliers : 2.99 % Allowed : 19.07 % Favored : 77.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.83 (0.34), residues: 656 helix: 1.13 (0.30), residues: 318 sheet: -0.09 (0.59), residues: 71 loop : 0.20 (0.40), residues: 267 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP G 590 HIS 0.004 0.001 HIS G 194 PHE 0.021 0.001 PHE G 572 TYR 0.012 0.001 TYR G 281 ARG 0.007 0.001 ARG G 404 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1312 Ramachandran restraints generated. 656 Oldfield, 0 Emsley, 656 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1312 Ramachandran restraints generated. 656 Oldfield, 0 Emsley, 656 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 96 residues out of total 585 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 80 time to evaluate : 0.616 Fit side-chains revert: symmetry clash REVERT: G 69 ARG cc_start: 0.7977 (OUTLIER) cc_final: 0.7623 (ttt-90) REVERT: G 380 MET cc_start: 0.8089 (OUTLIER) cc_final: 0.7374 (ttp) REVERT: G 459 GLN cc_start: 0.7653 (tp-100) cc_final: 0.7417 (tp40) outliers start: 16 outliers final: 6 residues processed: 89 average time/residue: 1.2162 time to fit residues: 113.0480 Evaluate side-chains 77 residues out of total 585 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 69 time to evaluate : 0.547 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 69 ARG Chi-restraints excluded: chain G residue 150 ILE Chi-restraints excluded: chain G residue 228 LYS Chi-restraints excluded: chain G residue 380 MET Chi-restraints excluded: chain G residue 385 LEU Chi-restraints excluded: chain G residue 426 GLU Chi-restraints excluded: chain G residue 431 ARG Chi-restraints excluded: chain G residue 512 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 65 random chunks: chunk 52 optimal weight: 0.8980 chunk 35 optimal weight: 0.9990 chunk 0 optimal weight: 30.0000 chunk 46 optimal weight: 1.9990 chunk 25 optimal weight: 0.9990 chunk 53 optimal weight: 0.8980 chunk 43 optimal weight: 0.5980 chunk 32 optimal weight: 1.9990 chunk 56 optimal weight: 4.9990 chunk 15 optimal weight: 2.9990 chunk 21 optimal weight: 1.9990 overall best weight: 0.8784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: G 140 GLN G 363 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7886 moved from start: 0.4145 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.030 5322 Z= 0.247 Angle : 0.558 6.466 7198 Z= 0.282 Chirality : 0.041 0.132 779 Planarity : 0.004 0.046 924 Dihedral : 5.445 66.325 722 Min Nonbonded Distance : 2.146 Molprobity Statistics. All-atom Clashscore : 7.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.29 % Favored : 97.71 % Rotamer: Outliers : 3.93 % Allowed : 20.00 % Favored : 76.07 % 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: 0.77 (0.34), residues: 656 helix: 1.15 (0.30), residues: 318 sheet: -0.24 (0.59), residues: 71 loop : 0.10 (0.39), residues: 267 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP G 590 HIS 0.003 0.001 HIS G 286 PHE 0.015 0.002 PHE G 391 TYR 0.013 0.001 TYR G 281 ARG 0.008 0.001 ARG G 404 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1312 Ramachandran restraints generated. 656 Oldfield, 0 Emsley, 656 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1312 Ramachandran restraints generated. 656 Oldfield, 0 Emsley, 656 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 96 residues out of total 585 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 75 time to evaluate : 0.686 Fit side-chains revert: symmetry clash REVERT: G 69 ARG cc_start: 0.7963 (OUTLIER) cc_final: 0.7623 (ttt-90) REVERT: G 380 MET cc_start: 0.8133 (OUTLIER) cc_final: 0.7412 (ttp) REVERT: G 504 GLU cc_start: 0.7580 (tm-30) cc_final: 0.7231 (tm-30) REVERT: G 630 PHE cc_start: 0.7643 (m-80) cc_final: 0.7352 (m-80) outliers start: 21 outliers final: 8 residues processed: 89 average time/residue: 1.2879 time to fit residues: 119.2907 Evaluate side-chains 78 residues out of total 585 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 68 time to evaluate : 0.587 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 69 ARG Chi-restraints excluded: chain G residue 150 ILE Chi-restraints excluded: chain G residue 228 LYS Chi-restraints excluded: chain G residue 295 ILE Chi-restraints excluded: chain G residue 380 MET Chi-restraints excluded: chain G residue 426 GLU Chi-restraints excluded: chain G residue 431 ARG Chi-restraints excluded: chain G residue 511 LEU Chi-restraints excluded: chain G residue 512 THR Chi-restraints excluded: chain G residue 574 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 65 random chunks: chunk 56 optimal weight: 3.9990 chunk 12 optimal weight: 4.9990 chunk 36 optimal weight: 2.9990 chunk 15 optimal weight: 3.9990 chunk 62 optimal weight: 0.2980 chunk 52 optimal weight: 0.6980 chunk 29 optimal weight: 0.5980 chunk 5 optimal weight: 2.9990 chunk 20 optimal weight: 1.9990 chunk 33 optimal weight: 0.7980 chunk 60 optimal weight: 3.9990 overall best weight: 0.8782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: G 459 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7892 moved from start: 0.4355 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.031 5322 Z= 0.246 Angle : 0.562 6.544 7198 Z= 0.284 Chirality : 0.041 0.130 779 Planarity : 0.004 0.046 924 Dihedral : 5.418 66.105 722 Min Nonbonded Distance : 2.142 Molprobity Statistics. All-atom Clashscore : 7.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.90 % Favored : 97.10 % Rotamer: Outliers : 4.30 % Allowed : 20.00 % Favored : 75.70 % 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: 0.74 (0.34), residues: 656 helix: 1.20 (0.30), residues: 317 sheet: -0.45 (0.59), residues: 73 loop : 0.05 (0.39), residues: 266 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP G 590 HIS 0.003 0.001 HIS G 286 PHE 0.014 0.001 PHE G 391 TYR 0.012 0.001 TYR G 281 ARG 0.008 0.001 ARG G 404 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1312 Ramachandran restraints generated. 656 Oldfield, 0 Emsley, 656 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1312 Ramachandran restraints generated. 656 Oldfield, 0 Emsley, 656 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 92 residues out of total 585 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 69 time to evaluate : 0.568 Fit side-chains revert: symmetry clash REVERT: G 69 ARG cc_start: 0.7982 (OUTLIER) cc_final: 0.7669 (ttt-90) REVERT: G 106 ARG cc_start: 0.7312 (ttt-90) cc_final: 0.5936 (tpt170) REVERT: G 380 MET cc_start: 0.8120 (OUTLIER) cc_final: 0.7400 (ttp) REVERT: G 437 LEU cc_start: 0.8808 (OUTLIER) cc_final: 0.8607 (tp) outliers start: 23 outliers final: 10 residues processed: 84 average time/residue: 1.3652 time to fit residues: 119.0729 Evaluate side-chains 79 residues out of total 585 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 66 time to evaluate : 0.606 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 69 ARG Chi-restraints excluded: chain G residue 102 LEU Chi-restraints excluded: chain G residue 228 LYS Chi-restraints excluded: chain G residue 295 ILE Chi-restraints excluded: chain G residue 344 LYS Chi-restraints excluded: chain G residue 380 MET Chi-restraints excluded: chain G residue 385 LEU Chi-restraints excluded: chain G residue 426 GLU Chi-restraints excluded: chain G residue 431 ARG Chi-restraints excluded: chain G residue 437 LEU Chi-restraints excluded: chain G residue 511 LEU Chi-restraints excluded: chain G residue 512 THR Chi-restraints excluded: chain G residue 574 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 65 random chunks: chunk 7 optimal weight: 3.9990 chunk 35 optimal weight: 0.6980 chunk 45 optimal weight: 1.9990 chunk 52 optimal weight: 1.9990 chunk 62 optimal weight: 2.9990 chunk 39 optimal weight: 3.9990 chunk 38 optimal weight: 0.7980 chunk 28 optimal weight: 2.9990 chunk 25 optimal weight: 0.6980 chunk 37 optimal weight: 0.7980 chunk 18 optimal weight: 0.9990 overall best weight: 0.7982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: G 459 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7890 moved from start: 0.4484 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.031 5322 Z= 0.234 Angle : 0.561 8.300 7198 Z= 0.282 Chirality : 0.041 0.132 779 Planarity : 0.004 0.046 924 Dihedral : 5.360 65.786 722 Min Nonbonded Distance : 2.149 Molprobity Statistics. All-atom Clashscore : 7.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.59 % Favored : 97.41 % Rotamer: Outliers : 3.74 % Allowed : 21.31 % Favored : 74.95 % 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: 0.75 (0.34), residues: 656 helix: 1.18 (0.30), residues: 318 sheet: -0.41 (0.59), residues: 73 loop : 0.08 (0.39), residues: 265 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP G 590 HIS 0.003 0.001 HIS G 194 PHE 0.014 0.001 PHE G 391 TYR 0.012 0.001 TYR G 281 ARG 0.008 0.000 ARG G 404 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1312 Ramachandran restraints generated. 656 Oldfield, 0 Emsley, 656 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1312 Ramachandran restraints generated. 656 Oldfield, 0 Emsley, 656 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 92 residues out of total 585 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 72 time to evaluate : 0.605 Fit side-chains revert: symmetry clash REVERT: G 69 ARG cc_start: 0.7979 (OUTLIER) cc_final: 0.7663 (ttt-90) REVERT: G 380 MET cc_start: 0.8131 (OUTLIER) cc_final: 0.7416 (ttp) REVERT: G 504 GLU cc_start: 0.7547 (tm-30) cc_final: 0.7257 (tm-30) outliers start: 20 outliers final: 11 residues processed: 82 average time/residue: 1.2992 time to fit residues: 110.9010 Evaluate side-chains 79 residues out of total 585 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 66 time to evaluate : 0.608 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 69 ARG Chi-restraints excluded: chain G residue 102 LEU Chi-restraints excluded: chain G residue 228 LYS Chi-restraints excluded: chain G residue 295 ILE Chi-restraints excluded: chain G residue 344 LYS Chi-restraints excluded: chain G residue 380 MET Chi-restraints excluded: chain G residue 385 LEU Chi-restraints excluded: chain G residue 426 GLU Chi-restraints excluded: chain G residue 431 ARG Chi-restraints excluded: chain G residue 501 SER Chi-restraints excluded: chain G residue 511 LEU Chi-restraints excluded: chain G residue 512 THR Chi-restraints excluded: chain G residue 574 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 65 random chunks: chunk 12 optimal weight: 0.9980 chunk 39 optimal weight: 2.9990 chunk 42 optimal weight: 0.1980 chunk 30 optimal weight: 1.9990 chunk 5 optimal weight: 3.9990 chunk 49 optimal weight: 0.0980 chunk 56 optimal weight: 0.9980 chunk 60 optimal weight: 6.9990 chunk 54 optimal weight: 7.9990 chunk 58 optimal weight: 0.9990 chunk 35 optimal weight: 0.7980 overall best weight: 0.6180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7874 moved from start: 0.4540 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 5322 Z= 0.204 Angle : 0.552 7.885 7198 Z= 0.277 Chirality : 0.040 0.136 779 Planarity : 0.004 0.046 924 Dihedral : 5.279 65.067 722 Min Nonbonded Distance : 2.156 Molprobity Statistics. All-atom Clashscore : 7.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.59 % Favored : 97.41 % Rotamer: Outliers : 3.74 % Allowed : 21.50 % Favored : 74.77 % 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: 0.79 (0.34), residues: 656 helix: 1.20 (0.30), residues: 320 sheet: -0.35 (0.59), residues: 73 loop : 0.10 (0.40), residues: 263 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP G 590 HIS 0.003 0.001 HIS G 262 PHE 0.013 0.001 PHE G 391 TYR 0.012 0.001 TYR G 651 ARG 0.009 0.000 ARG G 404 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1312 Ramachandran restraints generated. 656 Oldfield, 0 Emsley, 656 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1312 Ramachandran restraints generated. 656 Oldfield, 0 Emsley, 656 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 94 residues out of total 585 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 74 time to evaluate : 0.663 Fit side-chains revert: symmetry clash REVERT: G 69 ARG cc_start: 0.7968 (OUTLIER) cc_final: 0.7672 (ttt-90) REVERT: G 106 ARG cc_start: 0.7207 (ttt-90) cc_final: 0.5818 (tpt170) REVERT: G 380 MET cc_start: 0.8121 (OUTLIER) cc_final: 0.7413 (ttp) REVERT: G 400 HIS cc_start: 0.6415 (m-70) cc_final: 0.6056 (m90) REVERT: G 504 GLU cc_start: 0.7562 (tm-30) cc_final: 0.7275 (tm-30) outliers start: 20 outliers final: 10 residues processed: 87 average time/residue: 1.3503 time to fit residues: 122.1448 Evaluate side-chains 80 residues out of total 585 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 68 time to evaluate : 0.605 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 69 ARG Chi-restraints excluded: chain G residue 102 LEU Chi-restraints excluded: chain G residue 228 LYS Chi-restraints excluded: chain G residue 295 ILE Chi-restraints excluded: chain G residue 344 LYS Chi-restraints excluded: chain G residue 380 MET Chi-restraints excluded: chain G residue 385 LEU Chi-restraints excluded: chain G residue 426 GLU Chi-restraints excluded: chain G residue 431 ARG Chi-restraints excluded: chain G residue 501 SER Chi-restraints excluded: chain G residue 512 THR Chi-restraints excluded: chain G residue 574 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 65 random chunks: chunk 25 optimal weight: 0.9980 chunk 45 optimal weight: 1.9990 chunk 17 optimal weight: 1.9990 chunk 52 optimal weight: 1.9990 chunk 55 optimal weight: 6.9990 chunk 58 optimal weight: 0.7980 chunk 38 optimal weight: 0.7980 chunk 61 optimal weight: 2.9990 chunk 37 optimal weight: 0.6980 chunk 29 optimal weight: 0.9980 chunk 42 optimal weight: 0.6980 overall best weight: 0.7980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7887 moved from start: 0.4603 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 5322 Z= 0.237 Angle : 0.577 8.139 7198 Z= 0.290 Chirality : 0.041 0.139 779 Planarity : 0.004 0.047 924 Dihedral : 5.332 65.932 722 Min Nonbonded Distance : 2.150 Molprobity Statistics. All-atom Clashscore : 7.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.74 % Favored : 97.26 % Rotamer: Outliers : 2.80 % Allowed : 22.62 % Favored : 74.58 % 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: 0.82 (0.34), residues: 656 helix: 1.23 (0.30), residues: 317 sheet: -0.37 (0.59), residues: 73 loop : 0.13 (0.40), residues: 266 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP G 590 HIS 0.003 0.001 HIS G 262 PHE 0.014 0.001 PHE G 391 TYR 0.013 0.001 TYR G 651 ARG 0.008 0.001 ARG G 404 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1312 Ramachandran restraints generated. 656 Oldfield, 0 Emsley, 656 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1312 Ramachandran restraints generated. 656 Oldfield, 0 Emsley, 656 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 87 residues out of total 585 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 72 time to evaluate : 0.559 Fit side-chains revert: symmetry clash REVERT: G 69 ARG cc_start: 0.7984 (OUTLIER) cc_final: 0.7689 (ttt-90) REVERT: G 380 MET cc_start: 0.8128 (OUTLIER) cc_final: 0.7422 (ttp) REVERT: G 400 HIS cc_start: 0.6367 (m-70) cc_final: 0.6079 (m90) REVERT: G 504 GLU cc_start: 0.7577 (tm-30) cc_final: 0.7279 (tm-30) outliers start: 15 outliers final: 9 residues processed: 81 average time/residue: 1.2899 time to fit residues: 108.7276 Evaluate side-chains 78 residues out of total 585 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 67 time to evaluate : 0.656 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 69 ARG Chi-restraints excluded: chain G residue 228 LYS Chi-restraints excluded: chain G residue 295 ILE Chi-restraints excluded: chain G residue 344 LYS Chi-restraints excluded: chain G residue 380 MET Chi-restraints excluded: chain G residue 385 LEU Chi-restraints excluded: chain G residue 426 GLU Chi-restraints excluded: chain G residue 431 ARG Chi-restraints excluded: chain G residue 501 SER Chi-restraints excluded: chain G residue 512 THR Chi-restraints excluded: chain G residue 574 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 65 random chunks: chunk 64 optimal weight: 0.9990 chunk 59 optimal weight: 0.6980 chunk 51 optimal weight: 0.0980 chunk 5 optimal weight: 0.7980 chunk 39 optimal weight: 5.9990 chunk 31 optimal weight: 0.8980 chunk 40 optimal weight: 0.8980 chunk 54 optimal weight: 8.9990 chunk 15 optimal weight: 0.0980 chunk 47 optimal weight: 2.9990 chunk 7 optimal weight: 3.9990 overall best weight: 0.5180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** G 459 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7863 moved from start: 0.4669 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 5322 Z= 0.196 Angle : 0.564 8.515 7198 Z= 0.283 Chirality : 0.040 0.136 779 Planarity : 0.004 0.046 924 Dihedral : 5.218 64.463 722 Min Nonbonded Distance : 2.164 Molprobity Statistics. All-atom Clashscore : 8.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.59 % Favored : 97.41 % Rotamer: Outliers : 1.87 % Allowed : 24.30 % Favored : 73.83 % 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: 0.84 (0.34), residues: 656 helix: 1.19 (0.30), residues: 320 sheet: -0.43 (0.58), residues: 79 loop : 0.25 (0.41), residues: 257 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP G 590 HIS 0.002 0.001 HIS G 286 PHE 0.013 0.001 PHE G 391 TYR 0.017 0.001 TYR G 651 ARG 0.004 0.000 ARG G 431 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1312 Ramachandran restraints generated. 656 Oldfield, 0 Emsley, 656 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1312 Ramachandran restraints generated. 656 Oldfield, 0 Emsley, 656 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 81 residues out of total 585 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 71 time to evaluate : 0.586 Fit side-chains revert: symmetry clash REVERT: G 69 ARG cc_start: 0.7980 (OUTLIER) cc_final: 0.7678 (ttt-90) REVERT: G 106 ARG cc_start: 0.7132 (ttt-90) cc_final: 0.5817 (tpt170) REVERT: G 380 MET cc_start: 0.8120 (OUTLIER) cc_final: 0.7413 (ttp) REVERT: G 400 HIS cc_start: 0.6540 (m-70) cc_final: 0.6126 (m90) REVERT: G 504 GLU cc_start: 0.7544 (tm-30) cc_final: 0.7259 (tm-30) outliers start: 10 outliers final: 8 residues processed: 77 average time/residue: 1.3611 time to fit residues: 108.9279 Evaluate side-chains 81 residues out of total 585 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 71 time to evaluate : 0.598 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 69 ARG Chi-restraints excluded: chain G residue 228 LYS Chi-restraints excluded: chain G residue 295 ILE Chi-restraints excluded: chain G residue 344 LYS Chi-restraints excluded: chain G residue 380 MET Chi-restraints excluded: chain G residue 385 LEU Chi-restraints excluded: chain G residue 426 GLU Chi-restraints excluded: chain G residue 431 ARG Chi-restraints excluded: chain G residue 501 SER Chi-restraints excluded: chain G residue 512 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 65 random chunks: chunk 14 optimal weight: 0.9990 chunk 51 optimal weight: 0.8980 chunk 21 optimal weight: 0.4980 chunk 53 optimal weight: 2.9990 chunk 6 optimal weight: 1.9990 chunk 9 optimal weight: 4.9990 chunk 45 optimal weight: 0.7980 chunk 2 optimal weight: 0.6980 chunk 37 optimal weight: 0.8980 chunk 59 optimal weight: 0.4980 chunk 34 optimal weight: 0.7980 overall best weight: 0.6580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** G 459 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3930 r_free = 0.3930 target = 0.168375 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3575 r_free = 0.3575 target = 0.133450 restraints weight = 6246.689| |-----------------------------------------------------------------------------| r_work (start): 0.3527 rms_B_bonded: 2.11 r_work: 0.3346 rms_B_bonded: 2.84 restraints_weight: 0.5000 r_work: 0.3207 rms_B_bonded: 4.58 restraints_weight: 0.2500 r_work (final): 0.3207 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8327 moved from start: 0.4697 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 5322 Z= 0.218 Angle : 0.576 8.380 7198 Z= 0.288 Chirality : 0.040 0.138 779 Planarity : 0.004 0.046 924 Dihedral : 5.257 65.423 722 Min Nonbonded Distance : 2.162 Molprobity Statistics. All-atom Clashscore : 8.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.44 % Favored : 97.56 % Rotamer: Outliers : 2.24 % Allowed : 23.93 % Favored : 73.83 % 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: 0.86 (0.34), residues: 656 helix: 1.21 (0.30), residues: 320 sheet: -0.43 (0.58), residues: 79 loop : 0.26 (0.41), residues: 257 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP G 590 HIS 0.003 0.001 HIS G 262 PHE 0.013 0.001 PHE G 391 TYR 0.015 0.001 TYR G 651 ARG 0.006 0.000 ARG G 404 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2694.05 seconds wall clock time: 48 minutes 14.65 seconds (2894.65 seconds total)