Starting phenix.real_space_refine on Mon Nov 13 20:59:58 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8jpd_36476/11_2023/8jpd_36476_neut_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8jpd_36476/11_2023/8jpd_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_36476/11_2023/8jpd_36476.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8jpd_36476/11_2023/8jpd_36476.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8jpd_36476/11_2023/8jpd_36476_neut_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8jpd_36476/11_2023/8jpd_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: 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5144/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: 3.34, per 1000 atoms: 0.64 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: 2.02 Conformation dependent library (CDL) restraints added in 971.4 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: 1.24 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: 1.56 Time building geometry restraints manager: 2.19 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.17 - 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: 1.330 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: 0.000 Extract box with map and model: 7.070 Check model and map are aligned: 0.080 Set scattering table: 0.050 Process input model: 19.110 Find NCS groups from input model: 0.130 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:13.500 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 41.290 ------------------------------------------------------------------------------- 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 *********************** 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 : 0.590 Fit side-chains revert: symmetry clash outliers start: 2 outliers final: 2 residues processed: 146 average time/residue: 1.3144 time to fit residues: 198.8990 Evaluate side-chains 87 residues out of total 585 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 85 time to evaluate : 0.618 Switching outliers to nearest non-outliers outliers start: 2 outliers final: 1 residues processed: 1 average time/residue: 0.0486 time to fit residues: 0.9474 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 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: 0.7775 moved from start: 0.2747 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= 0.239 Angle : 0.590 5.820 7198 Z= 0.300 Chirality : 0.042 0.137 779 Planarity : 0.005 0.046 924 Dihedral : 5.467 64.464 722 Min Nonbonded Distance : 2.151 Molprobity Statistics. All-atom Clashscore : 6.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.44 % Favored : 97.56 % Rotamer: Outliers : 4.67 % Allowed : 14.39 % Favored : 80.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.11 (0.34), residues: 656 helix: 1.37 (0.30), residues: 318 sheet: 0.48 (0.64), residues: 67 loop : 0.18 (0.39), residues: 271 *********************** 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 121 residues out of total 585 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 96 time to evaluate : 0.615 Fit side-chains outliers start: 25 outliers final: 6 residues processed: 109 average time/residue: 1.2689 time to fit residues: 143.7416 Evaluate side-chains 77 residues out of total 585 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 71 time to evaluate : 0.552 Switching outliers to nearest non-outliers outliers start: 6 outliers final: 5 residues processed: 1 average time/residue: 0.0472 time to fit residues: 0.8563 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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: 1.9990 chunk 49 optimal weight: 8.9990 chunk 40 optimal weight: 0.0870 chunk 16 optimal weight: 2.9990 chunk 59 optimal weight: 3.9990 chunk 63 optimal weight: 1.9990 chunk 52 optimal weight: 0.6980 chunk 58 optimal weight: 0.9980 chunk 20 optimal weight: 1.9990 chunk 47 optimal weight: 0.7980 overall best weight: 0.9160 ------------------------------------------------------------------------------- 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 G 155 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: 0.7849 moved from start: 0.3370 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 5322 Z= 0.265 Angle : 0.570 6.411 7198 Z= 0.290 Chirality : 0.041 0.138 779 Planarity : 0.005 0.046 924 Dihedral : 5.473 66.599 722 Min Nonbonded Distance : 2.231 Molprobity Statistics. All-atom Clashscore : 5.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.13 % Favored : 97.87 % Rotamer: Outliers : 4.30 % Allowed : 17.01 % Favored : 78.69 % 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: 0.94 (0.34), residues: 656 helix: 1.26 (0.30), residues: 320 sheet: -0.09 (0.58), residues: 73 loop : 0.19 (0.40), residues: 263 *********************** 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 98 residues out of total 585 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 75 time to evaluate : 0.606 Fit side-chains revert: symmetry clash outliers start: 23 outliers final: 6 residues processed: 91 average time/residue: 1.2513 time to fit residues: 118.6278 Evaluate side-chains 74 residues out of total 585 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 68 time to evaluate : 0.610 Switching outliers to nearest non-outliers outliers start: 6 outliers final: 5 residues processed: 1 average time/residue: 0.0484 time to fit residues: 0.9330 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 65 random chunks: chunk 58 optimal weight: 1.9990 chunk 44 optimal weight: 0.0270 chunk 30 optimal weight: 0.9990 chunk 6 optimal weight: 0.9990 chunk 28 optimal weight: 2.9990 chunk 39 optimal weight: 4.9990 chunk 59 optimal weight: 0.7980 chunk 62 optimal weight: 1.9990 chunk 31 optimal weight: 0.9980 chunk 56 optimal weight: 0.9980 chunk 16 optimal weight: 0.9990 overall best weight: 0.7640 ------------------------------------------------------------------------------- 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 363 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7848 moved from start: 0.3801 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= 0.227 Angle : 0.556 7.340 7198 Z= 0.281 Chirality : 0.041 0.127 779 Planarity : 0.004 0.046 924 Dihedral : 5.368 65.460 722 Min Nonbonded Distance : 2.199 Molprobity Statistics. All-atom Clashscore : 5.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.13 % Favored : 97.87 % Rotamer: Outliers : 3.36 % Allowed : 18.69 % 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: 0.87 (0.34), residues: 656 helix: 1.18 (0.30), residues: 319 sheet: -0.09 (0.59), residues: 71 loop : 0.18 (0.39), residues: 266 *********************** 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 98 residues out of total 585 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 80 time to evaluate : 0.651 Fit side-chains revert: symmetry clash outliers start: 18 outliers final: 7 residues processed: 93 average time/residue: 1.3143 time to fit residues: 127.1665 Evaluate side-chains 74 residues out of total 585 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 67 time to evaluate : 0.619 Switching outliers to nearest non-outliers outliers start: 7 outliers final: 4 residues processed: 3 average time/residue: 0.7227 time to fit residues: 3.1635 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 65 random chunks: chunk 52 optimal weight: 0.9980 chunk 35 optimal weight: 0.9980 chunk 0 optimal weight: 30.0000 chunk 46 optimal weight: 0.9990 chunk 25 optimal weight: 0.2980 chunk 53 optimal weight: 0.9980 chunk 43 optimal weight: 0.8980 chunk 32 optimal weight: 0.5980 chunk 56 optimal weight: 0.9990 chunk 15 optimal weight: 2.9990 chunk 21 optimal weight: 0.4980 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 140 GLN G 155 GLN ** G 459 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7853 moved from start: 0.4042 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.025 5322 Z= 0.207 Angle : 0.543 6.764 7198 Z= 0.273 Chirality : 0.040 0.133 779 Planarity : 0.004 0.046 924 Dihedral : 5.301 65.262 722 Min Nonbonded Distance : 2.182 Molprobity Statistics. All-atom Clashscore : 6.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.44 % Favored : 97.56 % Rotamer: Outliers : 2.62 % Allowed : 21.50 % Favored : 75.89 % 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: 0.78 (0.34), residues: 656 helix: 1.17 (0.31), residues: 321 sheet: -0.35 (0.58), residues: 73 loop : 0.13 (0.40), residues: 262 *********************** 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 87 residues out of total 585 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 73 time to evaluate : 0.617 Fit side-chains revert: symmetry clash outliers start: 14 outliers final: 7 residues processed: 85 average time/residue: 1.2444 time to fit residues: 110.4335 Evaluate side-chains 72 residues out of total 585 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 65 time to evaluate : 0.616 Switching outliers to nearest non-outliers outliers start: 7 outliers final: 5 residues processed: 2 average time/residue: 1.0252 time to fit residues: 2.9921 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 65 random chunks: chunk 56 optimal weight: 4.9990 chunk 12 optimal weight: 0.0020 chunk 36 optimal weight: 0.9990 chunk 15 optimal weight: 1.9990 chunk 62 optimal weight: 0.3980 chunk 52 optimal weight: 0.9980 chunk 29 optimal weight: 0.9980 chunk 5 optimal weight: 2.9990 chunk 20 optimal weight: 0.9980 chunk 33 optimal weight: 2.9990 chunk 60 optimal weight: 4.9990 overall best weight: 0.6788 ------------------------------------------------------------------------------- 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: 0.7859 moved from start: 0.4248 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 5322 Z= 0.211 Angle : 0.543 7.045 7198 Z= 0.273 Chirality : 0.040 0.130 779 Planarity : 0.004 0.046 924 Dihedral : 5.261 65.411 722 Min Nonbonded Distance : 2.181 Molprobity Statistics. All-atom Clashscore : 7.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.29 % Favored : 97.71 % Rotamer: Outliers : 2.43 % Allowed : 23.18 % Favored : 74.39 % 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: 0.78 (0.34), residues: 656 helix: 1.18 (0.31), residues: 321 sheet: -0.38 (0.59), residues: 73 loop : 0.13 (0.40), residues: 262 *********************** 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 82 residues out of total 585 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 69 time to evaluate : 0.627 Fit side-chains revert: symmetry clash outliers start: 13 outliers final: 7 residues processed: 79 average time/residue: 1.2915 time to fit residues: 106.6013 Evaluate side-chains 74 residues out of total 585 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 67 time to evaluate : 1.017 Switching outliers to nearest non-outliers outliers start: 7 outliers final: 5 residues processed: 2 average time/residue: 1.2505 time to fit residues: 3.6165 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 65 random chunks: chunk 7 optimal weight: 2.9990 chunk 35 optimal weight: 0.4980 chunk 45 optimal weight: 2.9990 chunk 52 optimal weight: 0.7980 chunk 62 optimal weight: 0.8980 chunk 39 optimal weight: 3.9990 chunk 38 optimal weight: 0.4980 chunk 28 optimal weight: 2.9990 chunk 25 optimal weight: 0.9990 chunk 37 optimal weight: 0.5980 chunk 18 optimal weight: 0.9980 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 140 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7860 moved from start: 0.4356 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= 0.206 Angle : 0.545 7.015 7198 Z= 0.273 Chirality : 0.040 0.133 779 Planarity : 0.004 0.047 924 Dihedral : 5.233 65.171 722 Min Nonbonded Distance : 2.188 Molprobity Statistics. All-atom Clashscore : 7.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.29 % Favored : 97.71 % Rotamer: Outliers : 2.99 % Allowed : 22.80 % Favored : 74.21 % 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: 1.20 (0.31), residues: 321 sheet: -0.36 (0.59), residues: 73 loop : 0.16 (0.40), residues: 262 *********************** 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 84 residues out of total 585 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 68 time to evaluate : 0.641 Fit side-chains revert: symmetry clash outliers start: 16 outliers final: 8 residues processed: 81 average time/residue: 1.3188 time to fit residues: 111.3338 Evaluate side-chains 73 residues out of total 585 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 65 time to evaluate : 0.625 Switching outliers to nearest non-outliers outliers start: 8 outliers final: 7 residues processed: 1 average time/residue: 0.0504 time to fit residues: 0.9663 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 65 random chunks: chunk 12 optimal weight: 0.8980 chunk 39 optimal weight: 7.9990 chunk 42 optimal weight: 2.9990 chunk 30 optimal weight: 0.2980 chunk 5 optimal weight: 4.9990 chunk 49 optimal weight: 0.0270 chunk 56 optimal weight: 4.9990 chunk 60 optimal weight: 0.9980 chunk 54 optimal weight: 8.9990 chunk 58 optimal weight: 0.6980 chunk 35 optimal weight: 1.9990 overall best weight: 0.5838 ------------------------------------------------------------------------------- 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** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7852 moved from start: 0.4500 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 5322 Z= 0.197 Angle : 0.542 7.064 7198 Z= 0.272 Chirality : 0.040 0.136 779 Planarity : 0.004 0.046 924 Dihedral : 5.178 64.773 722 Min Nonbonded Distance : 2.180 Molprobity Statistics. All-atom Clashscore : 7.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.29 % Favored : 97.71 % Rotamer: Outliers : 2.80 % Allowed : 23.18 % Favored : 74.02 % 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: 0.92 (0.34), residues: 656 helix: 1.28 (0.30), residues: 321 sheet: -0.38 (0.58), residues: 79 loop : 0.26 (0.41), residues: 256 *********************** 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 88 residues out of total 585 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 73 time to evaluate : 0.587 Fit side-chains revert: symmetry clash outliers start: 15 outliers final: 7 residues processed: 82 average time/residue: 1.3878 time to fit residues: 118.4616 Evaluate side-chains 74 residues out of total 585 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 67 time to evaluate : 0.697 Switching outliers to nearest non-outliers outliers start: 7 outliers final: 5 residues processed: 2 average time/residue: 1.0674 time to fit residues: 3.1147 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 65 random chunks: chunk 25 optimal weight: 1.9990 chunk 45 optimal weight: 1.9990 chunk 17 optimal weight: 1.9990 chunk 52 optimal weight: 0.8980 chunk 55 optimal weight: 7.9990 chunk 58 optimal weight: 0.9990 chunk 38 optimal weight: 0.4980 chunk 61 optimal weight: 0.9990 chunk 37 optimal weight: 0.6980 chunk 29 optimal weight: 0.6980 chunk 42 optimal weight: 0.6980 overall best weight: 0.6980 ------------------------------------------------------------------------------- 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 363 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7866 moved from start: 0.4549 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 5322 Z= 0.216 Angle : 0.560 7.601 7198 Z= 0.281 Chirality : 0.040 0.136 779 Planarity : 0.004 0.046 924 Dihedral : 5.236 65.511 722 Min Nonbonded Distance : 2.182 Molprobity Statistics. All-atom Clashscore : 7.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.44 % Favored : 97.56 % Rotamer: Outliers : 1.87 % Allowed : 23.74 % Favored : 74.39 % 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 (0.34), residues: 656 helix: 1.27 (0.31), residues: 321 sheet: -0.39 (0.58), residues: 79 loop : 0.18 (0.41), residues: 256 *********************** 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 79 residues out of total 585 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 69 time to evaluate : 0.596 Fit side-chains revert: symmetry clash outliers start: 10 outliers final: 6 residues processed: 75 average time/residue: 1.2348 time to fit residues: 96.7112 Evaluate side-chains 71 residues out of total 585 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 65 time to evaluate : 0.616 Switching outliers to nearest non-outliers outliers start: 6 outliers final: 5 residues processed: 1 average time/residue: 0.0492 time to fit residues: 0.9491 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 65 random chunks: chunk 64 optimal weight: 0.8980 chunk 59 optimal weight: 0.1980 chunk 51 optimal weight: 0.9990 chunk 5 optimal weight: 0.7980 chunk 39 optimal weight: 0.7980 chunk 31 optimal weight: 0.0980 chunk 40 optimal weight: 0.9980 chunk 54 optimal weight: 7.9990 chunk 15 optimal weight: 3.9990 chunk 47 optimal weight: 0.0980 chunk 7 optimal weight: 3.9990 overall best weight: 0.3980 ------------------------------------------------------------------------------- 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** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7834 moved from start: 0.4600 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 5322 Z= 0.171 Angle : 0.540 8.672 7198 Z= 0.271 Chirality : 0.039 0.137 779 Planarity : 0.004 0.046 924 Dihedral : 5.099 63.820 722 Min Nonbonded Distance : 2.181 Molprobity Statistics. All-atom Clashscore : 8.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.59 % Favored : 97.41 % Rotamer: Outliers : 1.31 % Allowed : 23.74 % 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: 0.94 (0.34), residues: 656 helix: 1.27 (0.31), residues: 320 sheet: -0.28 (0.59), residues: 79 loop : 0.26 (0.41), residues: 257 ********************** 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 75 residues out of total 585 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 68 time to evaluate : 0.642 Fit side-chains revert: symmetry clash outliers start: 7 outliers final: 5 residues processed: 74 average time/residue: 1.3330 time to fit residues: 102.8034 Evaluate side-chains 70 residues out of total 585 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 65 time to evaluate : 0.629 Switching outliers to nearest non-outliers outliers start: 5 outliers final: 5 residues processed: 0 time to fit residues: 0.9046 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 65 random chunks: chunk 14 optimal weight: 5.9990 chunk 51 optimal weight: 0.6980 chunk 21 optimal weight: 0.5980 chunk 53 optimal weight: 2.9990 chunk 6 optimal weight: 0.5980 chunk 9 optimal weight: 0.9990 chunk 45 optimal weight: 2.9990 chunk 2 optimal weight: 0.3980 chunk 37 optimal weight: 0.5980 chunk 59 optimal weight: 0.0970 chunk 34 optimal weight: 1.9990 overall best weight: 0.4578 ------------------------------------------------------------------------------- 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** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3941 r_free = 0.3941 target = 0.169867 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3579 r_free = 0.3579 target = 0.133958 restraints weight = 6151.653| |-----------------------------------------------------------------------------| r_work (start): 0.3549 rms_B_bonded: 2.23 r_work: 0.3369 rms_B_bonded: 2.86 restraints_weight: 0.5000 r_work: 0.3229 rms_B_bonded: 4.65 restraints_weight: 0.2500 r_work (final): 0.3229 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8268 moved from start: 0.4679 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 5322 Z= 0.180 Angle : 0.543 8.466 7198 Z= 0.271 Chirality : 0.039 0.137 779 Planarity : 0.004 0.045 924 Dihedral : 5.104 64.349 722 Min Nonbonded Distance : 2.191 Molprobity Statistics. All-atom Clashscore : 7.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.59 % Favored : 97.41 % Rotamer: Outliers : 1.50 % Allowed : 23.74 % 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: 1.00 (0.34), residues: 656 helix: 1.35 (0.30), residues: 320 sheet: -0.23 (0.59), residues: 79 loop : 0.26 (0.41), residues: 257 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2687.34 seconds wall clock time: 48 minutes 17.50 seconds (2897.50 seconds total)