Starting phenix.real_space_refine on Fri Jul 19 01:11:24 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8jpd_36476/07_2024/8jpd_36476_neut.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8jpd_36476/07_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_36476/07_2024/8jpd_36476.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8jpd_36476/07_2024/8jpd_36476.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8jpd_36476/07_2024/8jpd_36476_neut.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8jpd_36476/07_2024/8jpd_36476_neut.cif" } 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-dev-5388/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: 3.98, per 1000 atoms: 0.77 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 1.1 seconds 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... Secondary structure from input PDB file: 34 helices and 4 sheets defined 55.2% alpha, 12.3% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.62 Creating SS restraints... Processing helix chain 'G' and resid 3 through 19 Processing helix chain 'G' and resid 23 through 28 removed outlier: 3.633A pdb=" N ALA G 28 " --> pdb=" O ALA G 25 " (cutoff:3.500A) Processing helix chain 'G' and resid 36 through 38 No H-bonds generated for 'chain 'G' and resid 36 through 38' Processing helix chain 'G' and resid 39 through 49 removed outlier: 4.176A pdb=" N LYS G 45 " --> pdb=" O SER G 41 " (cutoff:3.500A) Processing helix chain 'G' and resid 54 through 60 Processing helix chain 'G' and resid 61 through 76 removed outlier: 3.764A pdb=" N LEU G 76 " --> pdb=" O CYS G 72 " (cutoff:3.500A) Processing helix chain 'G' and resid 79 through 94 removed outlier: 3.687A pdb=" N LYS G 94 " --> pdb=" O LYS G 90 " (cutoff:3.500A) Processing helix chain 'G' and resid 97 through 113 removed outlier: 4.148A pdb=" N VAL G 103 " --> pdb=" O GLU G 99 " (cutoff:3.500A) Processing helix chain 'G' and resid 113 through 119 Processing helix chain 'G' and resid 125 through 138 removed outlier: 3.700A pdb=" N LYS G 138 " --> pdb=" O GLY G 134 " (cutoff:3.500A) Processing helix chain 'G' and resid 146 through 158 Processing helix chain 'G' and resid 159 through 168 removed outlier: 3.509A pdb=" N GLN G 163 " --> pdb=" O GLY G 159 " (cutoff:3.500A) Processing helix chain 'G' and resid 169 through 183 Processing helix chain 'G' and resid 187 through 189 No H-bonds generated for 'chain 'G' and resid 187 through 189' Processing helix chain 'G' and resid 224 through 230 Processing helix chain 'G' and resid 232 through 248 removed outlier: 3.779A pdb=" N THR G 248 " --> pdb=" O SER G 244 " (cutoff:3.500A) Processing helix chain 'G' and resid 278 through 287 removed outlier: 3.517A pdb=" N HIS G 282 " --> pdb=" O ASP G 278 " (cutoff:3.500A) Processing helix chain 'G' and resid 290 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 319 through 321 No H-bonds generated for 'chain 'G' and resid 319 through 321' Processing helix chain 'G' and resid 358 through 363 Processing helix chain 'G' and resid 370 through 387 removed outlier: 3.981A pdb=" N TRP G 374 " --> pdb=" O SER G 370 " (cutoff:3.500A) removed outlier: 3.765A pdb=" N PHE G 375 " --> pdb=" O SER G 371 " (cutoff:3.500A) Processing helix chain 'G' and resid 398 through 403 Processing helix chain 'G' and resid 404 through 408 removed outlier: 3.911A pdb=" N THR G 408 " --> pdb=" O MET G 405 " (cutoff:3.500A) Processing helix chain 'G' and resid 418 through 429 Processing helix chain 'G' and resid 443 through 449 removed outlier: 3.723A pdb=" N VAL G 447 " --> pdb=" O GLY G 443 " (cutoff:3.500A) Processing helix chain 'G' and resid 450 through 454 Processing helix chain 'G' and resid 457 through 464 Processing helix chain 'G' and resid 481 through 486 Processing helix chain 'G' and resid 489 through 494 Processing helix chain 'G' and resid 499 through 504 Processing helix chain 'G' and resid 505 through 507 No H-bonds generated for 'chain 'G' and resid 505 through 507' Processing helix chain 'G' and resid 513 through 525 Processing helix chain 'G' and resid 525 through 548 Processing helix chain 'G' and resid 636 through 659 Processing sheet with id=AA1, first strand: chain 'G' and resid 191 through 200 removed outlier: 4.646A pdb=" N GLY G 207 " --> pdb=" O HIS G 194 " (cutoff:3.500A) removed outlier: 4.911A pdb=" N ILE G 196 " --> pdb=" O VAL G 205 " (cutoff:3.500A) removed outlier: 7.381A pdb=" N VAL G 205 " --> pdb=" O ILE G 196 " (cutoff:3.500A) removed outlier: 7.628A pdb=" N GLY G 198 " --> pdb=" O GLY G 203 " (cutoff:3.500A) removed outlier: 7.782A pdb=" N GLY G 203 " --> pdb=" O GLY G 198 " (cutoff:3.500A) 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=AA2, first strand: chain 'G' and resid 313 through 314 Processing sheet with id=AA3, first strand: chain 'G' and resid 323 through 325 Processing sheet with id=AA4, first strand: chain 'G' and resid 597 through 602 removed outlier: 4.740A pdb=" N SER G 599 " --> pdb=" O TRP G 590 " (cutoff:3.500A) removed outlier: 5.554A pdb=" N TRP G 590 " --> pdb=" O SER G 599 " (cutoff:3.500A) removed outlier: 3.634A pdb=" N TYR G 582 " --> pdb=" O GLU G 589 " (cutoff:3.500A) removed outlier: 3.555A pdb=" N TYR G 580 " --> pdb=" O ARG G 591 " (cutoff:3.500A) removed outlier: 3.527A pdb=" N MET G 561 " --> pdb=" O LEU G 583 " (cutoff:3.500A) 268 hydrogen bonds defined for protein. 768 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: 1.54 Time building geometry restraints manager: 2.22 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: 1403 2.81 - 3.33: 5005 3.33 - 3.85: 8453 3.85 - 4.38: 10150 4.38 - 4.90: 17643 Nonbonded interactions: 42654 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 42649 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: 2.610 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: 0.190 Check model and map are aligned: 0.030 Set scattering table: 0.050 Process input model: 19.630 Find NCS groups from input model: 0.050 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: 0.010 Load rotamer database and sin/cos tables:11.790 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 34.380 ------------------------------------------------------------------------------- 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 : 0.524 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: 1.3058 time to fit residues: 197.6966 Evaluate side-chains 88 residues out of total 585 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 86 time to evaluate : 0.764 ------------------------------------------------------------------------------- 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: 3.9990 chunk 49 optimal weight: 2.9990 chunk 27 optimal weight: 1.9990 chunk 16 optimal weight: 0.7980 chunk 33 optimal weight: 0.9980 chunk 26 optimal weight: 0.6980 chunk 50 optimal weight: 0.7980 chunk 19 optimal weight: 0.7980 chunk 30 optimal weight: 3.9990 chunk 37 optimal weight: 0.9980 chunk 59 optimal weight: 0.3980 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 155 GLN ** G 434 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 508 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7765 moved from start: 0.2549 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 5322 Z= 0.225 Angle : 0.588 5.757 7198 Z= 0.304 Chirality : 0.042 0.142 779 Planarity : 0.004 0.044 924 Dihedral : 5.410 64.052 725 Min Nonbonded Distance : 2.147 Molprobity Statistics. All-atom Clashscore : 6.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.59 % Favored : 97.41 % Rotamer: Outliers : 4.30 % Allowed : 14.39 % 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: 1.17 (0.34), residues: 656 helix: 1.46 (0.30), residues: 322 sheet: 0.41 (0.65), residues: 67 loop : 0.16 (0.38), residues: 267 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.002 TRP G 590 HIS 0.003 0.001 HIS G 282 PHE 0.013 0.001 PHE G 391 TYR 0.017 0.002 TYR G 651 ARG 0.004 0.000 ARG G 404 *********************** 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 118 residues out of total 585 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 95 time to evaluate : 0.549 Fit side-chains REVERT: G 106 ARG cc_start: 0.7014 (ttt-90) cc_final: 0.5817 (tpt170) REVERT: G 114 MET cc_start: 0.7673 (tpt) cc_final: 0.7459 (tpt) REVERT: G 380 MET cc_start: 0.8063 (OUTLIER) cc_final: 0.7428 (ttt) outliers start: 23 outliers final: 6 residues processed: 108 average time/residue: 1.2342 time to fit residues: 138.7969 Evaluate side-chains 79 residues out of total 585 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 72 time to evaluate : 0.598 ------------------------------------------------------------------------------- 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 192 SER Chi-restraints excluded: chain G residue 228 LYS Chi-restraints excluded: chain G residue 380 MET Chi-restraints excluded: chain G residue 512 THR Chi-restraints excluded: chain G residue 602 THR 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: 4.9990 chunk 40 optimal weight: 1.9990 chunk 16 optimal weight: 2.9990 chunk 59 optimal weight: 5.9990 chunk 63 optimal weight: 2.9990 chunk 52 optimal weight: 0.9980 chunk 58 optimal weight: 1.9990 chunk 20 optimal weight: 2.9990 chunk 47 optimal weight: 5.9990 overall best weight: 1.7988 ------------------------------------------------------------------------------- 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 ** both conformations clash, **PLEASE CHECK MANUALLY** G 285 GLN G 434 ASN 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: 0.7925 moved from start: 0.3778 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.044 5322 Z= 0.430 Angle : 0.697 6.581 7198 Z= 0.358 Chirality : 0.046 0.141 779 Planarity : 0.005 0.052 924 Dihedral : 5.974 69.874 722 Min Nonbonded Distance : 2.140 Molprobity Statistics. All-atom Clashscore : 7.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.44 % Favored : 97.56 % Rotamer: Outliers : 4.86 % Allowed : 17.01 % Favored : 78.13 % 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: 0.53 (0.33), residues: 656 helix: 1.02 (0.29), residues: 329 sheet: -0.19 (0.59), residues: 71 loop : -0.24 (0.39), residues: 256 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.002 TRP G 590 HIS 0.006 0.002 HIS G 194 PHE 0.032 0.002 PHE G 572 TYR 0.012 0.002 TYR G 86 ARG 0.004 0.001 ARG G 69 *********************** 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 102 residues out of total 585 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 76 time to evaluate : 0.600 Fit side-chains revert: symmetry clash REVERT: G 69 ARG cc_start: 0.7995 (OUTLIER) cc_final: 0.7641 (ttt-90) REVERT: G 380 MET cc_start: 0.8340 (OUTLIER) cc_final: 0.7703 (ttt) REVERT: G 504 GLU cc_start: 0.7270 (OUTLIER) cc_final: 0.6794 (tm-30) REVERT: G 630 PHE cc_start: 0.7700 (m-80) cc_final: 0.7422 (m-80) outliers start: 26 outliers final: 8 residues processed: 96 average time/residue: 1.3495 time to fit residues: 134.6115 Evaluate side-chains 77 residues out of total 585 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 66 time to evaluate : 0.633 ------------------------------------------------------------------------------- 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 353 THR 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 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: 0.5980 chunk 44 optimal weight: 2.9990 chunk 30 optimal weight: 0.6980 chunk 6 optimal weight: 0.6980 chunk 28 optimal weight: 1.9990 chunk 39 optimal weight: 6.9990 chunk 59 optimal weight: 0.9980 chunk 62 optimal weight: 2.9990 chunk 31 optimal weight: 0.9990 chunk 56 optimal weight: 1.9990 chunk 16 optimal weight: 0.9980 overall best weight: 0.7980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: G 140 GLN ** G 459 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 508 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7878 moved from start: 0.3996 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 5322 Z= 0.225 Angle : 0.557 6.252 7198 Z= 0.285 Chirality : 0.041 0.131 779 Planarity : 0.004 0.046 924 Dihedral : 5.539 65.167 722 Min Nonbonded Distance : 2.168 Molprobity Statistics. All-atom Clashscore : 7.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.29 % Favored : 97.71 % Rotamer: Outliers : 3.18 % Allowed : 19.81 % Favored : 77.01 % 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: 0.85 (0.33), residues: 656 helix: 1.31 (0.30), residues: 324 sheet: -0.29 (0.58), residues: 71 loop : 0.00 (0.39), residues: 261 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP G 590 HIS 0.004 0.001 HIS G 194 PHE 0.019 0.001 PHE G 572 TYR 0.012 0.001 TYR G 281 ARG 0.006 0.000 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 94 residues out of total 585 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 77 time to evaluate : 0.624 Fit side-chains revert: symmetry clash REVERT: G 69 ARG cc_start: 0.7962 (OUTLIER) cc_final: 0.7626 (ttt-90) REVERT: G 437 LEU cc_start: 0.8566 (tp) cc_final: 0.8358 (tp) outliers start: 17 outliers final: 7 residues processed: 88 average time/residue: 1.2791 time to fit residues: 117.2795 Evaluate side-chains 72 residues out of total 585 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 64 time to evaluate : 0.620 ------------------------------------------------------------------------------- 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 363 GLN 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: 0.9990 chunk 35 optimal weight: 1.9990 chunk 0 optimal weight: 30.0000 chunk 46 optimal weight: 1.9990 chunk 25 optimal weight: 0.9990 chunk 53 optimal weight: 0.7980 chunk 43 optimal weight: 0.9980 chunk 32 optimal weight: 1.9990 chunk 56 optimal weight: 4.9990 chunk 15 optimal weight: 0.5980 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 459 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7890 moved from start: 0.4213 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.027 5322 Z= 0.246 Angle : 0.568 6.371 7198 Z= 0.291 Chirality : 0.041 0.132 779 Planarity : 0.004 0.046 924 Dihedral : 5.547 66.429 722 Min Nonbonded Distance : 2.158 Molprobity Statistics. All-atom Clashscore : 6.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.29 % Favored : 97.71 % Rotamer: Outliers : 3.93 % Allowed : 19.25 % Favored : 76.82 % 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: 0.89 (0.34), residues: 656 helix: 1.36 (0.30), residues: 325 sheet: -0.36 (0.58), residues: 71 loop : 0.02 (0.39), residues: 260 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP G 590 HIS 0.004 0.001 HIS G 194 PHE 0.016 0.001 PHE G 391 TYR 0.012 0.001 TYR G 281 ARG 0.007 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 92 residues out of total 585 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 71 time to evaluate : 0.623 Fit side-chains revert: symmetry clash REVERT: G 33 LEU cc_start: 0.8920 (OUTLIER) cc_final: 0.8662 (tt) REVERT: G 69 ARG cc_start: 0.7958 (OUTLIER) cc_final: 0.7628 (ttt-90) REVERT: G 363 GLN cc_start: 0.8276 (OUTLIER) cc_final: 0.7876 (mt0) REVERT: G 380 MET cc_start: 0.8277 (OUTLIER) cc_final: 0.7878 (ttp) REVERT: G 404 ARG cc_start: 0.6559 (mmm-85) cc_final: 0.6153 (tpp80) REVERT: G 504 GLU cc_start: 0.7542 (tm-30) cc_final: 0.7253 (tm-30) REVERT: G 630 PHE cc_start: 0.7645 (m-80) cc_final: 0.7353 (m-80) outliers start: 21 outliers final: 7 residues processed: 85 average time/residue: 1.2547 time to fit residues: 111.2460 Evaluate side-chains 77 residues out of total 585 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 66 time to evaluate : 0.524 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 33 LEU 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 363 GLN 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 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: 5.9990 chunk 12 optimal weight: 1.9990 chunk 36 optimal weight: 3.9990 chunk 15 optimal weight: 0.8980 chunk 62 optimal weight: 2.9990 chunk 52 optimal weight: 0.9990 chunk 29 optimal weight: 0.5980 chunk 5 optimal weight: 0.8980 chunk 20 optimal weight: 0.9990 chunk 33 optimal weight: 3.9990 chunk 60 optimal weight: 0.7980 overall best weight: 0.8382 ------------------------------------------------------------------------------- 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 ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7887 moved from start: 0.4378 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.026 5322 Z= 0.235 Angle : 0.557 6.246 7198 Z= 0.284 Chirality : 0.041 0.132 779 Planarity : 0.004 0.046 924 Dihedral : 5.466 65.789 722 Min Nonbonded Distance : 2.165 Molprobity Statistics. All-atom Clashscore : 7.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.29 % Favored : 97.71 % Rotamer: Outliers : 4.49 % Allowed : 19.25 % Favored : 76.26 % 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: 1.47 (0.30), residues: 323 sheet: -0.50 (0.58), residues: 73 loop : 0.13 (0.40), residues: 260 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 0.004 0.000 ARG G 431 *********************** 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 95 residues out of total 585 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 71 time to evaluate : 0.624 Fit side-chains revert: symmetry clash REVERT: G 33 LEU cc_start: 0.8915 (OUTLIER) cc_final: 0.8652 (tt) REVERT: G 69 ARG cc_start: 0.7973 (OUTLIER) cc_final: 0.7641 (ttt-90) REVERT: G 380 MET cc_start: 0.8293 (OUTLIER) cc_final: 0.7867 (ttp) REVERT: G 504 GLU cc_start: 0.7551 (tm-30) cc_final: 0.7268 (tm-30) outliers start: 24 outliers final: 8 residues processed: 86 average time/residue: 1.5525 time to fit residues: 138.9030 Evaluate side-chains 77 residues out of total 585 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 66 time to evaluate : 0.802 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 33 LEU 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 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 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: 2.9990 chunk 35 optimal weight: 0.6980 chunk 45 optimal weight: 2.9990 chunk 52 optimal weight: 1.9990 chunk 62 optimal weight: 0.6980 chunk 39 optimal weight: 1.9990 chunk 38 optimal weight: 0.7980 chunk 28 optimal weight: 0.6980 chunk 25 optimal weight: 0.9990 chunk 37 optimal weight: 0.5980 chunk 18 optimal weight: 0.0770 overall best weight: 0.5538 ------------------------------------------------------------------------------- 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: 0.7861 moved from start: 0.4494 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 5322 Z= 0.184 Angle : 0.541 6.311 7198 Z= 0.275 Chirality : 0.040 0.134 779 Planarity : 0.004 0.046 924 Dihedral : 5.314 64.521 722 Min Nonbonded Distance : 2.176 Molprobity Statistics. All-atom Clashscore : 7.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.44 % Favored : 97.56 % Rotamer: Outliers : 3.36 % Allowed : 21.68 % 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: 1.12 (0.34), residues: 656 helix: 1.56 (0.30), residues: 323 sheet: -0.52 (0.57), residues: 79 loop : 0.24 (0.40), residues: 254 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP G 590 HIS 0.002 0.001 HIS G 286 PHE 0.014 0.001 PHE G 391 TYR 0.011 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 89 residues out of total 585 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 71 time to evaluate : 0.588 Fit side-chains revert: symmetry clash REVERT: G 33 LEU cc_start: 0.8882 (OUTLIER) cc_final: 0.8599 (tt) REVERT: G 69 ARG cc_start: 0.7976 (OUTLIER) cc_final: 0.7663 (ttt-90) REVERT: G 106 ARG cc_start: 0.7259 (ttt-90) cc_final: 0.5950 (tpt170) REVERT: G 380 MET cc_start: 0.8287 (OUTLIER) cc_final: 0.7882 (ttp) REVERT: G 504 GLU cc_start: 0.7505 (tm-30) cc_final: 0.7226 (tm-30) outliers start: 18 outliers final: 8 residues processed: 80 average time/residue: 1.3145 time to fit residues: 109.3157 Evaluate side-chains 77 residues out of total 585 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 66 time to evaluate : 0.468 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 33 LEU 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 426 GLU Chi-restraints excluded: chain G residue 431 ARG Chi-restraints excluded: chain G residue 512 THR Chi-restraints excluded: chain G residue 574 THR Chi-restraints excluded: chain G residue 624 ILE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 65 random chunks: chunk 12 optimal weight: 2.9990 chunk 39 optimal weight: 7.9990 chunk 42 optimal weight: 2.9990 chunk 30 optimal weight: 0.7980 chunk 5 optimal weight: 4.9990 chunk 49 optimal weight: 4.9990 chunk 56 optimal weight: 1.9990 chunk 60 optimal weight: 5.9990 chunk 54 optimal weight: 3.9990 chunk 58 optimal weight: 0.8980 chunk 35 optimal weight: 0.1980 overall best weight: 1.3784 ------------------------------------------------------------------------------- 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 577 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7922 moved from start: 0.4605 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.035 5322 Z= 0.341 Angle : 0.633 9.177 7198 Z= 0.320 Chirality : 0.043 0.139 779 Planarity : 0.005 0.047 924 Dihedral : 5.624 67.867 722 Min Nonbonded Distance : 2.139 Molprobity Statistics. All-atom Clashscore : 7.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.74 % Favored : 97.26 % Rotamer: Outliers : 3.93 % Allowed : 21.12 % 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: 0.88 (0.34), residues: 656 helix: 1.38 (0.30), residues: 325 sheet: -0.56 (0.59), residues: 73 loop : 0.03 (0.39), residues: 258 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP G 590 HIS 0.004 0.001 HIS G 286 PHE 0.017 0.002 PHE G 391 TYR 0.014 0.002 TYR G 281 ARG 0.008 0.001 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 87 residues out of total 585 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 66 time to evaluate : 0.620 Fit side-chains revert: symmetry clash REVERT: G 33 LEU cc_start: 0.8952 (OUTLIER) cc_final: 0.8686 (tt) REVERT: G 69 ARG cc_start: 0.7963 (OUTLIER) cc_final: 0.7678 (ttt-90) REVERT: G 380 MET cc_start: 0.8277 (OUTLIER) cc_final: 0.7772 (ttp) REVERT: G 504 GLU cc_start: 0.7561 (tm-30) cc_final: 0.7213 (tm-30) outliers start: 21 outliers final: 8 residues processed: 76 average time/residue: 1.3306 time to fit residues: 105.6002 Evaluate side-chains 76 residues out of total 585 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 65 time to evaluate : 0.590 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 33 LEU 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 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: 1.9990 chunk 45 optimal weight: 0.7980 chunk 17 optimal weight: 0.7980 chunk 52 optimal weight: 0.4980 chunk 55 optimal weight: 6.9990 chunk 58 optimal weight: 0.6980 chunk 38 optimal weight: 0.6980 chunk 61 optimal weight: 0.9990 chunk 37 optimal weight: 0.5980 chunk 29 optimal weight: 0.5980 chunk 42 optimal weight: 0.8980 overall best weight: 0.6180 ------------------------------------------------------------------------------- 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: 0.7875 moved from start: 0.4637 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= 0.201 Angle : 0.566 8.375 7198 Z= 0.287 Chirality : 0.040 0.137 779 Planarity : 0.004 0.046 924 Dihedral : 5.382 64.717 722 Min Nonbonded Distance : 2.170 Molprobity Statistics. All-atom Clashscore : 8.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.59 % Favored : 97.41 % Rotamer: Outliers : 2.62 % Allowed : 22.43 % 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: 1.02 (0.34), residues: 656 helix: 1.50 (0.30), residues: 323 sheet: -0.66 (0.57), residues: 79 loop : 0.20 (0.41), residues: 254 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 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 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 82 residues out of total 585 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 68 time to evaluate : 0.603 Fit side-chains revert: symmetry clash REVERT: G 33 LEU cc_start: 0.8898 (OUTLIER) cc_final: 0.8631 (tt) REVERT: G 69 ARG cc_start: 0.7982 (OUTLIER) cc_final: 0.7671 (ttt-90) REVERT: G 380 MET cc_start: 0.8270 (OUTLIER) cc_final: 0.7812 (ttp) REVERT: G 504 GLU cc_start: 0.7523 (tm-30) cc_final: 0.7163 (tm-30) outliers start: 14 outliers final: 8 residues processed: 75 average time/residue: 1.3565 time to fit residues: 105.8235 Evaluate side-chains 76 residues out of total 585 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 65 time to evaluate : 0.585 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 33 LEU Chi-restraints excluded: chain G residue 69 ARG Chi-restraints excluded: chain G residue 228 LYS 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 512 THR Chi-restraints excluded: chain G residue 574 THR Chi-restraints excluded: chain G residue 624 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 65 random chunks: chunk 64 optimal weight: 0.6980 chunk 59 optimal weight: 2.9990 chunk 51 optimal weight: 1.9990 chunk 5 optimal weight: 4.9990 chunk 39 optimal weight: 5.9990 chunk 31 optimal weight: 0.8980 chunk 40 optimal weight: 4.9990 chunk 54 optimal weight: 0.0010 chunk 15 optimal weight: 3.9990 chunk 47 optimal weight: 0.6980 chunk 7 optimal weight: 3.9990 overall best weight: 0.8588 ------------------------------------------------------------------------------- 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: 0.7891 moved from start: 0.4711 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 5322 Z= 0.246 Angle : 0.596 8.972 7198 Z= 0.301 Chirality : 0.041 0.140 779 Planarity : 0.004 0.046 924 Dihedral : 5.470 66.359 722 Min Nonbonded Distance : 2.158 Molprobity Statistics. All-atom Clashscore : 8.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.74 % Favored : 97.26 % Rotamer: Outliers : 2.43 % Allowed : 22.99 % 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: 0.96 (0.34), residues: 656 helix: 1.46 (0.30), residues: 325 sheet: -0.56 (0.59), residues: 73 loop : 0.08 (0.40), residues: 258 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP G 590 HIS 0.003 0.001 HIS G 286 PHE 0.016 0.001 PHE G 391 TYR 0.013 0.001 TYR G 281 ARG 0.007 0.001 ARG G 404 ********************** 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 78 residues out of total 585 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 65 time to evaluate : 0.585 Fit side-chains revert: symmetry clash REVERT: G 33 LEU cc_start: 0.8924 (OUTLIER) cc_final: 0.8652 (tt) REVERT: G 69 ARG cc_start: 0.7993 (OUTLIER) cc_final: 0.7676 (ttt-90) REVERT: G 380 MET cc_start: 0.8275 (OUTLIER) cc_final: 0.7814 (ttp) outliers start: 13 outliers final: 7 residues processed: 72 average time/residue: 1.3691 time to fit residues: 102.7371 Evaluate side-chains 75 residues out of total 585 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 65 time to evaluate : 0.612 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 33 LEU Chi-restraints excluded: chain G residue 69 ARG Chi-restraints excluded: chain G residue 228 LYS 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 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 14 optimal weight: 0.9990 chunk 51 optimal weight: 1.9990 chunk 21 optimal weight: 0.8980 chunk 53 optimal weight: 0.7980 chunk 6 optimal weight: 0.7980 chunk 9 optimal weight: 0.6980 chunk 45 optimal weight: 1.9990 chunk 2 optimal weight: 0.8980 chunk 37 optimal weight: 0.9980 chunk 59 optimal weight: 1.9990 chunk 34 optimal weight: 0.8980 overall best weight: 0.8180 ------------------------------------------------------------------------------- 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 = 0.3924 r_free = 0.3924 target = 0.167532 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3570 r_free = 0.3570 target = 0.132946 restraints weight = 6231.117| |-----------------------------------------------------------------------------| r_work (start): 0.3531 rms_B_bonded: 2.20 r_work: 0.3352 rms_B_bonded: 2.78 restraints_weight: 0.5000 r_work: 0.3214 rms_B_bonded: 4.49 restraints_weight: 0.2500 r_work (final): 0.3214 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8322 moved from start: 0.4771 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 5322 Z= 0.237 Angle : 0.590 8.778 7198 Z= 0.299 Chirality : 0.041 0.141 779 Planarity : 0.004 0.046 924 Dihedral : 5.426 65.653 722 Min Nonbonded Distance : 2.162 Molprobity Statistics. All-atom Clashscore : 8.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.59 % Favored : 97.41 % Rotamer: Outliers : 2.24 % Allowed : 23.18 % 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: 0.97 (0.34), residues: 656 helix: 1.47 (0.30), residues: 325 sheet: -0.64 (0.57), residues: 79 loop : 0.15 (0.41), residues: 252 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP G 590 HIS 0.003 0.001 HIS G 194 PHE 0.015 0.001 PHE G 391 TYR 0.013 0.001 TYR G 281 ARG 0.009 0.001 ARG G 404 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2647.64 seconds wall clock time: 46 minutes 47.30 seconds (2807.30 seconds total)