Starting phenix.real_space_refine on Thu Jul 18 18:40:38 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8thr_41269/07_2024/8thr_41269.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8thr_41269/07_2024/8thr_41269.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.12 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8thr_41269/07_2024/8thr_41269.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8thr_41269/07_2024/8thr_41269.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8thr_41269/07_2024/8thr_41269.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8thr_41269/07_2024/8thr_41269.cif" } resolution = 3.12 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= 0.027 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 28 5.16 5 C 1954 2.51 5 N 454 2.21 5 O 501 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A ARG 19": "NH1" <-> "NH2" Residue "A ARG 155": "NH1" <-> "NH2" Residue "A ARG 189": "NH1" <-> "NH2" Residue "A ARG 217": "NH1" <-> "NH2" Residue "A ARG 274": "NH1" <-> "NH2" Residue "A ARG 326": "NH1" <-> "NH2" Residue "A ARG 357": "NH1" <-> "NH2" Residue "A ARG 413": "NH1" <-> "NH2" Residue "A ARG 471": "NH1" <-> "NH2" Time to flip residues: 0.01s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5388/modules/chem_data/mon_lib" Total number of atoms: 2937 Number of models: 1 Model: "" Number of chains: 2 Chain: "A" Number of atoms: 2914 Number of conformers: 1 Conformer: "" Number of residues, atoms: 389, 2914 Classifications: {'peptide': 389} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 23, 'TRANS': 365} Chain breaks: 1 Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 4 Chain: "A" Number of atoms: 23 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 23 Unusual residues: {'EBZ': 1} Classifications: {'undetermined': 1} Time building chain proxies: 3.37, per 1000 atoms: 1.15 Number of scatterers: 2937 At special positions: 0 Unit cell: (56.936, 71.817, 75.699, 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 28 16.00 O 501 8.00 N 454 7.00 C 1954 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: 1.04 Conformation dependent library (CDL) restraints added in 869.0 milliseconds 770 Ramachandran restraints generated. 385 Oldfield, 0 Emsley, 385 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 702 Finding SS restraints... Secondary structure from input PDB file: 23 helices and 0 sheets defined 89.2% alpha, 0.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.30 Creating SS restraints... Processing helix chain 'A' and resid 17 through 40 removed outlier: 4.139A pdb=" N LEU A 23 " --> pdb=" O ARG A 19 " (cutoff:3.500A) removed outlier: 3.744A pdb=" N PHE A 24 " --> pdb=" O LYS A 20 " (cutoff:3.500A) removed outlier: 3.859A pdb=" N ASP A 33 " --> pdb=" O ALA A 29 " (cutoff:3.500A) removed outlier: 3.549A pdb=" N THR A 38 " --> pdb=" O ASN A 34 " (cutoff:3.500A) removed outlier: 3.997A pdb=" N VAL A 40 " --> pdb=" O LEU A 36 " (cutoff:3.500A) Processing helix chain 'A' and resid 41 through 47 Proline residue: A 45 - end of helix Processing helix chain 'A' and resid 123 through 128 Processing helix chain 'A' and resid 128 through 157 removed outlier: 3.586A pdb=" N LEU A 134 " --> pdb=" O GLN A 130 " (cutoff:3.500A) removed outlier: 4.039A pdb=" N LYS A 138 " --> pdb=" O LEU A 134 " (cutoff:3.500A) removed outlier: 3.517A pdb=" N ALA A 139 " --> pdb=" O PHE A 135 " (cutoff:3.500A) Proline residue: A 147 - end of helix removed outlier: 3.942A pdb=" N ASN A 154 " --> pdb=" O GLY A 150 " (cutoff:3.500A) removed outlier: 3.840A pdb=" N ARG A 155 " --> pdb=" O LEU A 151 " (cutoff:3.500A) Processing helix chain 'A' and resid 158 through 177 removed outlier: 3.811A pdb=" N MET A 169 " --> pdb=" O GLY A 165 " (cutoff:3.500A) removed outlier: 3.876A pdb=" N ALA A 177 " --> pdb=" O THR A 173 " (cutoff:3.500A) Processing helix chain 'A' and resid 181 through 211 removed outlier: 3.574A pdb=" N LEU A 185 " --> pdb=" O SER A 181 " (cutoff:3.500A) removed outlier: 3.585A pdb=" N ALA A 202 " --> pdb=" O CYS A 198 " (cutoff:3.500A) Processing helix chain 'A' and resid 213 through 246 removed outlier: 3.750A pdb=" N GLY A 227 " --> pdb=" O ILE A 223 " (cutoff:3.500A) removed outlier: 4.365A pdb=" N LEU A 228 " --> pdb=" O ALA A 224 " (cutoff:3.500A) removed outlier: 3.599A pdb=" N LEU A 233 " --> pdb=" O ALA A 229 " (cutoff:3.500A) Proline residue: A 236 - end of helix Processing helix chain 'A' and resid 249 through 270 removed outlier: 3.929A pdb=" N LEU A 253 " --> pdb=" O THR A 249 " (cutoff:3.500A) removed outlier: 3.812A pdb=" N LEU A 255 " --> pdb=" O PRO A 251 " (cutoff:3.500A) Processing helix chain 'A' and resid 284 through 290 removed outlier: 3.743A pdb=" N LEU A 288 " --> pdb=" O PRO A 284 " (cutoff:3.500A) Processing helix chain 'A' and resid 291 through 312 removed outlier: 3.753A pdb=" N LEU A 295 " --> pdb=" O ASP A 291 " (cutoff:3.500A) removed outlier: 4.020A pdb=" N ALA A 297 " --> pdb=" O TYR A 293 " (cutoff:3.500A) removed outlier: 3.500A pdb=" N ASN A 305 " --> pdb=" O ILE A 301 " (cutoff:3.500A) removed outlier: 3.787A pdb=" N GLY A 307 " --> pdb=" O PHE A 303 " (cutoff:3.500A) removed outlier: 4.228A pdb=" N ILE A 308 " --> pdb=" O ALA A 304 " (cutoff:3.500A) removed outlier: 3.892A pdb=" N LEU A 311 " --> pdb=" O GLY A 307 " (cutoff:3.500A) Processing helix chain 'A' and resid 313 through 315 No H-bonds generated for 'chain 'A' and resid 313 through 315' Processing helix chain 'A' and resid 319 through 323 removed outlier: 3.900A pdb=" N THR A 322 " --> pdb=" O MET A 319 " (cutoff:3.500A) Processing helix chain 'A' and resid 324 through 330 Processing helix chain 'A' and resid 331 through 333 No H-bonds generated for 'chain 'A' and resid 331 through 333' Processing helix chain 'A' and resid 334 through 356 removed outlier: 3.911A pdb=" N LEU A 342 " --> pdb=" O SER A 338 " (cutoff:3.500A) removed outlier: 3.858A pdb=" N ILE A 350 " --> pdb=" O ASN A 346 " (cutoff:3.500A) removed outlier: 3.829A pdb=" N ALA A 352 " --> pdb=" O PHE A 348 " (cutoff:3.500A) removed outlier: 4.782A pdb=" N HIS A 353 " --> pdb=" O GLY A 349 " (cutoff:3.500A) removed outlier: 3.879A pdb=" N LYS A 354 " --> pdb=" O ILE A 350 " (cutoff:3.500A) Processing helix chain 'A' and resid 358 through 373 removed outlier: 3.577A pdb=" N GLY A 364 " --> pdb=" O CYS A 360 " (cutoff:3.500A) removed outlier: 4.059A pdb=" N ILE A 367 " --> pdb=" O LEU A 363 " (cutoff:3.500A) removed outlier: 3.894A pdb=" N VAL A 368 " --> pdb=" O GLY A 364 " (cutoff:3.500A) Processing helix chain 'A' and resid 374 through 378 Processing helix chain 'A' and resid 380 through 383 Processing helix chain 'A' and resid 384 through 414 Proline residue: A 404 - end of helix removed outlier: 3.834A pdb=" N GLY A 407 " --> pdb=" O MET A 403 " (cutoff:3.500A) Processing helix chain 'A' and resid 420 through 436 removed outlier: 4.293A pdb=" N GLY A 432 " --> pdb=" O ALA A 428 " (cutoff:3.500A) removed outlier: 4.995A pdb=" N TYR A 433 " --> pdb=" O PHE A 429 " (cutoff:3.500A) Processing helix chain 'A' and resid 440 through 445 removed outlier: 4.144A pdb=" N ALA A 444 " --> pdb=" O GLY A 440 " (cutoff:3.500A) removed outlier: 3.703A pdb=" N LYS A 445 " --> pdb=" O GLY A 441 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 440 through 445' Processing helix chain 'A' and resid 448 through 462 removed outlier: 3.944A pdb=" N LEU A 452 " --> pdb=" O GLY A 448 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N ASP A 460 " --> pdb=" O ILE A 456 " (cutoff:3.500A) Processing helix chain 'A' and resid 463 through 471 removed outlier: 3.642A pdb=" N CYS A 467 " --> pdb=" O ALA A 464 " (cutoff:3.500A) removed outlier: 3.660A pdb=" N PHE A 469 " --> pdb=" O LEU A 466 " (cutoff:3.500A) 207 hydrogen bonds defined for protein. 582 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: 0.66 Time building geometry restraints manager: 1.09 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.32: 498 1.32 - 1.45: 745 1.45 - 1.57: 1716 1.57 - 1.70: 0 1.70 - 1.82: 48 Bond restraints: 3007 Sorted by residual: bond pdb=" CA VAL A 220 " pdb=" CB VAL A 220 " ideal model delta sigma weight residual 1.539 1.491 0.049 1.20e-02 6.94e+03 1.65e+01 bond pdb=" N PRO A 437 " pdb=" CD PRO A 437 " ideal model delta sigma weight residual 1.473 1.427 0.046 1.40e-02 5.10e+03 1.09e+01 bond pdb=" N PRO A 313 " pdb=" CD PRO A 313 " ideal model delta sigma weight residual 1.473 1.428 0.045 1.40e-02 5.10e+03 1.02e+01 bond pdb=" CA TYR A 418 " pdb=" CB TYR A 418 " ideal model delta sigma weight residual 1.530 1.484 0.046 1.51e-02 4.39e+03 9.44e+00 bond pdb=" CB THR A 140 " pdb=" OG1 THR A 140 " ideal model delta sigma weight residual 1.433 1.385 0.048 1.60e-02 3.91e+03 8.97e+00 ... (remaining 3002 not shown) Histogram of bond angle deviations from ideal: 98.06 - 105.52: 104 105.52 - 112.98: 1403 112.98 - 120.44: 1563 120.44 - 127.90: 996 127.90 - 135.36: 24 Bond angle restraints: 4090 Sorted by residual: angle pdb=" N MET A 319 " pdb=" CA MET A 319 " pdb=" C MET A 319 " ideal model delta sigma weight residual 111.40 118.41 -7.01 1.22e+00 6.72e-01 3.30e+01 angle pdb=" N VAL A 427 " pdb=" CA VAL A 427 " pdb=" CB VAL A 427 " ideal model delta sigma weight residual 110.54 118.23 -7.69 1.36e+00 5.41e-01 3.20e+01 angle pdb=" N SER A 420 " pdb=" CA SER A 420 " pdb=" C SER A 420 " ideal model delta sigma weight residual 112.04 120.07 -8.03 1.44e+00 4.82e-01 3.11e+01 angle pdb=" CA ILE A 455 " pdb=" C ILE A 455 " pdb=" N ILE A 456 " ideal model delta sigma weight residual 117.28 123.73 -6.45 1.16e+00 7.43e-01 3.09e+01 angle pdb=" CA ASN A 154 " pdb=" CB ASN A 154 " pdb=" CG ASN A 154 " ideal model delta sigma weight residual 112.60 118.14 -5.54 1.00e+00 1.00e+00 3.07e+01 ... (remaining 4085 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.30: 1616 16.30 - 32.60: 141 32.60 - 48.90: 25 48.90 - 65.19: 7 65.19 - 81.49: 1 Dihedral angle restraints: 1790 sinusoidal: 689 harmonic: 1101 Sorted by residual: dihedral pdb=" CA CYS A 360 " pdb=" C CYS A 360 " pdb=" N ALA A 361 " pdb=" CA ALA A 361 " ideal model delta harmonic sigma weight residual 180.00 153.16 26.84 0 5.00e+00 4.00e-02 2.88e+01 dihedral pdb=" CA ILE A 156 " pdb=" C ILE A 156 " pdb=" N GLY A 157 " pdb=" CA GLY A 157 " ideal model delta harmonic sigma weight residual 180.00 -155.51 -24.49 0 5.00e+00 4.00e-02 2.40e+01 dihedral pdb=" CA ASN A 128 " pdb=" C ASN A 128 " pdb=" N VAL A 129 " pdb=" CA VAL A 129 " ideal model delta harmonic sigma weight residual -180.00 -156.54 -23.46 0 5.00e+00 4.00e-02 2.20e+01 ... (remaining 1787 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.089: 288 0.089 - 0.179: 155 0.179 - 0.268: 34 0.268 - 0.358: 8 0.358 - 0.447: 2 Chirality restraints: 487 Sorted by residual: chirality pdb=" CA SER A 420 " pdb=" N SER A 420 " pdb=" C SER A 420 " pdb=" CB SER A 420 " both_signs ideal model delta sigma weight residual False 2.51 2.06 0.45 2.00e-01 2.50e+01 4.99e+00 chirality pdb=" CA LEU A 152 " pdb=" N LEU A 152 " pdb=" C LEU A 152 " pdb=" CB LEU A 152 " both_signs ideal model delta sigma weight residual False 2.51 2.14 0.37 2.00e-01 2.50e+01 3.36e+00 chirality pdb=" CB THR A 140 " pdb=" CA THR A 140 " pdb=" OG1 THR A 140 " pdb=" CG2 THR A 140 " both_signs ideal model delta sigma weight residual False 2.55 2.23 0.32 2.00e-01 2.50e+01 2.55e+00 ... (remaining 484 not shown) Planarity restraints: 501 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB PHE A 176 " 0.112 2.00e-02 2.50e+03 7.03e-02 8.64e+01 pdb=" CG PHE A 176 " -0.068 2.00e-02 2.50e+03 pdb=" CD1 PHE A 176 " -0.075 2.00e-02 2.50e+03 pdb=" CD2 PHE A 176 " -0.072 2.00e-02 2.50e+03 pdb=" CE1 PHE A 176 " 0.015 2.00e-02 2.50e+03 pdb=" CE2 PHE A 176 " 0.009 2.00e-02 2.50e+03 pdb=" CZ PHE A 176 " 0.079 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C05 EBZ A 601 " -0.062 2.00e-02 2.50e+03 5.00e-02 6.24e+01 pdb=" C06 EBZ A 601 " -0.039 2.00e-02 2.50e+03 pdb=" C07 EBZ A 601 " -0.019 2.00e-02 2.50e+03 pdb=" C09 EBZ A 601 " 0.017 2.00e-02 2.50e+03 pdb=" C14 EBZ A 601 " 0.098 2.00e-02 2.50e+03 pdb=" C15 EBZ A 601 " 0.028 2.00e-02 2.50e+03 pdb=" C16 EBZ A 601 " -0.010 2.00e-02 2.50e+03 pdb=" C17 EBZ A 601 " -0.015 2.00e-02 2.50e+03 pdb=" O01 EBZ A 601 " 0.065 2.00e-02 2.50e+03 pdb=" O02 EBZ A 601 " -0.063 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYR A 422 " 0.091 2.00e-02 2.50e+03 4.75e-02 4.51e+01 pdb=" CG TYR A 422 " -0.041 2.00e-02 2.50e+03 pdb=" CD1 TYR A 422 " -0.031 2.00e-02 2.50e+03 pdb=" CD2 TYR A 422 " -0.050 2.00e-02 2.50e+03 pdb=" CE1 TYR A 422 " -0.024 2.00e-02 2.50e+03 pdb=" CE2 TYR A 422 " -0.005 2.00e-02 2.50e+03 pdb=" CZ TYR A 422 " -0.003 2.00e-02 2.50e+03 pdb=" OH TYR A 422 " 0.064 2.00e-02 2.50e+03 ... (remaining 498 not shown) Histogram of nonbonded interaction distances: 2.54 - 3.01: 1517 3.01 - 3.48: 3458 3.48 - 3.95: 4867 3.95 - 4.43: 5561 4.43 - 4.90: 9114 Nonbonded interactions: 24517 Sorted by model distance: nonbonded pdb=" OD1 ASP A 411 " pdb=" OH TYR A 418 " model vdw 2.537 2.440 nonbonded pdb=" O SER A 420 " pdb=" N ALA A 423 " model vdw 2.561 2.520 nonbonded pdb=" N THR A 249 " pdb=" N ALA A 250 " model vdw 2.562 2.560 nonbonded pdb=" O ILE A 455 " pdb=" CA ILE A 456 " model vdw 2.574 2.776 nonbonded pdb=" OD1 ASP A 411 " pdb=" OG SER A 416 " model vdw 2.601 2.440 ... (remaining 24512 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: 2.280 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: 0.120 Check model and map are aligned: 0.020 Set scattering table: 0.040 Process input model: 14.020 Find NCS groups from input model: 0.020 Set up NCS constraints: 0.010 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:2.790 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 19.300 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7194 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 : 0.012 0.049 3007 Z= 0.790 Angle : 1.889 9.388 4090 Z= 1.258 Chirality : 0.108 0.447 487 Planarity : 0.014 0.070 501 Dihedral : 13.084 81.492 1088 Min Nonbonded Distance : 2.537 Molprobity Statistics. All-atom Clashscore : 4.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.08 % Favored : 97.92 % Rotamer: Outliers : 0.96 % Allowed : 7.03 % Favored : 92.01 % Cbeta Deviations : 0.28 % 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: -3.14 (0.37), residues: 385 helix: -1.94 (0.25), residues: 275 sheet: None (None), residues: 0 loop : -1.95 (0.61), residues: 110 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.070 0.016 TRP A 451 HIS 0.003 0.002 HIS A 353 PHE 0.112 0.016 PHE A 176 TYR 0.091 0.015 TYR A 422 ARG 0.004 0.001 ARG A 413 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 770 Ramachandran restraints generated. 385 Oldfield, 0 Emsley, 385 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 770 Ramachandran restraints generated. 385 Oldfield, 0 Emsley, 385 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 84 residues out of total 314 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 81 time to evaluate : 0.298 Fit side-chains revert: symmetry clash REVERT: A 443 ILE cc_start: 0.7773 (mt) cc_final: 0.7455 (mt) outliers start: 3 outliers final: 0 residues processed: 83 average time/residue: 0.1093 time to fit residues: 11.7773 Evaluate side-chains 67 residues out of total 314 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 67 time to evaluate : 0.308 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 38 random chunks: chunk 32 optimal weight: 0.7980 chunk 28 optimal weight: 0.3980 chunk 15 optimal weight: 0.5980 chunk 9 optimal weight: 0.7980 chunk 19 optimal weight: 0.9990 chunk 29 optimal weight: 0.7980 chunk 11 optimal weight: 0.5980 chunk 18 optimal weight: 0.9980 chunk 22 optimal weight: 0.0980 chunk 34 optimal weight: 0.6980 chunk 10 optimal weight: 0.7980 overall best weight: 0.4780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 34 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 128 ASN A 154 ASN A 192 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7092 moved from start: 0.2304 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.033 3007 Z= 0.296 Angle : 0.816 7.981 4090 Z= 0.403 Chirality : 0.047 0.174 487 Planarity : 0.006 0.058 501 Dihedral : 7.440 25.955 441 Min Nonbonded Distance : 2.202 Molprobity Statistics. All-atom Clashscore : 9.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.34 % Favored : 97.66 % Rotamer: Outliers : 2.88 % Allowed : 14.38 % Favored : 82.75 % 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: -1.09 (0.42), residues: 385 helix: -0.28 (0.30), residues: 282 sheet: None (None), residues: 0 loop : -1.66 (0.67), residues: 103 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.002 TRP A 451 HIS 0.002 0.001 HIS A 353 PHE 0.018 0.002 PHE A 238 TYR 0.017 0.002 TYR A 422 ARG 0.002 0.000 ARG A 189 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 770 Ramachandran restraints generated. 385 Oldfield, 0 Emsley, 385 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 770 Ramachandran restraints generated. 385 Oldfield, 0 Emsley, 385 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 80 residues out of total 314 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 71 time to evaluate : 0.313 Fit side-chains REVERT: A 288 LEU cc_start: 0.8043 (mt) cc_final: 0.7815 (mp) REVERT: A 433 TYR cc_start: 0.8445 (m-80) cc_final: 0.8223 (m-80) REVERT: A 443 ILE cc_start: 0.7834 (mt) cc_final: 0.7475 (mt) outliers start: 9 outliers final: 3 residues processed: 77 average time/residue: 0.0915 time to fit residues: 9.3985 Evaluate side-chains 68 residues out of total 314 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 65 time to evaluate : 0.272 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 128 ASN Chi-restraints excluded: chain A residue 283 THR Chi-restraints excluded: chain A residue 339 ILE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 38 random chunks: chunk 28 optimal weight: 0.0870 chunk 23 optimal weight: 0.7980 chunk 9 optimal weight: 1.9990 chunk 34 optimal weight: 0.5980 chunk 37 optimal weight: 0.5980 chunk 30 optimal weight: 0.4980 chunk 11 optimal weight: 2.9990 chunk 27 optimal weight: 0.8980 chunk 25 optimal weight: 0.5980 chunk 17 optimal weight: 0.5980 chunk 3 optimal weight: 2.9990 overall best weight: 0.4758 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 128 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7095 moved from start: 0.2634 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 3007 Z= 0.284 Angle : 0.783 7.742 4090 Z= 0.383 Chirality : 0.046 0.149 487 Planarity : 0.006 0.062 501 Dihedral : 7.097 25.468 441 Min Nonbonded Distance : 2.195 Molprobity Statistics. All-atom Clashscore : 9.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.56 % Favored : 98.44 % Rotamer: Outliers : 2.88 % Allowed : 16.29 % Favored : 80.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.85 (0.42), residues: 385 helix: -0.00 (0.30), residues: 277 sheet: None (None), residues: 0 loop : -1.81 (0.62), residues: 108 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP A 328 HIS 0.002 0.001 HIS A 414 PHE 0.015 0.002 PHE A 238 TYR 0.021 0.002 TYR A 422 ARG 0.001 0.000 ARG A 189 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 770 Ramachandran restraints generated. 385 Oldfield, 0 Emsley, 385 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 770 Ramachandran restraints generated. 385 Oldfield, 0 Emsley, 385 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 75 residues out of total 314 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 66 time to evaluate : 0.271 Fit side-chains REVERT: A 196 SER cc_start: 0.8269 (t) cc_final: 0.8040 (p) REVERT: A 244 GLU cc_start: 0.6603 (OUTLIER) cc_final: 0.6263 (tp30) REVERT: A 443 ILE cc_start: 0.7858 (mt) cc_final: 0.7522 (mt) outliers start: 9 outliers final: 5 residues processed: 70 average time/residue: 0.0912 time to fit residues: 8.4520 Evaluate side-chains 70 residues out of total 314 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 64 time to evaluate : 0.298 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 44 ILE Chi-restraints excluded: chain A residue 244 GLU Chi-restraints excluded: chain A residue 253 LEU Chi-restraints excluded: chain A residue 283 THR Chi-restraints excluded: chain A residue 339 ILE Chi-restraints excluded: chain A residue 395 ILE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 38 random chunks: chunk 16 optimal weight: 0.8980 chunk 23 optimal weight: 0.0770 chunk 34 optimal weight: 0.9980 chunk 36 optimal weight: 0.9990 chunk 18 optimal weight: 4.9990 chunk 32 optimal weight: 0.5980 chunk 9 optimal weight: 0.7980 chunk 30 optimal weight: 0.5980 chunk 20 optimal weight: 0.3980 chunk 0 optimal weight: 0.8980 chunk 27 optimal weight: 0.8980 overall best weight: 0.4938 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7106 moved from start: 0.2904 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.031 3007 Z= 0.277 Angle : 0.770 7.465 4090 Z= 0.373 Chirality : 0.046 0.147 487 Planarity : 0.006 0.065 501 Dihedral : 6.780 24.699 441 Min Nonbonded Distance : 2.184 Molprobity Statistics. All-atom Clashscore : 11.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.34 % Favored : 97.66 % Rotamer: Outliers : 2.56 % Allowed : 21.41 % Favored : 76.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.67 (0.43), residues: 385 helix: 0.14 (0.31), residues: 280 sheet: None (None), residues: 0 loop : -1.82 (0.64), residues: 105 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP A 328 HIS 0.003 0.001 HIS A 414 PHE 0.013 0.002 PHE A 238 TYR 0.019 0.002 TYR A 422 ARG 0.001 0.000 ARG A 189 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 770 Ramachandran restraints generated. 385 Oldfield, 0 Emsley, 385 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 770 Ramachandran restraints generated. 385 Oldfield, 0 Emsley, 385 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 75 residues out of total 314 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 67 time to evaluate : 0.299 Fit side-chains REVERT: A 323 MET cc_start: 0.6213 (ppp) cc_final: 0.5710 (ppp) outliers start: 8 outliers final: 2 residues processed: 70 average time/residue: 0.0992 time to fit residues: 9.1424 Evaluate side-chains 66 residues out of total 314 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 64 time to evaluate : 0.299 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 253 LEU Chi-restraints excluded: chain A residue 283 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 38 random chunks: chunk 15 optimal weight: 0.0370 chunk 31 optimal weight: 0.5980 chunk 25 optimal weight: 0.5980 chunk 0 optimal weight: 0.9990 chunk 18 optimal weight: 4.9990 chunk 32 optimal weight: 0.6980 chunk 9 optimal weight: 1.9990 chunk 12 optimal weight: 0.5980 chunk 33 optimal weight: 0.7980 chunk 7 optimal weight: 0.0970 chunk 21 optimal weight: 0.5980 overall best weight: 0.3856 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7087 moved from start: 0.3132 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.033 3007 Z= 0.249 Angle : 0.739 8.019 4090 Z= 0.357 Chirality : 0.044 0.139 487 Planarity : 0.006 0.065 501 Dihedral : 6.549 23.599 441 Min Nonbonded Distance : 2.174 Molprobity Statistics. All-atom Clashscore : 11.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.86 % Favored : 97.14 % Rotamer: Outliers : 4.15 % Allowed : 21.09 % Favored : 74.76 % 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: -0.40 (0.43), residues: 385 helix: 0.34 (0.31), residues: 274 sheet: None (None), residues: 0 loop : -1.63 (0.62), residues: 111 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.003 0.001 TRP A 328 HIS 0.002 0.001 HIS A 414 PHE 0.011 0.001 PHE A 238 TYR 0.019 0.002 TYR A 422 ARG 0.001 0.000 ARG A 189 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 770 Ramachandran restraints generated. 385 Oldfield, 0 Emsley, 385 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 770 Ramachandran restraints generated. 385 Oldfield, 0 Emsley, 385 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 80 residues out of total 314 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 67 time to evaluate : 0.286 Fit side-chains REVERT: A 185 LEU cc_start: 0.5949 (tp) cc_final: 0.5699 (tp) REVERT: A 405 ILE cc_start: 0.7059 (OUTLIER) cc_final: 0.6619 (mm) outliers start: 13 outliers final: 7 residues processed: 74 average time/residue: 0.0900 time to fit residues: 8.8299 Evaluate side-chains 74 residues out of total 314 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 66 time to evaluate : 0.299 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 137 SER Chi-restraints excluded: chain A residue 253 LEU Chi-restraints excluded: chain A residue 283 THR Chi-restraints excluded: chain A residue 339 ILE Chi-restraints excluded: chain A residue 355 MET Chi-restraints excluded: chain A residue 366 ILE Chi-restraints excluded: chain A residue 395 ILE Chi-restraints excluded: chain A residue 405 ILE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 38 random chunks: chunk 9 optimal weight: 1.9990 chunk 36 optimal weight: 0.6980 chunk 30 optimal weight: 0.9990 chunk 17 optimal weight: 0.5980 chunk 3 optimal weight: 2.9990 chunk 12 optimal weight: 0.9990 chunk 19 optimal weight: 0.2980 chunk 35 optimal weight: 0.0770 chunk 4 optimal weight: 0.9990 chunk 20 optimal weight: 0.8980 chunk 26 optimal weight: 0.9980 overall best weight: 0.5138 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7113 moved from start: 0.3276 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.033 3007 Z= 0.282 Angle : 0.772 8.249 4090 Z= 0.372 Chirality : 0.046 0.171 487 Planarity : 0.006 0.066 501 Dihedral : 6.605 23.615 441 Min Nonbonded Distance : 2.191 Molprobity Statistics. All-atom Clashscore : 12.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.64 % Favored : 96.36 % Rotamer: Outliers : 5.11 % Allowed : 19.81 % Favored : 75.08 % 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: -0.49 (0.43), residues: 385 helix: 0.27 (0.31), residues: 274 sheet: None (None), residues: 0 loop : -1.68 (0.61), residues: 111 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.003 0.001 TRP A 358 HIS 0.003 0.001 HIS A 414 PHE 0.011 0.002 PHE A 178 TYR 0.020 0.002 TYR A 422 ARG 0.001 0.000 ARG A 189 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 770 Ramachandran restraints generated. 385 Oldfield, 0 Emsley, 385 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 770 Ramachandran restraints generated. 385 Oldfield, 0 Emsley, 385 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 82 residues out of total 314 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 66 time to evaluate : 0.236 Fit side-chains REVERT: A 185 LEU cc_start: 0.5991 (tp) cc_final: 0.5697 (tp) REVERT: A 405 ILE cc_start: 0.7093 (OUTLIER) cc_final: 0.6679 (mm) outliers start: 16 outliers final: 10 residues processed: 74 average time/residue: 0.0953 time to fit residues: 9.2720 Evaluate side-chains 75 residues out of total 314 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 64 time to evaluate : 0.231 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 137 SER Chi-restraints excluded: chain A residue 245 PHE Chi-restraints excluded: chain A residue 249 THR Chi-restraints excluded: chain A residue 253 LEU Chi-restraints excluded: chain A residue 280 GLN Chi-restraints excluded: chain A residue 283 THR Chi-restraints excluded: chain A residue 339 ILE Chi-restraints excluded: chain A residue 355 MET Chi-restraints excluded: chain A residue 366 ILE Chi-restraints excluded: chain A residue 395 ILE Chi-restraints excluded: chain A residue 405 ILE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 38 random chunks: chunk 20 optimal weight: 0.2980 chunk 30 optimal weight: 0.9980 chunk 36 optimal weight: 0.8980 chunk 22 optimal weight: 0.8980 chunk 16 optimal weight: 0.5980 chunk 14 optimal weight: 0.5980 chunk 21 optimal weight: 0.6980 chunk 11 optimal weight: 1.9990 chunk 7 optimal weight: 0.7980 chunk 23 optimal weight: 0.9980 chunk 24 optimal weight: 0.5980 overall best weight: 0.5580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7125 moved from start: 0.3401 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.034 3007 Z= 0.294 Angle : 0.773 8.921 4090 Z= 0.373 Chirality : 0.046 0.178 487 Planarity : 0.006 0.066 501 Dihedral : 6.658 23.682 441 Min Nonbonded Distance : 2.186 Molprobity Statistics. All-atom Clashscore : 12.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.64 % Favored : 96.36 % Rotamer: Outliers : 5.11 % Allowed : 21.41 % Favored : 73.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.60 (0.43), residues: 385 helix: 0.28 (0.31), residues: 273 sheet: None (None), residues: 0 loop : -1.96 (0.60), residues: 112 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP A 318 HIS 0.003 0.001 HIS A 414 PHE 0.025 0.002 PHE A 429 TYR 0.019 0.002 TYR A 422 ARG 0.001 0.000 ARG A 189 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 770 Ramachandran restraints generated. 385 Oldfield, 0 Emsley, 385 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 770 Ramachandran restraints generated. 385 Oldfield, 0 Emsley, 385 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 80 residues out of total 314 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 64 time to evaluate : 0.269 Fit side-chains REVERT: A 405 ILE cc_start: 0.7148 (OUTLIER) cc_final: 0.6749 (mm) outliers start: 16 outliers final: 11 residues processed: 72 average time/residue: 0.0930 time to fit residues: 8.9221 Evaluate side-chains 75 residues out of total 314 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 63 time to evaluate : 0.311 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 137 SER Chi-restraints excluded: chain A residue 245 PHE Chi-restraints excluded: chain A residue 249 THR Chi-restraints excluded: chain A residue 253 LEU Chi-restraints excluded: chain A residue 280 GLN Chi-restraints excluded: chain A residue 283 THR Chi-restraints excluded: chain A residue 339 ILE Chi-restraints excluded: chain A residue 350 ILE Chi-restraints excluded: chain A residue 355 MET Chi-restraints excluded: chain A residue 366 ILE Chi-restraints excluded: chain A residue 395 ILE Chi-restraints excluded: chain A residue 405 ILE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 38 random chunks: chunk 18 optimal weight: 0.0370 chunk 3 optimal weight: 0.0670 chunk 28 optimal weight: 0.6980 chunk 33 optimal weight: 0.3980 chunk 35 optimal weight: 0.5980 chunk 32 optimal weight: 0.9990 chunk 34 optimal weight: 0.7980 chunk 20 optimal weight: 0.3980 chunk 14 optimal weight: 0.9990 chunk 26 optimal weight: 0.7980 chunk 10 optimal weight: 0.6980 overall best weight: 0.2996 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7064 moved from start: 0.3641 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 3007 Z= 0.221 Angle : 0.752 9.723 4090 Z= 0.357 Chirality : 0.044 0.198 487 Planarity : 0.006 0.065 501 Dihedral : 6.532 23.559 441 Min Nonbonded Distance : 2.173 Molprobity Statistics. All-atom Clashscore : 12.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.64 % Favored : 96.36 % Rotamer: Outliers : 5.11 % Allowed : 21.73 % Favored : 73.16 % 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: -0.39 (0.43), residues: 385 helix: 0.44 (0.31), residues: 276 sheet: None (None), residues: 0 loop : -1.96 (0.62), residues: 109 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.003 0.001 TRP A 451 HIS 0.002 0.001 HIS A 414 PHE 0.020 0.001 PHE A 429 TYR 0.017 0.002 TYR A 422 ARG 0.001 0.000 ARG A 189 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 770 Ramachandran restraints generated. 385 Oldfield, 0 Emsley, 385 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 770 Ramachandran restraints generated. 385 Oldfield, 0 Emsley, 385 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 83 residues out of total 314 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 67 time to evaluate : 0.310 Fit side-chains REVERT: A 185 LEU cc_start: 0.5811 (tp) cc_final: 0.5559 (tp) REVERT: A 319 MET cc_start: 0.4005 (mmm) cc_final: 0.3684 (mmp) REVERT: A 405 ILE cc_start: 0.7039 (OUTLIER) cc_final: 0.6590 (mm) outliers start: 16 outliers final: 10 residues processed: 77 average time/residue: 0.1134 time to fit residues: 11.1835 Evaluate side-chains 77 residues out of total 314 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 66 time to evaluate : 0.280 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 245 PHE Chi-restraints excluded: chain A residue 249 THR Chi-restraints excluded: chain A residue 253 LEU Chi-restraints excluded: chain A residue 280 GLN Chi-restraints excluded: chain A residue 283 THR Chi-restraints excluded: chain A residue 339 ILE Chi-restraints excluded: chain A residue 350 ILE Chi-restraints excluded: chain A residue 355 MET Chi-restraints excluded: chain A residue 366 ILE Chi-restraints excluded: chain A residue 395 ILE Chi-restraints excluded: chain A residue 405 ILE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 38 random chunks: chunk 30 optimal weight: 0.9990 chunk 32 optimal weight: 0.6980 chunk 34 optimal weight: 0.9990 chunk 22 optimal weight: 0.5980 chunk 36 optimal weight: 0.6980 chunk 17 optimal weight: 0.5980 chunk 25 optimal weight: 0.5980 chunk 37 optimal weight: 0.5980 chunk 3 optimal weight: 0.0570 chunk 23 optimal weight: 2.9990 chunk 18 optimal weight: 0.7980 overall best weight: 0.4898 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7107 moved from start: 0.3638 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.034 3007 Z= 0.279 Angle : 0.789 10.150 4090 Z= 0.375 Chirality : 0.046 0.199 487 Planarity : 0.006 0.065 501 Dihedral : 6.588 24.549 441 Min Nonbonded Distance : 2.168 Molprobity Statistics. All-atom Clashscore : 13.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.38 % Favored : 96.62 % Rotamer: Outliers : 5.11 % Allowed : 21.09 % Favored : 73.80 % 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 (0.43), residues: 385 helix: 0.34 (0.31), residues: 276 sheet: None (None), residues: 0 loop : -2.02 (0.61), residues: 109 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.003 0.001 TRP A 328 HIS 0.003 0.001 HIS A 414 PHE 0.019 0.002 PHE A 429 TYR 0.020 0.002 TYR A 422 ARG 0.006 0.000 ARG A 189 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 770 Ramachandran restraints generated. 385 Oldfield, 0 Emsley, 385 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 770 Ramachandran restraints generated. 385 Oldfield, 0 Emsley, 385 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 83 residues out of total 314 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 67 time to evaluate : 0.302 Fit side-chains REVERT: A 405 ILE cc_start: 0.7154 (OUTLIER) cc_final: 0.6731 (mm) outliers start: 16 outliers final: 11 residues processed: 75 average time/residue: 0.0944 time to fit residues: 9.4552 Evaluate side-chains 77 residues out of total 314 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 65 time to evaluate : 0.261 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 128 ASN Chi-restraints excluded: chain A residue 152 LEU Chi-restraints excluded: chain A residue 245 PHE Chi-restraints excluded: chain A residue 249 THR Chi-restraints excluded: chain A residue 253 LEU Chi-restraints excluded: chain A residue 280 GLN Chi-restraints excluded: chain A residue 283 THR Chi-restraints excluded: chain A residue 339 ILE Chi-restraints excluded: chain A residue 350 ILE Chi-restraints excluded: chain A residue 355 MET Chi-restraints excluded: chain A residue 395 ILE Chi-restraints excluded: chain A residue 405 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 38 random chunks: chunk 23 optimal weight: 3.9990 chunk 32 optimal weight: 0.4980 chunk 9 optimal weight: 1.9990 chunk 27 optimal weight: 0.4980 chunk 4 optimal weight: 0.5980 chunk 8 optimal weight: 0.2980 chunk 30 optimal weight: 0.6980 chunk 12 optimal weight: 0.7980 chunk 31 optimal weight: 0.0980 chunk 3 optimal weight: 0.0670 chunk 5 optimal weight: 0.6980 overall best weight: 0.2918 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7058 moved from start: 0.3865 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.032 3007 Z= 0.232 Angle : 0.814 11.443 4090 Z= 0.376 Chirality : 0.046 0.203 487 Planarity : 0.006 0.064 501 Dihedral : 6.472 25.386 441 Min Nonbonded Distance : 2.192 Molprobity Statistics. All-atom Clashscore : 15.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.16 % Favored : 95.84 % Rotamer: Outliers : 3.83 % Allowed : 22.68 % Favored : 73.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.34 (0.44), residues: 385 helix: 0.50 (0.32), residues: 276 sheet: None (None), residues: 0 loop : -2.03 (0.60), residues: 109 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.003 0.001 TRP A 451 HIS 0.002 0.001 HIS A 414 PHE 0.020 0.002 PHE A 429 TYR 0.017 0.002 TYR A 422 ARG 0.006 0.000 ARG A 189 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 770 Ramachandran restraints generated. 385 Oldfield, 0 Emsley, 385 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 770 Ramachandran restraints generated. 385 Oldfield, 0 Emsley, 385 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 79 residues out of total 314 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 67 time to evaluate : 0.270 Fit side-chains REVERT: A 185 LEU cc_start: 0.5862 (tp) cc_final: 0.5596 (tp) REVERT: A 405 ILE cc_start: 0.7077 (OUTLIER) cc_final: 0.6631 (mm) outliers start: 12 outliers final: 9 residues processed: 74 average time/residue: 0.0821 time to fit residues: 8.0521 Evaluate side-chains 76 residues out of total 314 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 66 time to evaluate : 0.303 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 128 ASN Chi-restraints excluded: chain A residue 249 THR Chi-restraints excluded: chain A residue 253 LEU Chi-restraints excluded: chain A residue 280 GLN Chi-restraints excluded: chain A residue 283 THR Chi-restraints excluded: chain A residue 339 ILE Chi-restraints excluded: chain A residue 350 ILE Chi-restraints excluded: chain A residue 355 MET Chi-restraints excluded: chain A residue 395 ILE Chi-restraints excluded: chain A residue 405 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 38 random chunks: chunk 26 optimal weight: 0.6980 chunk 1 optimal weight: 0.7980 chunk 21 optimal weight: 0.9980 chunk 34 optimal weight: 0.5980 chunk 20 optimal weight: 0.0370 chunk 25 optimal weight: 0.5980 chunk 24 optimal weight: 0.9980 chunk 23 optimal weight: 0.7980 chunk 14 optimal weight: 0.6980 chunk 37 optimal weight: 0.3980 chunk 0 optimal weight: 0.1980 overall best weight: 0.3658 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4062 r_free = 0.4062 target = 0.143518 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 27)----------------| | r_work = 0.3936 r_free = 0.3936 target = 0.132788 restraints weight = 4927.977| |-----------------------------------------------------------------------------| r_work (start): 0.3938 rms_B_bonded: 2.22 r_work: 0.3844 rms_B_bonded: 2.84 restraints_weight: 0.5000 r_work (final): 0.3844 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6972 moved from start: 0.3895 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 3007 Z= 0.253 Angle : 0.817 10.513 4090 Z= 0.375 Chirality : 0.046 0.195 487 Planarity : 0.006 0.065 501 Dihedral : 6.458 24.085 441 Min Nonbonded Distance : 2.198 Molprobity Statistics. All-atom Clashscore : 14.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.90 % Favored : 96.10 % Rotamer: Outliers : 3.83 % Allowed : 22.68 % Favored : 73.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.32 (0.44), residues: 385 helix: 0.50 (0.32), residues: 276 sheet: None (None), residues: 0 loop : -1.96 (0.61), residues: 109 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.003 0.001 TRP A 328 HIS 0.002 0.001 HIS A 414 PHE 0.020 0.002 PHE A 348 TYR 0.019 0.002 TYR A 422 ARG 0.006 0.000 ARG A 189 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1159.54 seconds wall clock time: 22 minutes 51.33 seconds (1371.33 seconds total)