Starting phenix.real_space_refine on Fri Aug 2 19:21:19 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8q3f_18126/08_2024/8q3f_18126.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8q3f_18126/08_2024/8q3f_18126.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.77 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8q3f_18126/08_2024/8q3f_18126.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8q3f_18126/08_2024/8q3f_18126.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8q3f_18126/08_2024/8q3f_18126.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8q3f_18126/08_2024/8q3f_18126.cif" } resolution = 3.77 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= 0.002 sd= 0.009 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 41 5.16 5 C 2903 2.51 5 N 776 2.21 5 O 879 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped None Time to flip residues: 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/chem_data/mon_lib" Total number of atoms: 4599 Number of models: 1 Model: "" Number of chains: 1 Chain: "A" Number of atoms: 4599 Number of conformers: 1 Conformer: "" Number of residues, atoms: 578, 4599 Classifications: {'peptide': 578} Link IDs: {'PTRANS': 24, 'TRANS': 553} Time building chain proxies: 3.55, per 1000 atoms: 0.77 Number of scatterers: 4599 At special positions: 0 Unit cell: (67.08, 97.18, 104.06, 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 41 16.00 O 879 8.00 N 776 7.00 C 2903 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=13, symmetry=0 Simple disulfide: pdb=" SG CYS A 53 " - pdb=" SG CYS A 62 " distance=2.03 Simple disulfide: pdb=" SG CYS A 124 " - pdb=" SG CYS A 169 " distance=2.03 Simple disulfide: pdb=" SG CYS A 168 " - pdb=" SG CYS A 177 " distance=2.03 Simple disulfide: pdb=" SG CYS A 200 " - pdb=" SG CYS A 246 " distance=2.04 Simple disulfide: pdb=" SG CYS A 245 " - pdb=" SG CYS A 253 " distance=2.03 Simple disulfide: pdb=" SG CYS A 265 " - pdb=" SG CYS A 279 " distance=2.03 Simple disulfide: pdb=" SG CYS A 278 " - pdb=" SG CYS A 289 " distance=2.03 Simple disulfide: pdb=" SG CYS A 316 " - pdb=" SG CYS A 361 " distance=2.03 Simple disulfide: pdb=" SG CYS A 360 " - pdb=" SG CYS A 369 " distance=2.03 Simple disulfide: pdb=" SG CYS A 392 " - pdb=" SG CYS A 438 " distance=2.03 Simple disulfide: pdb=" SG CYS A 437 " - pdb=" SG CYS A 448 " distance=2.03 Simple disulfide: pdb=" SG CYS A 461 " - pdb=" SG CYS A 477 " distance=2.03 Simple disulfide: pdb=" SG CYS A 476 " - pdb=" SG CYS A 487 " distance=2.03 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: 1.73 Conformation dependent library (CDL) restraints added in 986.1 milliseconds 1152 Ramachandran restraints generated. 576 Oldfield, 0 Emsley, 576 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1134 Finding SS restraints... Secondary structure from input PDB file: 30 helices and 0 sheets defined 70.8% alpha, 0.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.49 Creating SS restraints... Processing helix chain 'A' and resid 15 through 31 removed outlier: 3.654A pdb=" N LYS A 20 " --> pdb=" O GLU A 16 " (cutoff:3.500A) removed outlier: 3.909A pdb=" N ALA A 21 " --> pdb=" O GLU A 17 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N VAL A 23 " --> pdb=" O PHE A 19 " (cutoff:3.500A) removed outlier: 3.710A pdb=" N LEU A 24 " --> pdb=" O LYS A 20 " (cutoff:3.500A) removed outlier: 3.583A pdb=" N ILE A 25 " --> pdb=" O ALA A 21 " (cutoff:3.500A) removed outlier: 3.688A pdb=" N ALA A 26 " --> pdb=" O LEU A 22 " (cutoff:3.500A) Processing helix chain 'A' and resid 36 through 54 removed outlier: 3.701A pdb=" N VAL A 40 " --> pdb=" O PHE A 36 " (cutoff:3.500A) removed outlier: 3.821A pdb=" N LYS A 41 " --> pdb=" O GLU A 37 " (cutoff:3.500A) Processing helix chain 'A' and resid 65 through 78 removed outlier: 3.787A pdb=" N LEU A 74 " --> pdb=" O PHE A 70 " (cutoff:3.500A) removed outlier: 3.911A pdb=" N CYS A 75 " --> pdb=" O GLY A 71 " (cutoff:3.500A) removed outlier: 4.060A pdb=" N THR A 76 " --> pdb=" O ASP A 72 " (cutoff:3.500A) removed outlier: 3.895A pdb=" N VAL A 77 " --> pdb=" O LYS A 73 " (cutoff:3.500A) Processing helix chain 'A' and resid 84 through 88 removed outlier: 4.300A pdb=" N MET A 87 " --> pdb=" O TYR A 84 " (cutoff:3.500A) Processing helix chain 'A' and resid 98 through 103 Processing helix chain 'A' and resid 119 through 130 removed outlier: 4.377A pdb=" N MET A 123 " --> pdb=" O GLU A 119 " (cutoff:3.500A) Processing helix chain 'A' and resid 130 through 143 Processing helix chain 'A' and resid 150 through 152 No H-bonds generated for 'chain 'A' and resid 150 through 152' Processing helix chain 'A' and resid 153 through 166 Processing helix chain 'A' and resid 174 through 206 removed outlier: 4.057A pdb=" N LEU A 178 " --> pdb=" O LYS A 174 " (cutoff:3.500A) Proline residue: A 180 - end of helix Processing helix chain 'A' and resid 208 through 223 Processing helix chain 'A' and resid 227 through 244 removed outlier: 3.789A pdb=" N VAL A 231 " --> pdb=" O GLU A 227 " (cutoff:3.500A) Processing helix chain 'A' and resid 249 through 267 Processing helix chain 'A' and resid 282 through 291 removed outlier: 3.833A pdb=" N ILE A 290 " --> pdb=" O LYS A 286 " (cutoff:3.500A) removed outlier: 4.511A pdb=" N ALA A 291 " --> pdb=" O SER A 287 " (cutoff:3.500A) Processing helix chain 'A' and resid 305 through 310 removed outlier: 3.656A pdb=" N PHE A 309 " --> pdb=" O LEU A 305 " (cutoff:3.500A) Processing helix chain 'A' and resid 315 through 322 Processing helix chain 'A' and resid 323 through 336 Processing helix chain 'A' and resid 342 through 361 removed outlier: 3.855A pdb=" N LYS A 359 " --> pdb=" O THR A 355 " (cutoff:3.500A) Processing helix chain 'A' and resid 376 through 399 removed outlier: 3.976A pdb=" N LEU A 380 " --> pdb=" O GLU A 376 " (cutoff:3.500A) removed outlier: 3.810A pdb=" N GLU A 383 " --> pdb=" O PRO A 379 " (cutoff:3.500A) Proline residue: A 384 - end of helix Processing helix chain 'A' and resid 399 through 412 removed outlier: 3.548A pdb=" N TYR A 411 " --> pdb=" O LEU A 407 " (cutoff:3.500A) removed outlier: 3.646A pdb=" N THR A 412 " --> pdb=" O LEU A 408 " (cutoff:3.500A) Processing helix chain 'A' and resid 419 through 437 removed outlier: 3.702A pdb=" N LEU A 423 " --> pdb=" O SER A 419 " (cutoff:3.500A) removed outlier: 3.750A pdb=" N CYS A 437 " --> pdb=" O VAL A 433 " (cutoff:3.500A) Processing helix chain 'A' and resid 445 through 450 Processing helix chain 'A' and resid 452 through 467 removed outlier: 3.935A pdb=" N VAL A 456 " --> pdb=" O TYR A 452 " (cutoff:3.500A) removed outlier: 3.509A pdb=" N ASN A 458 " --> pdb=" O SER A 454 " (cutoff:3.500A) removed outlier: 3.738A pdb=" N LYS A 466 " --> pdb=" O VAL A 462 " (cutoff:3.500A) removed outlier: 3.907A pdb=" N THR A 467 " --> pdb=" O LEU A 463 " (cutoff:3.500A) Processing helix chain 'A' and resid 471 through 478 Processing helix chain 'A' and resid 480 through 482 No H-bonds generated for 'chain 'A' and resid 480 through 482' Processing helix chain 'A' and resid 483 through 490 Processing helix chain 'A' and resid 510 through 516 removed outlier: 4.300A pdb=" N CYS A 514 " --> pdb=" O ALA A 511 " (cutoff:3.500A) Processing helix chain 'A' and resid 517 through 536 Processing helix chain 'A' and resid 540 through 561 removed outlier: 3.586A pdb=" N LYS A 545 " --> pdb=" O LYS A 541 " (cutoff:3.500A) removed outlier: 4.779A pdb=" N ALA A 546 " --> pdb=" O GLU A 542 " (cutoff:3.500A) removed outlier: 3.930A pdb=" N CYS A 558 " --> pdb=" O PHE A 554 " (cutoff:3.500A) removed outlier: 3.566A pdb=" N LYS A 560 " --> pdb=" O GLU A 556 " (cutoff:3.500A) Processing helix chain 'A' and resid 565 through 578 removed outlier: 3.593A pdb=" N LYS A 573 " --> pdb=" O ALA A 569 " (cutoff:3.500A) 251 hydrogen bonds defined for protein. 741 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: 1.17 Time building geometry restraints manager: 1.92 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 1145 1.33 - 1.46: 1038 1.46 - 1.58: 2458 1.58 - 1.71: 0 1.71 - 1.83: 47 Bond restraints: 4688 Sorted by residual: bond pdb=" C GLU A 95 " pdb=" N PRO A 96 " ideal model delta sigma weight residual 1.334 1.400 -0.066 2.34e-02 1.83e+03 8.06e+00 bond pdb=" C THR A 420 " pdb=" N PRO A 421 " ideal model delta sigma weight residual 1.337 1.367 -0.030 1.24e-02 6.50e+03 5.91e+00 bond pdb=" C GLU A 383 " pdb=" N PRO A 384 " ideal model delta sigma weight residual 1.337 1.365 -0.028 1.24e-02 6.50e+03 5.20e+00 bond pdb=" C LEU A 179 " pdb=" N PRO A 180 " ideal model delta sigma weight residual 1.336 1.358 -0.022 1.25e-02 6.40e+03 3.12e+00 bond pdb=" C MET A 446 " pdb=" N PRO A 447 " ideal model delta sigma weight residual 1.336 1.356 -0.021 1.23e-02 6.61e+03 2.86e+00 ... (remaining 4683 not shown) Histogram of bond angle deviations from ideal: 96.21 - 104.24: 71 104.24 - 112.27: 2147 112.27 - 120.30: 2392 120.30 - 128.33: 1685 128.33 - 136.36: 29 Bond angle restraints: 6324 Sorted by residual: angle pdb=" C GLU A 95 " pdb=" N PRO A 96 " pdb=" CA PRO A 96 " ideal model delta sigma weight residual 120.96 114.15 6.81 1.41e+00 5.03e-01 2.33e+01 angle pdb=" CG1 VAL A 415 " pdb=" CB VAL A 415 " pdb=" CG2 VAL A 415 " ideal model delta sigma weight residual 110.80 101.30 9.50 2.20e+00 2.07e-01 1.86e+01 angle pdb=" N GLN A 526 " pdb=" CA GLN A 526 " pdb=" CB GLN A 526 " ideal model delta sigma weight residual 110.40 116.91 -6.51 1.63e+00 3.76e-01 1.59e+01 angle pdb=" CA PRO A 384 " pdb=" N PRO A 384 " pdb=" CD PRO A 384 " ideal model delta sigma weight residual 112.00 106.58 5.42 1.40e+00 5.10e-01 1.50e+01 angle pdb=" CA PRO A 421 " pdb=" N PRO A 421 " pdb=" CD PRO A 421 " ideal model delta sigma weight residual 112.00 106.70 5.30 1.40e+00 5.10e-01 1.44e+01 ... (remaining 6319 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.61: 2582 17.61 - 35.21: 306 35.21 - 52.82: 48 52.82 - 70.43: 6 70.43 - 88.03: 10 Dihedral angle restraints: 2952 sinusoidal: 1223 harmonic: 1729 Sorted by residual: dihedral pdb=" CB CYS A 124 " pdb=" SG CYS A 124 " pdb=" SG CYS A 169 " pdb=" CB CYS A 169 " ideal model delta sinusoidal sigma weight residual 93.00 174.01 -81.01 1 1.00e+01 1.00e-02 8.10e+01 dihedral pdb=" CB CYS A 461 " pdb=" SG CYS A 461 " pdb=" SG CYS A 477 " pdb=" CB CYS A 477 " ideal model delta sinusoidal sigma weight residual 93.00 170.04 -77.04 1 1.00e+01 1.00e-02 7.45e+01 dihedral pdb=" CB CYS A 392 " pdb=" SG CYS A 392 " pdb=" SG CYS A 438 " pdb=" CB CYS A 438 " ideal model delta sinusoidal sigma weight residual -86.00 -159.69 73.69 1 1.00e+01 1.00e-02 6.90e+01 ... (remaining 2949 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.067: 553 0.067 - 0.134: 115 0.134 - 0.201: 22 0.201 - 0.268: 10 0.268 - 0.335: 3 Chirality restraints: 703 Sorted by residual: chirality pdb=" CB VAL A 418 " pdb=" CA VAL A 418 " pdb=" CG1 VAL A 418 " pdb=" CG2 VAL A 418 " both_signs ideal model delta sigma weight residual False -2.63 -2.29 -0.33 2.00e-01 2.50e+01 2.80e+00 chirality pdb=" CG LEU A 154 " pdb=" CB LEU A 154 " pdb=" CD1 LEU A 154 " pdb=" CD2 LEU A 154 " both_signs ideal model delta sigma weight residual False -2.59 -2.29 -0.30 2.00e-01 2.50e+01 2.26e+00 chirality pdb=" CB VAL A 381 " pdb=" CA VAL A 381 " pdb=" CG1 VAL A 381 " pdb=" CG2 VAL A 381 " both_signs ideal model delta sigma weight residual False -2.63 -2.35 -0.28 2.00e-01 2.50e+01 1.98e+00 ... (remaining 700 not shown) Planarity restraints: 824 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ALA A 151 " 0.050 5.00e-02 4.00e+02 7.36e-02 8.68e+00 pdb=" N PRO A 152 " -0.127 5.00e-02 4.00e+02 pdb=" CA PRO A 152 " 0.036 5.00e-02 4.00e+02 pdb=" CD PRO A 152 " 0.042 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C LYS A 281 " 0.046 5.00e-02 4.00e+02 7.03e-02 7.91e+00 pdb=" N PRO A 282 " -0.122 5.00e-02 4.00e+02 pdb=" CA PRO A 282 " 0.037 5.00e-02 4.00e+02 pdb=" CD PRO A 282 " 0.039 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C CYS A 34 " 0.042 5.00e-02 4.00e+02 6.25e-02 6.25e+00 pdb=" N PRO A 35 " -0.108 5.00e-02 4.00e+02 pdb=" CA PRO A 35 " 0.031 5.00e-02 4.00e+02 pdb=" CD PRO A 35 " 0.035 5.00e-02 4.00e+02 ... (remaining 821 not shown) Histogram of nonbonded interaction distances: 2.34 - 2.85: 1525 2.85 - 3.36: 4096 3.36 - 3.88: 7405 3.88 - 4.39: 7696 4.39 - 4.90: 13195 Nonbonded interactions: 33917 Sorted by model distance: nonbonded pdb=" O VAL A 235 " pdb=" OG1 THR A 239 " model vdw 2.339 3.040 nonbonded pdb=" O ALA A 226 " pdb=" OH TYR A 332 " model vdw 2.375 3.040 nonbonded pdb=" O SER A 5 " pdb=" OG SER A 5 " model vdw 2.398 3.040 nonbonded pdb=" O SER A 232 " pdb=" OG1 THR A 236 " model vdw 2.404 3.040 nonbonded pdb=" O CYS A 514 " pdb=" NH2 ARG A 521 " model vdw 2.425 3.120 ... (remaining 33912 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=0.00 max=1.00 mean=0.87 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.380 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.210 Check model and map are aligned: 0.040 Set scattering table: 0.050 Process input model: 18.260 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: 0.000 Load rotamer database and sin/cos tables:2.980 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 23.000 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8023 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 : 0.005 0.066 4688 Z= 0.343 Angle : 1.118 11.803 6324 Z= 0.575 Chirality : 0.065 0.335 703 Planarity : 0.008 0.074 824 Dihedral : 15.048 88.031 1779 Min Nonbonded Distance : 2.339 Molprobity Statistics. All-atom Clashscore : 3.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.12 % Favored : 96.88 % Rotamer: Outliers : 0.00 % Allowed : 0.79 % Favored : 99.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -5.05 (0.22), residues: 576 helix: -3.30 (0.16), residues: 400 sheet: None (None), residues: 0 loop : -2.91 (0.33), residues: 176 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.002 TRP A 214 HIS 0.005 0.001 HIS A 39 PHE 0.042 0.002 PHE A 149 TYR 0.025 0.002 TYR A 411 ARG 0.004 0.000 ARG A 98 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1152 Ramachandran restraints generated. 576 Oldfield, 0 Emsley, 576 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1152 Ramachandran restraints generated. 576 Oldfield, 0 Emsley, 576 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 8 residues out of total 506 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 8 time to evaluate : 0.573 Fit side-chains REVERT: A 87 MET cc_start: 0.8679 (mmp) cc_final: 0.8461 (mmm) outliers start: 0 outliers final: 0 residues processed: 8 average time/residue: 0.1522 time to fit residues: 2.4506 Evaluate side-chains 6 residues out of total 506 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 6 time to evaluate : 0.553 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 57 random chunks: chunk 48 optimal weight: 4.9990 chunk 43 optimal weight: 9.9990 chunk 23 optimal weight: 0.8980 chunk 14 optimal weight: 0.9990 chunk 29 optimal weight: 6.9990 chunk 44 optimal weight: 0.3980 chunk 17 optimal weight: 0.2980 chunk 27 optimal weight: 3.9990 chunk 33 optimal weight: 3.9990 chunk 51 optimal weight: 5.9990 chunk 28 optimal weight: 0.7980 overall best weight: 0.6782 ------------------------------------------------------------------------------- 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: 0.8013 moved from start: 0.1196 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.028 4688 Z= 0.120 Angle : 0.506 6.231 6324 Z= 0.265 Chirality : 0.037 0.125 703 Planarity : 0.004 0.042 824 Dihedral : 4.347 20.573 619 Min Nonbonded Distance : 2.555 Molprobity Statistics. All-atom Clashscore : 2.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.08 % Favored : 97.92 % Rotamer: Outliers : 0.00 % Allowed : 6.13 % Favored : 93.87 % 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: -1.80 (0.32), residues: 576 helix: -0.63 (0.25), residues: 386 sheet: None (None), residues: 0 loop : -2.21 (0.39), residues: 190 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP A 214 HIS 0.002 0.000 HIS A 535 PHE 0.027 0.001 PHE A 554 TYR 0.009 0.001 TYR A 370 ARG 0.003 0.000 ARG A 98 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1152 Ramachandran restraints generated. 576 Oldfield, 0 Emsley, 576 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1152 Ramachandran restraints generated. 576 Oldfield, 0 Emsley, 576 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 10 residues out of total 506 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 10 time to evaluate : 0.553 Fit side-chains REVERT: A 87 MET cc_start: 0.8702 (mmp) cc_final: 0.8489 (mmm) REVERT: A 123 MET cc_start: 0.8842 (pmm) cc_final: 0.8620 (pmm) REVERT: A 446 MET cc_start: 0.7183 (mmm) cc_final: 0.6894 (mmt) REVERT: A 465 GLU cc_start: 0.9109 (tm-30) cc_final: 0.8873 (tm-30) outliers start: 0 outliers final: 0 residues processed: 10 average time/residue: 0.1400 time to fit residues: 2.5730 Evaluate side-chains 8 residues out of total 506 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 8 time to evaluate : 0.527 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 57 random chunks: chunk 16 optimal weight: 9.9990 chunk 43 optimal weight: 9.9990 chunk 35 optimal weight: 6.9990 chunk 14 optimal weight: 0.1980 chunk 51 optimal weight: 0.1980 chunk 56 optimal weight: 0.9990 chunk 46 optimal weight: 0.1980 chunk 17 optimal weight: 1.9990 chunk 41 optimal weight: 6.9990 chunk 38 optimal weight: 0.9980 chunk 26 optimal weight: 0.7980 overall best weight: 0.4780 ------------------------------------------------------------------------------- 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: 0.8000 moved from start: 0.1524 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.026 4688 Z= 0.103 Angle : 0.479 7.683 6324 Z= 0.243 Chirality : 0.037 0.128 703 Planarity : 0.003 0.038 824 Dihedral : 3.842 17.079 619 Min Nonbonded Distance : 2.602 Molprobity Statistics. All-atom Clashscore : 2.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.08 % Favored : 97.92 % Rotamer: Outliers : 0.20 % Allowed : 9.68 % Favored : 90.12 % 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: -0.45 (0.35), residues: 576 helix: 0.47 (0.27), residues: 388 sheet: None (None), residues: 0 loop : -1.86 (0.41), residues: 188 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.003 0.001 TRP A 214 HIS 0.002 0.000 HIS A 535 PHE 0.024 0.001 PHE A 554 TYR 0.009 0.001 TYR A 370 ARG 0.002 0.000 ARG A 98 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1152 Ramachandran restraints generated. 576 Oldfield, 0 Emsley, 576 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1152 Ramachandran restraints generated. 576 Oldfield, 0 Emsley, 576 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 10 residues out of total 506 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 9 time to evaluate : 0.576 Fit side-chains REVERT: A 87 MET cc_start: 0.8809 (mmp) cc_final: 0.8608 (mmm) REVERT: A 123 MET cc_start: 0.8833 (pmm) cc_final: 0.8444 (pmm) REVERT: A 446 MET cc_start: 0.7141 (mmm) cc_final: 0.6859 (mmt) outliers start: 1 outliers final: 0 residues processed: 9 average time/residue: 0.1402 time to fit residues: 2.4748 Evaluate side-chains 6 residues out of total 506 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 6 time to evaluate : 0.560 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 57 random chunks: chunk 5 optimal weight: 10.0000 chunk 24 optimal weight: 8.9990 chunk 34 optimal weight: 0.9990 chunk 52 optimal weight: 0.9980 chunk 55 optimal weight: 5.9990 chunk 27 optimal weight: 8.9990 chunk 49 optimal weight: 9.9990 chunk 14 optimal weight: 3.9990 chunk 45 optimal weight: 2.9990 chunk 31 optimal weight: 8.9990 chunk 0 optimal weight: 10.0000 overall best weight: 2.9988 ------------------------------------------------------------------------------- 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: 0.8103 moved from start: 0.2063 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.025 4688 Z= 0.261 Angle : 0.578 6.572 6324 Z= 0.302 Chirality : 0.040 0.125 703 Planarity : 0.004 0.037 824 Dihedral : 4.019 17.037 619 Min Nonbonded Distance : 2.500 Molprobity Statistics. All-atom Clashscore : 5.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.95 % Favored : 97.05 % Rotamer: Outliers : 0.79 % Allowed : 10.87 % Favored : 88.34 % 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: 0.02 (0.36), residues: 576 helix: 0.75 (0.27), residues: 402 sheet: None (None), residues: 0 loop : -1.66 (0.44), residues: 174 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.002 TRP A 214 HIS 0.004 0.001 HIS A 39 PHE 0.034 0.002 PHE A 554 TYR 0.014 0.002 TYR A 411 ARG 0.002 0.000 ARG A 222 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1152 Ramachandran restraints generated. 576 Oldfield, 0 Emsley, 576 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1152 Ramachandran restraints generated. 576 Oldfield, 0 Emsley, 576 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 11 residues out of total 506 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 7 time to evaluate : 0.580 Fit side-chains revert: symmetry clash REVERT: A 87 MET cc_start: 0.9009 (mmp) cc_final: 0.8652 (tpp) REVERT: A 123 MET cc_start: 0.9021 (pmm) cc_final: 0.8790 (pmm) outliers start: 4 outliers final: 2 residues processed: 11 average time/residue: 0.1413 time to fit residues: 2.9892 Evaluate side-chains 8 residues out of total 506 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 6 time to evaluate : 0.568 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 457 LEU Chi-restraints excluded: chain A residue 526 GLN Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 57 random chunks: chunk 41 optimal weight: 2.9990 chunk 22 optimal weight: 2.9990 chunk 47 optimal weight: 8.9990 chunk 38 optimal weight: 0.9980 chunk 0 optimal weight: 10.0000 chunk 28 optimal weight: 9.9990 chunk 49 optimal weight: 4.9990 chunk 13 optimal weight: 1.9990 chunk 18 optimal weight: 7.9990 chunk 10 optimal weight: 8.9990 chunk 32 optimal weight: 0.9990 overall best weight: 1.9988 ------------------------------------------------------------------------------- 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: 0.8086 moved from start: 0.2216 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.025 4688 Z= 0.186 Angle : 0.506 6.353 6324 Z= 0.264 Chirality : 0.039 0.131 703 Planarity : 0.003 0.038 824 Dihedral : 3.883 14.804 619 Min Nonbonded Distance : 2.532 Molprobity Statistics. All-atom Clashscore : 5.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.95 % Favored : 97.05 % Rotamer: Outliers : 0.20 % Allowed : 12.25 % Favored : 87.55 % 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 (0.36), residues: 576 helix: 1.07 (0.27), residues: 402 sheet: None (None), residues: 0 loop : -1.59 (0.44), residues: 174 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.002 TRP A 214 HIS 0.003 0.001 HIS A 464 PHE 0.039 0.001 PHE A 554 TYR 0.012 0.001 TYR A 370 ARG 0.001 0.000 ARG A 145 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1152 Ramachandran restraints generated. 576 Oldfield, 0 Emsley, 576 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1152 Ramachandran restraints generated. 576 Oldfield, 0 Emsley, 576 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 8 residues out of total 506 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 7 time to evaluate : 0.570 Fit side-chains revert: symmetry clash REVERT: A 87 MET cc_start: 0.9101 (mmp) cc_final: 0.8762 (tpp) REVERT: A 123 MET cc_start: 0.9089 (pmm) cc_final: 0.8696 (pmm) outliers start: 1 outliers final: 1 residues processed: 8 average time/residue: 0.1409 time to fit residues: 2.3196 Evaluate side-chains 7 residues out of total 506 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 6 time to evaluate : 0.579 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 526 GLN Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 57 random chunks: chunk 13 optimal weight: 2.9990 chunk 55 optimal weight: 3.9990 chunk 45 optimal weight: 2.9990 chunk 25 optimal weight: 0.7980 chunk 4 optimal weight: 1.9990 chunk 18 optimal weight: 8.9990 chunk 28 optimal weight: 8.9990 chunk 53 optimal weight: 3.9990 chunk 6 optimal weight: 1.9990 chunk 31 optimal weight: 9.9990 chunk 40 optimal weight: 3.9990 overall best weight: 2.1588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 67 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8100 moved from start: 0.2455 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.025 4688 Z= 0.200 Angle : 0.519 6.432 6324 Z= 0.271 Chirality : 0.039 0.128 703 Planarity : 0.003 0.037 824 Dihedral : 3.907 17.619 619 Min Nonbonded Distance : 2.576 Molprobity Statistics. All-atom Clashscore : 5.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.12 % Favored : 96.88 % Rotamer: Outliers : 0.99 % Allowed : 12.65 % Favored : 86.36 % 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: 0.64 (0.36), residues: 576 helix: 1.25 (0.27), residues: 402 sheet: None (None), residues: 0 loop : -1.52 (0.45), residues: 174 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.002 TRP A 214 HIS 0.003 0.001 HIS A 464 PHE 0.019 0.001 PHE A 554 TYR 0.012 0.001 TYR A 370 ARG 0.001 0.000 ARG A 197 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1152 Ramachandran restraints generated. 576 Oldfield, 0 Emsley, 576 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1152 Ramachandran restraints generated. 576 Oldfield, 0 Emsley, 576 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 12 residues out of total 506 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 7 time to evaluate : 0.683 Fit side-chains revert: symmetry clash REVERT: A 87 MET cc_start: 0.9117 (mmp) cc_final: 0.8779 (tpp) REVERT: A 123 MET cc_start: 0.9108 (pmm) cc_final: 0.8661 (pmm) outliers start: 5 outliers final: 3 residues processed: 12 average time/residue: 0.1447 time to fit residues: 3.2899 Evaluate side-chains 9 residues out of total 506 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 6 time to evaluate : 0.622 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 7 VAL Chi-restraints excluded: chain A residue 457 LEU Chi-restraints excluded: chain A residue 526 GLN Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 57 random chunks: chunk 31 optimal weight: 5.9990 chunk 46 optimal weight: 3.9990 chunk 30 optimal weight: 2.9990 chunk 54 optimal weight: 5.9990 chunk 34 optimal weight: 0.9980 chunk 33 optimal weight: 0.9990 chunk 25 optimal weight: 0.9980 chunk 21 optimal weight: 0.8980 chunk 32 optimal weight: 0.9980 chunk 16 optimal weight: 20.0000 chunk 10 optimal weight: 1.9990 overall best weight: 0.9782 ------------------------------------------------------------------------------- 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: 0.8061 moved from start: 0.2454 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.026 4688 Z= 0.124 Angle : 0.477 6.284 6324 Z= 0.248 Chirality : 0.038 0.128 703 Planarity : 0.003 0.034 824 Dihedral : 3.784 13.833 619 Min Nonbonded Distance : 2.613 Molprobity Statistics. All-atom Clashscore : 4.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.08 % Favored : 97.92 % Rotamer: Outliers : 0.40 % Allowed : 13.83 % Favored : 85.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.98 (0.37), residues: 576 helix: 1.61 (0.28), residues: 390 sheet: None (None), residues: 0 loop : -1.46 (0.44), residues: 186 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.002 TRP A 214 HIS 0.002 0.000 HIS A 535 PHE 0.021 0.001 PHE A 554 TYR 0.011 0.001 TYR A 370 ARG 0.001 0.000 ARG A 145 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1152 Ramachandran restraints generated. 576 Oldfield, 0 Emsley, 576 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1152 Ramachandran restraints generated. 576 Oldfield, 0 Emsley, 576 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 11 residues out of total 506 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 9 time to evaluate : 0.597 Fit side-chains revert: symmetry clash REVERT: A 87 MET cc_start: 0.9133 (mmp) cc_final: 0.8777 (tpp) REVERT: A 123 MET cc_start: 0.9106 (pmm) cc_final: 0.8647 (pmm) outliers start: 2 outliers final: 2 residues processed: 11 average time/residue: 0.1245 time to fit residues: 2.7259 Evaluate side-chains 9 residues out of total 506 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 7 time to evaluate : 0.589 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 7 VAL Chi-restraints excluded: chain A residue 526 GLN Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 57 random chunks: chunk 10 optimal weight: 1.9990 chunk 34 optimal weight: 0.9980 chunk 37 optimal weight: 5.9990 chunk 27 optimal weight: 10.0000 chunk 5 optimal weight: 6.9990 chunk 43 optimal weight: 2.9990 chunk 49 optimal weight: 7.9990 chunk 52 optimal weight: 0.8980 chunk 48 optimal weight: 2.9990 chunk 51 optimal weight: 0.0670 chunk 30 optimal weight: 0.7980 overall best weight: 0.9520 ------------------------------------------------------------------------------- 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: 0.8057 moved from start: 0.2519 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.026 4688 Z= 0.125 Angle : 0.485 7.517 6324 Z= 0.246 Chirality : 0.038 0.127 703 Planarity : 0.003 0.035 824 Dihedral : 3.683 13.438 619 Min Nonbonded Distance : 2.630 Molprobity Statistics. All-atom Clashscore : 4.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.08 % Favored : 97.92 % Rotamer: Outliers : 0.79 % Allowed : 13.83 % Favored : 85.38 % 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: 1.08 (0.37), residues: 576 helix: 1.65 (0.28), residues: 394 sheet: None (None), residues: 0 loop : -1.40 (0.45), residues: 182 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.002 TRP A 214 HIS 0.002 0.000 HIS A 464 PHE 0.017 0.001 PHE A 149 TYR 0.011 0.001 TYR A 370 ARG 0.001 0.000 ARG A 145 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1152 Ramachandran restraints generated. 576 Oldfield, 0 Emsley, 576 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1152 Ramachandran restraints generated. 576 Oldfield, 0 Emsley, 576 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 12 residues out of total 506 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 8 time to evaluate : 0.537 Fit side-chains revert: symmetry clash REVERT: A 87 MET cc_start: 0.9122 (mmp) cc_final: 0.8766 (tpp) REVERT: A 123 MET cc_start: 0.9073 (pmm) cc_final: 0.8654 (pmm) outliers start: 4 outliers final: 3 residues processed: 12 average time/residue: 0.1287 time to fit residues: 2.8734 Evaluate side-chains 10 residues out of total 506 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 7 time to evaluate : 0.663 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 7 VAL Chi-restraints excluded: chain A residue 457 LEU Chi-restraints excluded: chain A residue 526 GLN Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 57 random chunks: chunk 22 optimal weight: 0.3980 chunk 40 optimal weight: 0.8980 chunk 15 optimal weight: 0.4980 chunk 46 optimal weight: 0.9990 chunk 48 optimal weight: 7.9990 chunk 51 optimal weight: 0.4980 chunk 33 optimal weight: 0.9980 chunk 54 optimal weight: 1.9990 chunk 25 optimal weight: 0.9990 chunk 37 optimal weight: 0.8980 chunk 56 optimal weight: 3.9990 overall best weight: 0.6380 ------------------------------------------------------------------------------- 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: 0.8041 moved from start: 0.2553 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.026 4688 Z= 0.112 Angle : 0.492 8.895 6324 Z= 0.246 Chirality : 0.039 0.221 703 Planarity : 0.003 0.035 824 Dihedral : 3.647 13.866 619 Min Nonbonded Distance : 2.637 Molprobity Statistics. All-atom Clashscore : 4.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.91 % Favored : 98.09 % Rotamer: Outliers : 0.99 % Allowed : 13.64 % Favored : 85.38 % 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: 1.24 (0.37), residues: 576 helix: 1.76 (0.28), residues: 394 sheet: None (None), residues: 0 loop : -1.32 (0.45), residues: 182 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.002 TRP A 214 HIS 0.001 0.000 HIS A 535 PHE 0.018 0.001 PHE A 554 TYR 0.010 0.001 TYR A 370 ARG 0.001 0.000 ARG A 145 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1152 Ramachandran restraints generated. 576 Oldfield, 0 Emsley, 576 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1152 Ramachandran restraints generated. 576 Oldfield, 0 Emsley, 576 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 12 residues out of total 506 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 7 time to evaluate : 0.587 Fit side-chains revert: symmetry clash REVERT: A 87 MET cc_start: 0.9118 (mmp) cc_final: 0.8805 (tpt) REVERT: A 123 MET cc_start: 0.9071 (OUTLIER) cc_final: 0.8642 (pmm) outliers start: 5 outliers final: 4 residues processed: 11 average time/residue: 0.1242 time to fit residues: 2.7063 Evaluate side-chains 12 residues out of total 506 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 7 time to evaluate : 0.566 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 7 VAL Chi-restraints excluded: chain A residue 123 MET Chi-restraints excluded: chain A residue 438 CYS Chi-restraints excluded: chain A residue 457 LEU Chi-restraints excluded: chain A residue 526 GLN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 57 random chunks: chunk 52 optimal weight: 0.8980 chunk 45 optimal weight: 1.9990 chunk 4 optimal weight: 2.9990 chunk 34 optimal weight: 0.9980 chunk 27 optimal weight: 8.9990 chunk 35 optimal weight: 0.0870 chunk 48 optimal weight: 0.9980 chunk 13 optimal weight: 5.9990 chunk 41 optimal weight: 0.0170 chunk 6 optimal weight: 0.0060 chunk 12 optimal weight: 0.9990 overall best weight: 0.4012 ------------------------------------------------------------------------------- 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: 0.8008 moved from start: 0.2629 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.033 4688 Z= 0.106 Angle : 0.475 7.206 6324 Z= 0.238 Chirality : 0.038 0.253 703 Planarity : 0.003 0.035 824 Dihedral : 3.446 12.640 619 Min Nonbonded Distance : 2.642 Molprobity Statistics. All-atom Clashscore : 3.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.91 % Favored : 98.09 % Rotamer: Outliers : 1.19 % Allowed : 13.83 % Favored : 84.98 % 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: 1.45 (0.37), residues: 576 helix: 1.92 (0.28), residues: 389 sheet: None (None), residues: 0 loop : -1.14 (0.45), residues: 187 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.002 TRP A 214 HIS 0.001 0.000 HIS A 535 PHE 0.013 0.001 PHE A 554 TYR 0.009 0.000 TYR A 370 ARG 0.001 0.000 ARG A 337 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1152 Ramachandran restraints generated. 576 Oldfield, 0 Emsley, 576 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1152 Ramachandran restraints generated. 576 Oldfield, 0 Emsley, 576 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 13 residues out of total 506 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 7 time to evaluate : 0.600 Fit side-chains revert: symmetry clash REVERT: A 87 MET cc_start: 0.9125 (mmp) cc_final: 0.8804 (tpt) REVERT: A 123 MET cc_start: 0.9058 (OUTLIER) cc_final: 0.8614 (pmm) outliers start: 6 outliers final: 3 residues processed: 12 average time/residue: 0.1227 time to fit residues: 2.8138 Evaluate side-chains 11 residues out of total 506 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 7 time to evaluate : 0.573 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 123 MET Chi-restraints excluded: chain A residue 438 CYS Chi-restraints excluded: chain A residue 457 LEU Chi-restraints excluded: chain A residue 526 GLN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 57 random chunks: chunk 45 optimal weight: 1.9990 chunk 18 optimal weight: 0.9980 chunk 46 optimal weight: 3.9990 chunk 5 optimal weight: 3.9990 chunk 8 optimal weight: 0.0980 chunk 39 optimal weight: 1.9990 chunk 2 optimal weight: 0.0570 chunk 32 optimal weight: 0.9980 chunk 51 optimal weight: 0.9980 chunk 30 optimal weight: 0.8980 chunk 38 optimal weight: 0.9980 overall best weight: 0.6098 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 386 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3441 r_free = 0.3441 target = 0.052643 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3103 r_free = 0.3103 target = 0.042664 restraints weight = 34303.593| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3148 r_free = 0.3148 target = 0.043911 restraints weight = 17794.324| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3177 r_free = 0.3177 target = 0.044717 restraints weight = 11835.841| |-----------------------------------------------------------------------------| r_work (final): 0.3166 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3165 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3165 r_free = 0.3165 target_work(ls_wunit_k1) = 0.044 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 609 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3164 r_free = 0.3164 target_work(ls_wunit_k1) = 0.044 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 611 | |-----------------------------------------------------------------------------| r_final: 0.3164 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8065 moved from start: 0.2670 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.030 4688 Z= 0.109 Angle : 0.485 7.354 6324 Z= 0.244 Chirality : 0.038 0.214 703 Planarity : 0.003 0.034 824 Dihedral : 3.416 12.222 619 Min Nonbonded Distance : 2.640 Molprobity Statistics. All-atom Clashscore : 3.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.56 % Favored : 98.44 % Rotamer: Outliers : 0.99 % Allowed : 14.03 % Favored : 84.98 % 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: 1.55 (0.37), residues: 576 helix: 2.03 (0.28), residues: 385 sheet: None (None), residues: 0 loop : -1.12 (0.44), residues: 191 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 214 HIS 0.002 0.000 HIS A 535 PHE 0.014 0.001 PHE A 554 TYR 0.009 0.001 TYR A 370 ARG 0.001 0.000 ARG A 145 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1103.77 seconds wall clock time: 20 minutes 37.15 seconds (1237.15 seconds total)