Starting phenix.real_space_refine on Tue Feb 13 12:56:04 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7zdq_14666/02_2024/7zdq_14666.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7zdq_14666/02_2024/7zdq_14666.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.2 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7zdq_14666/02_2024/7zdq_14666.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7zdq_14666/02_2024/7zdq_14666.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7zdq_14666/02_2024/7zdq_14666.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7zdq_14666/02_2024/7zdq_14666.pdb" } resolution = 3.2 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= 0.000 sd= 0.006 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 33 5.16 5 C 4010 2.51 5 N 1037 2.21 5 O 1184 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-5238/modules/chem_data/mon_lib" Total number of atoms: 6264 Number of models: 1 Model: "" Number of chains: 3 Chain: "A" Number of atoms: 4877 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 597, 4870 Classifications: {'peptide': 597} Link IDs: {'PCIS': 1, 'PTRANS': 26, 'TRANS': 569} Conformer: "B" Number of residues, atoms: 597, 4870 Classifications: {'peptide': 597} Link IDs: {'PCIS': 1, 'PTRANS': 26, 'TRANS': 569} bond proxies already assigned to first conformer: 4998 Chain: "B" Number of atoms: 1345 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 166, 1339 Classifications: {'peptide': 166} Link IDs: {'PTRANS': 8, 'TRANS': 157} Chain breaks: 2 Conformer: "B" Number of residues, atoms: 166, 1339 Classifications: {'peptide': 166} Link IDs: {'PTRANS': 8, 'TRANS': 157} Chain breaks: 2 bond proxies already assigned to first conformer: 1370 Chain: "A" Number of atoms: 42 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 42 Unusual residues: {'NAG': 3} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Time building chain proxies: 6.41, per 1000 atoms: 1.02 Number of scatterers: 6264 At special positions: 0 Unit cell: (96.025, 98.53, 91.85, 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 33 16.00 O 1184 8.00 N 1037 7.00 C 4010 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=5, symmetry=0 Simple disulfide: pdb=" SG CYS A 133 " - pdb=" SG CYS A 141 " distance=2.04 Simple disulfide: pdb=" SG CYS A 344 " - pdb=" SG CYS A 361 " distance=2.03 Simple disulfide: pdb=" SG CYS A 530 " - pdb=" SG CYS A 542 " distance=2.03 Simple disulfide: pdb=" SG CYS B 379 " - pdb=" SG CYS B 432 " distance=2.03 Simple disulfide: pdb=" SG CYS B 480 " - pdb=" SG CYS B 488 " 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 Links applied NAG-ASN " NAG A 701 " - " ASN A 546 " " NAG A 702 " - " ASN A 90 " " NAG A 703 " - " ASN A 53 " Time building additional restraints: 2.36 Conformation dependent library (CDL) restraints added in 2.3 seconds 1514 Ramachandran restraints generated. 757 Oldfield, 0 Emsley, 757 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1438 Finding SS restraints... Secondary structure from input PDB file: 37 helices and 5 sheets defined 58.7% alpha, 5.5% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.61 Creating SS restraints... Processing helix chain 'A' and resid 20 through 37 removed outlier: 3.543A pdb=" N HIS A 34 " --> pdb=" O ASP A 30 " (cutoff:3.500A) Processing helix chain 'A' and resid 39 through 53 removed outlier: 3.827A pdb=" N SER A 43 " --> pdb=" O LEU A 39 " (cutoff:3.500A) Processing helix chain 'A' and resid 55 through 81 Processing helix chain 'A' and resid 90 through 102 removed outlier: 3.566A pdb=" N GLN A 102 " --> pdb=" O GLN A 98 " (cutoff:3.500A) Processing helix chain 'A' and resid 103 through 108 removed outlier: 3.538A pdb=" N SER A 106 " --> pdb=" O ASN A 103 " (cutoff:3.500A) Processing helix chain 'A' and resid 109 through 130 Processing helix chain 'A' and resid 146 through 155 removed outlier: 3.608A pdb=" N ILE A 151 " --> pdb=" O GLY A 147 " (cutoff:3.500A) Processing helix chain 'A' and resid 157 through 194 removed outlier: 3.986A pdb=" N LYS A 174 " --> pdb=" O SER A 170 " (cutoff:3.500A) Proline residue: A 178 - end of helix Processing helix chain 'A' and resid 198 through 205 Processing helix chain 'A' and resid 206 through 208 No H-bonds generated for 'chain 'A' and resid 206 through 208' Processing helix chain 'A' and resid 218 through 252 removed outlier: 3.692A pdb=" N LEU A 222 " --> pdb=" O SER A 218 " (cutoff:3.500A) removed outlier: 4.169A pdb=" N ILE A 223 " --> pdb=" O ARG A 219 " (cutoff:3.500A) removed outlier: 3.765A pdb=" N GLU A 224 " --> pdb=" O GLY A 220 " (cutoff:3.500A) Proline residue: A 235 - end of helix Processing helix chain 'A' and resid 275 through 277 No H-bonds generated for 'chain 'A' and resid 275 through 277' Processing helix chain 'A' and resid 278 through 283 Processing helix chain 'A' and resid 293 through 300 Processing helix chain 'A' and resid 303 through 319 Processing helix chain 'A' and resid 324 through 331 removed outlier: 3.687A pdb=" N TRP A 328 " --> pdb=" O THR A 324 " (cutoff:3.500A) removed outlier: 3.544A pdb=" N SER A 331 " --> pdb=" O PHE A 327 " (cutoff:3.500A) Processing helix chain 'A' and resid 365 through 386 Processing helix chain 'A' and resid 400 through 414 removed outlier: 3.584A pdb=" N THR A 414 " --> pdb=" O LEU A 410 " (cutoff:3.500A) Processing helix chain 'A' and resid 414 through 421 Processing helix chain 'A' and resid 431 through 447 Processing helix chain 'A' and resid 449 through 466 Processing helix chain 'A' and resid 469 through 471 No H-bonds generated for 'chain 'A' and resid 469 through 471' Processing helix chain 'A' and resid 472 through 484 Processing helix chain 'A' and resid 499 through 502 Processing helix chain 'A' and resid 503 through 508 Processing helix chain 'A' and resid 512 through 533 removed outlier: 4.401A pdb=" N TYR A 516 " --> pdb=" O PHE A 512 " (cutoff:3.500A) Processing helix chain 'A' and resid 538 through 542 Processing helix chain 'A' and resid 547 through 559 Processing helix chain 'A' and resid 565 through 575 Processing helix chain 'A' and resid 581 through 588 removed outlier: 3.538A pdb=" N PHE A 588 " --> pdb=" O LEU A 584 " (cutoff:3.500A) Processing helix chain 'A' and resid 588 through 599 Processing helix chain 'B' and resid 339 through 343 Processing helix chain 'B' and resid 368 through 372 removed outlier: 4.063A pdb=" N ALA B 372 " --> pdb=" O TYR B 369 " (cutoff:3.500A) Processing helix chain 'B' and resid 405 through 411 removed outlier: 4.268A pdb=" N ARG B 408 " --> pdb=" O ASP B 405 " (cutoff:3.500A) removed outlier: 3.829A pdb=" N ALA B 411 " --> pdb=" O ARG B 408 " (cutoff:3.500A) Processing helix chain 'B' and resid 416 through 422 Processing helix chain 'B' and resid 438 through 443 Processing helix chain 'B' and resid 502 through 505 Processing sheet with id=AA1, first strand: chain 'A' and resid 262 through 263 removed outlier: 5.948A pdb=" N LEU A 262 " --> pdb=" O VAL A 488 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA1 Processing sheet with id=AA2, first strand: chain 'A' and resid 347 through 350 Processing sheet with id=AA3, first strand: chain 'B' and resid 354 through 358 Processing sheet with id=AA4, first strand: chain 'B' and resid 452 through 454 Processing sheet with id=AA5, first strand: chain 'B' and resid 473 through 474 removed outlier: 3.521A pdb=" N TYR B 489 " --> pdb=" O TYR B 473 " (cutoff:3.500A) 317 hydrogen bonds defined for protein. 907 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: 1.63 Time building geometry restraints manager: 2.58 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.35: 2010 1.35 - 1.47: 1677 1.47 - 1.59: 2701 1.59 - 1.70: 0 1.70 - 1.82: 54 Bond restraints: 6442 Sorted by residual: bond pdb=" C GLU A 589 " pdb=" N PRO A 590 " ideal model delta sigma weight residual 1.335 1.356 -0.021 1.36e-02 5.41e+03 2.31e+00 bond pdb=" C1 NAG A 702 " pdb=" O5 NAG A 702 " ideal model delta sigma weight residual 1.406 1.435 -0.029 2.00e-02 2.50e+03 2.08e+00 bond pdb=" C1 NAG A 701 " pdb=" O5 NAG A 701 " ideal model delta sigma weight residual 1.406 1.433 -0.027 2.00e-02 2.50e+03 1.86e+00 bond pdb=" C1 NAG A 703 " pdb=" O5 NAG A 703 " ideal model delta sigma weight residual 1.406 1.432 -0.026 2.00e-02 2.50e+03 1.71e+00 bond pdb=" C5 NAG A 701 " pdb=" O5 NAG A 701 " ideal model delta sigma weight residual 1.413 1.436 -0.023 2.00e-02 2.50e+03 1.33e+00 ... (remaining 6437 not shown) Histogram of bond angle deviations from ideal: 99.63 - 106.50: 194 106.50 - 113.38: 3329 113.38 - 120.25: 2352 120.25 - 127.12: 2784 127.12 - 134.00: 93 Bond angle restraints: 8752 Sorted by residual: angle pdb=" N LEU A 39 " pdb=" CA LEU A 39 " pdb=" C LEU A 39 " ideal model delta sigma weight residual 113.41 108.45 4.96 1.22e+00 6.72e-01 1.65e+01 angle pdb=" N ILE A 259 " pdb=" CA ILE A 259 " pdb=" C ILE A 259 " ideal model delta sigma weight residual 113.20 109.47 3.73 9.60e-01 1.09e+00 1.51e+01 angle pdb=" C PRO A 389 " pdb=" N PHE A 390 " pdb=" CA PHE A 390 " ideal model delta sigma weight residual 120.82 124.88 -4.06 1.50e+00 4.44e-01 7.34e+00 angle pdb=" CA ALA A 614 " pdb=" C ALA A 614 " pdb=" N ASP A 615 " ideal model delta sigma weight residual 119.26 116.40 2.86 1.14e+00 7.69e-01 6.31e+00 angle pdb=" C ALA A 614 " pdb=" N ASP A 615 " pdb=" CA ASP A 615 " ideal model delta sigma weight residual 121.70 126.14 -4.44 1.80e+00 3.09e-01 6.09e+00 ... (remaining 8747 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 18.00: 3432 18.00 - 36.00: 313 36.00 - 54.00: 57 54.00 - 71.99: 18 71.99 - 89.99: 11 Dihedral angle restraints: 3831 sinusoidal: 1587 harmonic: 2244 Sorted by residual: dihedral pdb=" CB CYS A 133 " pdb=" SG CYS A 133 " pdb=" SG CYS A 141 " pdb=" CB CYS A 141 " ideal model delta sinusoidal sigma weight residual 93.00 25.70 67.30 1 1.00e+01 1.00e-02 5.90e+01 dihedral pdb=" CB CYS A 530 " pdb=" SG CYS A 530 " pdb=" SG CYS A 542 " pdb=" CB CYS A 542 " ideal model delta sinusoidal sigma weight residual -86.00 -122.22 36.22 1 1.00e+01 1.00e-02 1.85e+01 dihedral pdb=" CA CYS A 344 " pdb=" C CYS A 344 " pdb=" N HIS A 345 " pdb=" CA HIS A 345 " ideal model delta harmonic sigma weight residual 180.00 162.64 17.36 0 5.00e+00 4.00e-02 1.21e+01 ... (remaining 3828 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.035: 644 0.035 - 0.070: 184 0.070 - 0.105: 73 0.105 - 0.140: 14 0.140 - 0.175: 1 Chirality restraints: 916 Sorted by residual: chirality pdb=" CB ILE B 410 " pdb=" CA ILE B 410 " pdb=" CG1 ILE B 410 " pdb=" CG2 ILE B 410 " both_signs ideal model delta sigma weight residual False 2.64 2.82 -0.17 2.00e-01 2.50e+01 7.66e-01 chirality pdb=" CA ILE B 434 " pdb=" N ILE B 434 " pdb=" C ILE B 434 " pdb=" CB ILE B 434 " both_signs ideal model delta sigma weight residual False 2.43 2.56 -0.12 2.00e-01 2.50e+01 3.86e-01 chirality pdb=" CA TYR A 385 " pdb=" N TYR A 385 " pdb=" C TYR A 385 " pdb=" CB TYR A 385 " both_signs ideal model delta sigma weight residual False 2.51 2.39 0.12 2.00e-01 2.50e+01 3.80e-01 ... (remaining 913 not shown) Planarity restraints: 1135 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C HIS A 345 " -0.052 5.00e-02 4.00e+02 7.73e-02 9.55e+00 pdb=" N PRO A 346 " 0.134 5.00e-02 4.00e+02 pdb=" CA PRO A 346 " -0.039 5.00e-02 4.00e+02 pdb=" CD PRO A 346 " -0.043 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CG GLU A 171 " -0.008 2.00e-02 2.50e+03 1.55e-02 2.41e+00 pdb=" CD GLU A 171 " 0.027 2.00e-02 2.50e+03 pdb=" OE1 GLU A 171 " -0.010 2.00e-02 2.50e+03 pdb=" OE2 GLU A 171 " -0.010 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C ASP A 499 " 0.026 5.00e-02 4.00e+02 3.88e-02 2.40e+00 pdb=" N PRO A 500 " -0.067 5.00e-02 4.00e+02 pdb=" CA PRO A 500 " 0.020 5.00e-02 4.00e+02 pdb=" CD PRO A 500 " 0.022 5.00e-02 4.00e+02 ... (remaining 1132 not shown) Histogram of nonbonded interaction distances: 2.21 - 2.75: 655 2.75 - 3.29: 6118 3.29 - 3.82: 10709 3.82 - 4.36: 12709 4.36 - 4.90: 21987 Nonbonded interactions: 52178 Sorted by model distance: nonbonded pdb=" O ASN B 439 " pdb=" OG SER B 443 " model vdw 2.212 2.440 nonbonded pdb=" OE1 GLU B 406 " pdb=" OH TYR B 495 " model vdw 2.226 2.440 nonbonded pdb=" OG SER A 425 " pdb=" OD1 ASP A 427 " model vdw 2.232 2.440 nonbonded pdb=" OG1 THR A 229 " pdb=" OH TYR A 516 " model vdw 2.249 2.440 nonbonded pdb=" O ASP A 431 " pdb=" OG1 THR A 434 " model vdw 2.277 2.440 ... (remaining 52173 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=0.50 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: 0.530 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: 1.620 Check model and map are aligned: 0.100 Set scattering table: 0.060 Process input model: 24.140 Find NCS groups from input model: 0.160 Set up NCS constraints: 0.030 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:2.840 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 29.480 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7858 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 : 0.003 0.045 6442 Z= 0.180 Angle : 0.555 6.676 8752 Z= 0.315 Chirality : 0.040 0.175 916 Planarity : 0.004 0.077 1132 Dihedral : 15.107 89.992 2378 Min Nonbonded Distance : 2.212 Molprobity Statistics. All-atom Clashscore : 6.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.25 % Favored : 97.75 % Rotamer: Outliers : 0.15 % Allowed : 0.45 % Favored : 99.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.86 % 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: 1.48 (0.31), residues: 757 helix: 2.02 (0.27), residues: 394 sheet: 1.39 (0.85), residues: 39 loop : -0.37 (0.35), residues: 324 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 165 HIS 0.005 0.001 HIS A 374 PHE 0.021 0.001 PHE A 369 TYR 0.008 0.001 TYR A 381 ARG 0.006 0.000 ARG B 457 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1514 Ramachandran restraints generated. 757 Oldfield, 0 Emsley, 757 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1514 Ramachandran restraints generated. 757 Oldfield, 0 Emsley, 757 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 90 residues out of total 668 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 90 time to evaluate : 0.661 Fit side-chains REVERT: A 483 GLU cc_start: 0.7026 (mp0) cc_final: 0.6688 (mp0) REVERT: A 568 LEU cc_start: 0.7999 (tt) cc_final: 0.7580 (mp) outliers start: 0 outliers final: 0 residues processed: 90 average time/residue: 0.2181 time to fit residues: 25.4746 Evaluate side-chains 77 residues out of total 668 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 77 time to evaluate : 0.676 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 75 random chunks: chunk 63 optimal weight: 10.0000 chunk 56 optimal weight: 4.9990 chunk 31 optimal weight: 0.9990 chunk 19 optimal weight: 0.7980 chunk 38 optimal weight: 0.9990 chunk 30 optimal weight: 0.4980 chunk 58 optimal weight: 2.9990 chunk 22 optimal weight: 0.7980 chunk 35 optimal weight: 3.9990 chunk 43 optimal weight: 0.7980 chunk 68 optimal weight: 7.9990 overall best weight: 0.7782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 137 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 580 ASN B 498 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7887 moved from start: 0.0672 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.033 6442 Z= 0.152 Angle : 0.473 6.015 8752 Z= 0.247 Chirality : 0.039 0.158 916 Planarity : 0.004 0.054 1132 Dihedral : 3.854 24.608 896 Min Nonbonded Distance : 2.185 Molprobity Statistics. All-atom Clashscore : 6.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.65 % Favored : 97.35 % Rotamer: Outliers : 0.89 % Allowed : 4.46 % Favored : 94.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.86 % 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: 1.57 (0.32), residues: 757 helix: 1.99 (0.26), residues: 404 sheet: 0.67 (0.75), residues: 50 loop : -0.15 (0.38), residues: 303 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 165 HIS 0.003 0.001 HIS A 374 PHE 0.021 0.001 PHE A 369 TYR 0.025 0.001 TYR A 385 ARG 0.003 0.000 ARG B 457 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1514 Ramachandran restraints generated. 757 Oldfield, 0 Emsley, 757 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1514 Ramachandran restraints generated. 757 Oldfield, 0 Emsley, 757 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 87 residues out of total 668 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 82 time to evaluate : 0.731 Fit side-chains REVERT: A 492 PRO cc_start: 0.7540 (Cg_exo) cc_final: 0.7264 (Cg_endo) outliers start: 5 outliers final: 3 residues processed: 85 average time/residue: 0.2063 time to fit residues: 23.4141 Evaluate side-chains 80 residues out of total 668 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 77 time to evaluate : 0.723 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 91 LEU Chi-restraints excluded: chain A residue 347 THR Chi-restraints excluded: chain A residue 432 ASN Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 75 random chunks: chunk 37 optimal weight: 1.9990 chunk 21 optimal weight: 5.9990 chunk 56 optimal weight: 0.9990 chunk 46 optimal weight: 4.9990 chunk 18 optimal weight: 0.7980 chunk 68 optimal weight: 8.9990 chunk 73 optimal weight: 2.9990 chunk 60 optimal weight: 6.9990 chunk 67 optimal weight: 5.9990 chunk 23 optimal weight: 3.9990 chunk 54 optimal weight: 0.9990 overall best weight: 1.5588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 137 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7965 moved from start: 0.1054 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 6442 Z= 0.213 Angle : 0.515 5.969 8752 Z= 0.269 Chirality : 0.041 0.141 916 Planarity : 0.004 0.046 1132 Dihedral : 3.934 21.340 896 Min Nonbonded Distance : 2.189 Molprobity Statistics. All-atom Clashscore : 6.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.05 % Favored : 96.95 % Rotamer: Outliers : 1.19 % Allowed : 5.21 % Favored : 93.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.86 % 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: 1.39 (0.31), residues: 757 helix: 1.90 (0.26), residues: 398 sheet: 0.52 (0.75), residues: 51 loop : -0.27 (0.37), residues: 308 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A 165 HIS 0.005 0.001 HIS A 241 PHE 0.020 0.002 PHE A 369 TYR 0.028 0.002 TYR A 385 ARG 0.002 0.000 ARG A 169 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1514 Ramachandran restraints generated. 757 Oldfield, 0 Emsley, 757 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1514 Ramachandran restraints generated. 757 Oldfield, 0 Emsley, 757 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 82 residues out of total 668 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 75 time to evaluate : 0.860 Fit side-chains REVERT: A 492 PRO cc_start: 0.7482 (Cg_exo) cc_final: 0.7184 (Cg_endo) outliers start: 7 outliers final: 4 residues processed: 79 average time/residue: 0.2124 time to fit residues: 22.3707 Evaluate side-chains 76 residues out of total 668 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 72 time to evaluate : 0.680 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 91 LEU Chi-restraints excluded: chain A residue 347 THR Chi-restraints excluded: chain A residue 432 ASN Chi-restraints excluded: chain A residue 568 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 75 random chunks: chunk 67 optimal weight: 0.9980 chunk 51 optimal weight: 1.9990 chunk 35 optimal weight: 8.9990 chunk 7 optimal weight: 4.9990 chunk 32 optimal weight: 0.6980 chunk 45 optimal weight: 0.6980 chunk 68 optimal weight: 0.0570 chunk 72 optimal weight: 2.9990 chunk 64 optimal weight: 1.9990 chunk 19 optimal weight: 0.2980 chunk 60 optimal weight: 3.9990 overall best weight: 0.5498 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 137 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 401 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7887 moved from start: 0.0992 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.032 6442 Z= 0.134 Angle : 0.459 5.914 8752 Z= 0.238 Chirality : 0.039 0.125 916 Planarity : 0.003 0.042 1132 Dihedral : 3.646 19.019 896 Min Nonbonded Distance : 2.218 Molprobity Statistics. All-atom Clashscore : 5.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.38 % Favored : 97.62 % Rotamer: Outliers : 0.74 % Allowed : 6.40 % Favored : 92.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.86 % 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: 1.59 (0.31), residues: 757 helix: 2.10 (0.26), residues: 398 sheet: 0.42 (0.74), residues: 51 loop : -0.19 (0.37), residues: 308 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 165 HIS 0.003 0.001 HIS A 374 PHE 0.019 0.001 PHE A 369 TYR 0.021 0.001 TYR A 385 ARG 0.002 0.000 ARG B 457 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1514 Ramachandran restraints generated. 757 Oldfield, 0 Emsley, 757 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1514 Ramachandran restraints generated. 757 Oldfield, 0 Emsley, 757 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 85 residues out of total 668 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 81 time to evaluate : 0.673 Fit side-chains REVERT: A 216 ASP cc_start: 0.7527 (m-30) cc_final: 0.7273 (m-30) REVERT: A 492 PRO cc_start: 0.7395 (Cg_exo) cc_final: 0.7108 (Cg_endo) REVERT: A 548 THR cc_start: 0.7832 (m) cc_final: 0.7307 (p) outliers start: 4 outliers final: 4 residues processed: 83 average time/residue: 0.2024 time to fit residues: 22.3810 Evaluate side-chains 81 residues out of total 668 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 77 time to evaluate : 0.692 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 91 LEU Chi-restraints excluded: chain A residue 347 THR Chi-restraints excluded: chain A residue 432 ASN Chi-restraints excluded: chain A residue 568 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 75 random chunks: chunk 41 optimal weight: 2.9990 chunk 1 optimal weight: 1.9990 chunk 53 optimal weight: 1.9990 chunk 29 optimal weight: 0.9980 chunk 61 optimal weight: 0.0980 chunk 50 optimal weight: 3.9990 chunk 0 optimal weight: 6.9990 chunk 37 optimal weight: 1.9990 chunk 65 optimal weight: 2.9990 chunk 18 optimal weight: 1.9990 chunk 24 optimal weight: 0.8980 overall best weight: 1.1984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 137 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7938 moved from start: 0.1116 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 6442 Z= 0.180 Angle : 0.481 5.979 8752 Z= 0.251 Chirality : 0.040 0.127 916 Planarity : 0.003 0.038 1132 Dihedral : 3.725 21.021 896 Min Nonbonded Distance : 2.198 Molprobity Statistics. All-atom Clashscore : 6.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.78 % Favored : 97.22 % Rotamer: Outliers : 0.74 % Allowed : 7.29 % Favored : 91.96 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.86 % 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: 1.53 (0.31), residues: 757 helix: 2.04 (0.26), residues: 398 sheet: 0.41 (0.75), residues: 51 loop : -0.21 (0.37), residues: 308 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 165 HIS 0.004 0.001 HIS A 241 PHE 0.019 0.001 PHE A 369 TYR 0.024 0.001 TYR A 385 ARG 0.002 0.000 ARG B 457 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1514 Ramachandran restraints generated. 757 Oldfield, 0 Emsley, 757 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1514 Ramachandran restraints generated. 757 Oldfield, 0 Emsley, 757 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 82 residues out of total 668 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 78 time to evaluate : 0.723 Fit side-chains REVERT: A 492 PRO cc_start: 0.7449 (Cg_exo) cc_final: 0.7173 (Cg_endo) REVERT: A 548 THR cc_start: 0.7848 (m) cc_final: 0.7327 (p) outliers start: 4 outliers final: 4 residues processed: 80 average time/residue: 0.1903 time to fit residues: 20.3179 Evaluate side-chains 80 residues out of total 668 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 76 time to evaluate : 0.691 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 91 LEU Chi-restraints excluded: chain A residue 347 THR Chi-restraints excluded: chain A residue 432 ASN Chi-restraints excluded: chain A residue 568 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 75 random chunks: chunk 65 optimal weight: 4.9990 chunk 14 optimal weight: 6.9990 chunk 42 optimal weight: 0.9990 chunk 17 optimal weight: 0.6980 chunk 72 optimal weight: 0.9990 chunk 60 optimal weight: 4.9990 chunk 33 optimal weight: 4.9990 chunk 6 optimal weight: 0.3980 chunk 24 optimal weight: 0.7980 chunk 38 optimal weight: 2.9990 chunk 69 optimal weight: 0.9980 overall best weight: 0.7782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 137 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7910 moved from start: 0.1141 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.031 6442 Z= 0.146 Angle : 0.454 5.944 8752 Z= 0.238 Chirality : 0.039 0.121 916 Planarity : 0.003 0.037 1132 Dihedral : 3.617 19.318 896 Min Nonbonded Distance : 2.216 Molprobity Statistics. All-atom Clashscore : 5.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.91 % Favored : 97.09 % Rotamer: Outliers : 1.04 % Allowed : 7.44 % Favored : 91.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.86 % 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: 1.61 (0.31), residues: 757 helix: 2.11 (0.26), residues: 400 sheet: 0.37 (0.74), residues: 51 loop : -0.17 (0.37), residues: 306 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 165 HIS 0.003 0.001 HIS A 374 PHE 0.019 0.001 PHE A 369 TYR 0.021 0.001 TYR A 385 ARG 0.002 0.000 ARG B 457 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1514 Ramachandran restraints generated. 757 Oldfield, 0 Emsley, 757 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1514 Ramachandran restraints generated. 757 Oldfield, 0 Emsley, 757 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 85 residues out of total 668 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 79 time to evaluate : 0.667 Fit side-chains REVERT: A 202 TYR cc_start: 0.8107 (t80) cc_final: 0.7704 (t80) REVERT: A 492 PRO cc_start: 0.7407 (Cg_exo) cc_final: 0.7124 (Cg_endo) REVERT: A 548 THR cc_start: 0.7828 (m) cc_final: 0.7298 (p) outliers start: 6 outliers final: 5 residues processed: 82 average time/residue: 0.2064 time to fit residues: 22.8006 Evaluate side-chains 80 residues out of total 668 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 75 time to evaluate : 0.587 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 91 LEU Chi-restraints excluded: chain A residue 347 THR Chi-restraints excluded: chain A residue 432 ASN Chi-restraints excluded: chain A residue 568 LEU Chi-restraints excluded: chain A residue 571 GLU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 75 random chunks: chunk 8 optimal weight: 10.0000 chunk 41 optimal weight: 4.9990 chunk 52 optimal weight: 6.9990 chunk 61 optimal weight: 8.9990 chunk 40 optimal weight: 1.9990 chunk 72 optimal weight: 5.9990 chunk 45 optimal weight: 0.9990 chunk 44 optimal weight: 1.9990 chunk 33 optimal weight: 0.8980 chunk 28 optimal weight: 4.9990 chunk 43 optimal weight: 2.9990 overall best weight: 1.7788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 137 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7981 moved from start: 0.1369 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 6442 Z= 0.229 Angle : 0.509 5.995 8752 Z= 0.268 Chirality : 0.041 0.138 916 Planarity : 0.004 0.035 1132 Dihedral : 3.903 21.857 896 Min Nonbonded Distance : 2.193 Molprobity Statistics. All-atom Clashscore : 6.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.05 % Favored : 96.95 % Rotamer: Outliers : 1.04 % Allowed : 7.74 % Favored : 91.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.86 % 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: 1.38 (0.31), residues: 757 helix: 1.91 (0.26), residues: 399 sheet: 0.40 (0.75), residues: 51 loop : -0.28 (0.36), residues: 307 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 165 HIS 0.005 0.001 HIS A 241 PHE 0.018 0.002 PHE A 369 TYR 0.026 0.002 TYR A 385 ARG 0.002 0.000 ARG A 169 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1514 Ramachandran restraints generated. 757 Oldfield, 0 Emsley, 757 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1514 Ramachandran restraints generated. 757 Oldfield, 0 Emsley, 757 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 84 residues out of total 668 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 78 time to evaluate : 0.703 Fit side-chains REVERT: A 492 PRO cc_start: 0.7521 (Cg_exo) cc_final: 0.7257 (Cg_endo) REVERT: A 548 THR cc_start: 0.7864 (m) cc_final: 0.7366 (p) outliers start: 6 outliers final: 5 residues processed: 81 average time/residue: 0.1821 time to fit residues: 19.9311 Evaluate side-chains 81 residues out of total 668 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 76 time to evaluate : 0.688 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 91 LEU Chi-restraints excluded: chain A residue 347 THR Chi-restraints excluded: chain A residue 432 ASN Chi-restraints excluded: chain A residue 568 LEU Chi-restraints excluded: chain A residue 571 GLU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 75 random chunks: chunk 21 optimal weight: 0.7980 chunk 14 optimal weight: 6.9990 chunk 45 optimal weight: 3.9990 chunk 49 optimal weight: 0.6980 chunk 35 optimal weight: 5.9990 chunk 6 optimal weight: 0.7980 chunk 56 optimal weight: 0.8980 chunk 65 optimal weight: 2.9990 chunk 69 optimal weight: 6.9990 chunk 63 optimal weight: 5.9990 chunk 67 optimal weight: 9.9990 overall best weight: 1.2382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 137 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7956 moved from start: 0.1335 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 6442 Z= 0.182 Angle : 0.480 5.988 8752 Z= 0.253 Chirality : 0.040 0.128 916 Planarity : 0.003 0.035 1132 Dihedral : 3.823 20.258 896 Min Nonbonded Distance : 2.194 Molprobity Statistics. All-atom Clashscore : 6.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.52 % Favored : 97.48 % Rotamer: Outliers : 0.89 % Allowed : 8.33 % Favored : 90.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.86 % 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: 1.44 (0.31), residues: 757 helix: 1.97 (0.26), residues: 399 sheet: 0.36 (0.75), residues: 51 loop : -0.26 (0.36), residues: 307 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 165 HIS 0.004 0.001 HIS A 241 PHE 0.018 0.001 PHE A 369 TYR 0.023 0.001 TYR A 385 ARG 0.006 0.000 ARG B 457 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1514 Ramachandran restraints generated. 757 Oldfield, 0 Emsley, 757 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1514 Ramachandran restraints generated. 757 Oldfield, 0 Emsley, 757 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 84 residues out of total 668 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 79 time to evaluate : 0.732 Fit side-chains REVERT: A 492 PRO cc_start: 0.7495 (Cg_exo) cc_final: 0.7223 (Cg_endo) REVERT: A 548 THR cc_start: 0.7876 (m) cc_final: 0.7372 (p) outliers start: 5 outliers final: 4 residues processed: 81 average time/residue: 0.1881 time to fit residues: 20.7225 Evaluate side-chains 83 residues out of total 668 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 79 time to evaluate : 0.705 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 91 LEU Chi-restraints excluded: chain A residue 347 THR Chi-restraints excluded: chain A residue 432 ASN Chi-restraints excluded: chain A residue 568 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 75 random chunks: chunk 69 optimal weight: 0.9990 chunk 40 optimal weight: 8.9990 chunk 29 optimal weight: 0.9990 chunk 52 optimal weight: 3.9990 chunk 20 optimal weight: 2.9990 chunk 60 optimal weight: 5.9990 chunk 63 optimal weight: 9.9990 chunk 67 optimal weight: 0.8980 chunk 44 optimal weight: 1.9990 chunk 71 optimal weight: 5.9990 chunk 43 optimal weight: 0.9980 overall best weight: 1.1786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 137 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7951 moved from start: 0.1346 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 6442 Z= 0.179 Angle : 0.475 5.980 8752 Z= 0.250 Chirality : 0.040 0.127 916 Planarity : 0.003 0.034 1132 Dihedral : 3.793 21.395 896 Min Nonbonded Distance : 2.198 Molprobity Statistics. All-atom Clashscore : 6.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.91 % Favored : 97.09 % Rotamer: Outliers : 0.74 % Allowed : 8.48 % Favored : 90.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.86 % 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 (0.31), residues: 757 helix: 1.98 (0.26), residues: 399 sheet: 0.33 (0.75), residues: 51 loop : -0.25 (0.36), residues: 307 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 165 HIS 0.003 0.001 HIS A 241 PHE 0.018 0.001 PHE A 369 TYR 0.023 0.001 TYR A 385 ARG 0.002 0.000 ARG A 169 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1514 Ramachandran restraints generated. 757 Oldfield, 0 Emsley, 757 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1514 Ramachandran restraints generated. 757 Oldfield, 0 Emsley, 757 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 83 residues out of total 668 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 79 time to evaluate : 0.706 Fit side-chains REVERT: A 492 PRO cc_start: 0.7447 (Cg_exo) cc_final: 0.7180 (Cg_endo) REVERT: A 548 THR cc_start: 0.7869 (m) cc_final: 0.7364 (p) outliers start: 4 outliers final: 4 residues processed: 81 average time/residue: 0.1798 time to fit residues: 19.6571 Evaluate side-chains 82 residues out of total 668 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 78 time to evaluate : 0.709 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 91 LEU Chi-restraints excluded: chain A residue 347 THR Chi-restraints excluded: chain A residue 432 ASN Chi-restraints excluded: chain A residue 568 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 75 random chunks: chunk 33 optimal weight: 3.9990 chunk 49 optimal weight: 0.0770 chunk 74 optimal weight: 0.5980 chunk 68 optimal weight: 4.9990 chunk 59 optimal weight: 5.9990 chunk 6 optimal weight: 5.9990 chunk 45 optimal weight: 0.0370 chunk 36 optimal weight: 2.9990 chunk 47 optimal weight: 8.9990 chunk 63 optimal weight: 0.0770 chunk 18 optimal weight: 0.9980 overall best weight: 0.3574 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 137 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 239 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7872 moved from start: 0.1318 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.031 6442 Z= 0.128 Angle : 0.440 5.905 8752 Z= 0.230 Chirality : 0.038 0.121 916 Planarity : 0.003 0.036 1132 Dihedral : 3.553 19.469 896 Min Nonbonded Distance : 2.221 Molprobity Statistics. All-atom Clashscore : 5.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.52 % Favored : 97.48 % Rotamer: Outliers : 0.60 % Allowed : 8.63 % Favored : 90.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.86 % 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: 1.74 (0.31), residues: 757 helix: 2.29 (0.26), residues: 393 sheet: 0.86 (0.83), residues: 40 loop : -0.22 (0.35), residues: 324 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 165 HIS 0.002 0.001 HIS A 374 PHE 0.019 0.001 PHE A 369 TYR 0.018 0.001 TYR A 385 ARG 0.002 0.000 ARG B 457 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1514 Ramachandran restraints generated. 757 Oldfield, 0 Emsley, 757 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1514 Ramachandran restraints generated. 757 Oldfield, 0 Emsley, 757 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 80 residues out of total 668 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 77 time to evaluate : 0.740 Fit side-chains REVERT: A 202 TYR cc_start: 0.8100 (t80) cc_final: 0.7731 (t80) REVERT: A 492 PRO cc_start: 0.7502 (Cg_exo) cc_final: 0.7256 (Cg_endo) REVERT: A 548 THR cc_start: 0.7786 (m) cc_final: 0.7254 (p) outliers start: 3 outliers final: 3 residues processed: 79 average time/residue: 0.1829 time to fit residues: 19.7395 Evaluate side-chains 78 residues out of total 668 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 75 time to evaluate : 0.717 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 347 THR Chi-restraints excluded: chain A residue 432 ASN Chi-restraints excluded: chain A residue 568 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 75 random chunks: chunk 54 optimal weight: 5.9990 chunk 8 optimal weight: 7.9990 chunk 16 optimal weight: 0.9990 chunk 59 optimal weight: 6.9990 chunk 24 optimal weight: 7.9990 chunk 61 optimal weight: 9.9990 chunk 7 optimal weight: 5.9990 chunk 10 optimal weight: 0.6980 chunk 52 optimal weight: 5.9990 chunk 3 optimal weight: 4.9990 chunk 43 optimal weight: 0.9980 overall best weight: 2.7386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 137 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3612 r_free = 0.3612 target = 0.150661 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3285 r_free = 0.3285 target = 0.123379 restraints weight = 14333.183| |-----------------------------------------------------------------------------| r_work (start): 0.3270 rms_B_bonded: 2.92 r_work: 0.3049 rms_B_bonded: 3.54 restraints_weight: 0.5000 r_work (final): 0.3049 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3034 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3034 r_free = 0.3034 target_work(ls_wunit_k1) = 0.104 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3034 r_free = 0.3034 target_work(ls_wunit_k1) = 0.104 | | occupancies: max = 1.00 min = 0.40 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3034 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8210 moved from start: 0.1525 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.052 6442 Z= 0.320 Angle : 0.560 6.078 8752 Z= 0.296 Chirality : 0.044 0.147 916 Planarity : 0.004 0.033 1132 Dihedral : 4.079 22.297 896 Min Nonbonded Distance : 2.186 Molprobity Statistics. All-atom Clashscore : 6.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.18 % Favored : 96.82 % Rotamer: Outliers : 0.60 % Allowed : 8.48 % Favored : 90.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.86 % 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: 1.18 (0.31), residues: 757 helix: 1.74 (0.26), residues: 399 sheet: 0.43 (0.75), residues: 51 loop : -0.40 (0.36), residues: 307 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.002 TRP A 165 HIS 0.007 0.001 HIS A 241 PHE 0.021 0.002 PHE A 400 TYR 0.029 0.002 TYR A 385 ARG 0.003 0.001 ARG B 457 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1606.77 seconds wall clock time: 29 minutes 53.02 seconds (1793.02 seconds total)