Starting phenix.real_space_refine on Fri Apr 5 17:18:16 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8wfj_37493/04_2024/8wfj_37493_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8wfj_37493/04_2024/8wfj_37493.map Found restraint, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8wfj_37493/04_2024/8wfj_37493_ligands.cif Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.35 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { restraint_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8wfj_37493/04_2024/8wfj_37493_ligands.cif" default_restraint = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8wfj_37493/04_2024/8wfj_37493_ligands.cif" real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8wfj_37493/04_2024/8wfj_37493.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8wfj_37493/04_2024/8wfj_37493.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8wfj_37493/04_2024/8wfj_37493_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8wfj_37493/04_2024/8wfj_37493_updated.pdb" } resolution = 3.35 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= 0.154 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: 5 Type Number sf(0) Gaussians S 34 5.16 5 C 2780 2.51 5 N 639 2.21 5 O 694 1.98 5 F 1 1.80 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A GLU 303": "OE1" <-> "OE2" Time to flip residues: 0.01s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5288/modules/chem_data/mon_lib" Total number of atoms: 4148 Number of models: 1 Model: "" Number of chains: 2 Chain: "A" Number of atoms: 4119 Number of conformers: 1 Conformer: "" Number of residues, atoms: 518, 4119 Classifications: {'peptide': 518} Incomplete info: {'truncation_to_alanine': 4} Link IDs: {'PTRANS': 23, 'TRANS': 494} Chain breaks: 2 Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "A" Number of atoms: 29 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 29 Unusual residues: {'W5F': 1} Classifications: {'undetermined': 1} Time building chain proxies: 2.84, per 1000 atoms: 0.68 Number of scatterers: 4148 At special positions: 0 Unit cell: (81.18, 68.88, 94.3, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 34 16.00 F 1 9.00 O 694 8.00 N 639 7.00 C 2780 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=1, symmetry=0 Simple disulfide: pdb=" SG CYS A 166 " - pdb=" SG CYS A 175 " distance=2.27 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: 1.57 Conformation dependent library (CDL) restraints added in 727.7 milliseconds 1024 Ramachandran restraints generated. 512 Oldfield, 0 Emsley, 512 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 946 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 27 helices and 0 sheets defined 65.8% alpha, 0.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.06 Creating SS restraints... Processing helix chain 'A' and resid 55 through 63 removed outlier: 3.917A pdb=" N ALA A 63 " --> pdb=" O SER A 59 " (cutoff:3.500A) Processing helix chain 'A' and resid 66 through 69 No H-bonds generated for 'chain 'A' and resid 66 through 69' Processing helix chain 'A' and resid 71 through 79 Processing helix chain 'A' and resid 82 through 94 removed outlier: 4.357A pdb=" N PHE A 86 " --> pdb=" O GLY A 82 " (cutoff:3.500A) Proline residue: A 87 - end of helix Processing helix chain 'A' and resid 97 through 109 Processing helix chain 'A' and resid 122 through 140 removed outlier: 4.294A pdb=" N GLY A 126 " --> pdb=" O MET A 123 " (cutoff:3.500A) removed outlier: 3.596A pdb=" N ILE A 140 " --> pdb=" O TYR A 137 " (cutoff:3.500A) Processing helix chain 'A' and resid 142 through 156 Processing helix chain 'A' and resid 210 through 217 Processing helix chain 'A' and resid 234 through 252 removed outlier: 3.562A pdb=" N LEU A 251 " --> pdb=" O VAL A 247 " (cutoff:3.500A) removed outlier: 3.830A pdb=" N ILE A 252 " --> pdb=" O PHE A 248 " (cutoff:3.500A) Processing helix chain 'A' and resid 268 through 278 Processing helix chain 'A' and resid 288 through 294 removed outlier: 3.653A pdb=" N TYR A 292 " --> pdb=" O ASP A 288 " (cutoff:3.500A) removed outlier: 4.005A pdb=" N TYR A 293 " --> pdb=" O GLY A 289 " (cutoff:3.500A) Processing helix chain 'A' and resid 304 through 318 removed outlier: 4.124A pdb=" N LEU A 318 " --> pdb=" O ILE A 314 " (cutoff:3.500A) Processing helix chain 'A' and resid 324 through 330 Processing helix chain 'A' and resid 338 through 371 removed outlier: 3.568A pdb=" N ILE A 363 " --> pdb=" O VAL A 359 " (cutoff:3.500A) removed outlier: 3.624A pdb=" N PHE A 366 " --> pdb=" O SER A 362 " (cutoff:3.500A) Processing helix chain 'A' and resid 375 through 377 No H-bonds generated for 'chain 'A' and resid 375 through 377' Processing helix chain 'A' and resid 390 through 396 removed outlier: 3.712A pdb=" N LEU A 396 " --> pdb=" O GLU A 392 " (cutoff:3.500A) Processing helix chain 'A' and resid 400 through 432 Processing helix chain 'A' and resid 443 through 457 removed outlier: 4.064A pdb=" N PHE A 455 " --> pdb=" O ALA A 451 " (cutoff:3.500A) Processing helix chain 'A' and resid 460 through 462 No H-bonds generated for 'chain 'A' and resid 460 through 462' Processing helix chain 'A' and resid 466 through 494 removed outlier: 4.068A pdb=" N ALA A 478 " --> pdb=" O ASP A 474 " (cutoff:3.500A) removed outlier: 4.983A pdb=" N SER A 479 " --> pdb=" O ASN A 475 " (cutoff:3.500A) removed outlier: 4.649A pdb=" N PHE A 480 " --> pdb=" O TYR A 476 " (cutoff:3.500A) removed outlier: 4.422A pdb=" N SER A 481 " --> pdb=" O ALA A 477 " (cutoff:3.500A) removed outlier: 6.459A pdb=" N LEU A 482 " --> pdb=" O ALA A 478 " (cutoff:3.500A) removed outlier: 5.239A pdb=" N VAL A 483 " --> pdb=" O SER A 479 " (cutoff:3.500A) removed outlier: 3.528A pdb=" N ILE A 493 " --> pdb=" O MET A 489 " (cutoff:3.500A) removed outlier: 3.852A pdb=" N MET A 494 " --> pdb=" O CYS A 490 " (cutoff:3.500A) Processing helix chain 'A' and resid 499 through 509 removed outlier: 3.513A pdb=" N MET A 508 " --> pdb=" O GLN A 504 " (cutoff:3.500A) removed outlier: 3.593A pdb=" N MET A 509 " --> pdb=" O ASP A 505 " (cutoff:3.500A) Processing helix chain 'A' and resid 516 through 523 removed outlier: 3.535A pdb=" N ARG A 523 " --> pdb=" O GLN A 519 " (cutoff:3.500A) Processing helix chain 'A' and resid 525 through 536 Processing helix chain 'A' and resid 544 through 546 No H-bonds generated for 'chain 'A' and resid 544 through 546' Processing helix chain 'A' and resid 553 through 566 removed outlier: 3.741A pdb=" N SER A 566 " --> pdb=" O MET A 562 " (cutoff:3.500A) Processing helix chain 'A' and resid 568 through 580 Processing helix chain 'A' and resid 588 through 594 209 hydrogen bonds defined for protein. 585 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: 1.14 Time building geometry restraints manager: 1.74 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 1206 1.34 - 1.46: 934 1.46 - 1.58: 2091 1.58 - 1.70: 0 1.70 - 1.81: 52 Bond restraints: 4283 Sorted by residual: bond pdb=" CB ASN A 171 " pdb=" CG ASN A 171 " ideal model delta sigma weight residual 1.516 1.549 -0.033 2.50e-02 1.60e+03 1.70e+00 bond pdb=" C CYS A 166 " pdb=" O CYS A 166 " ideal model delta sigma weight residual 1.235 1.220 0.015 1.33e-02 5.65e+03 1.34e+00 bond pdb=" CA CYS A 166 " pdb=" CB CYS A 166 " ideal model delta sigma weight residual 1.531 1.547 -0.016 1.69e-02 3.50e+03 9.37e-01 bond pdb=" N CYS A 166 " pdb=" CA CYS A 166 " ideal model delta sigma weight residual 1.456 1.468 -0.013 1.32e-02 5.74e+03 9.27e-01 bond pdb=" CA CYS A 166 " pdb=" C CYS A 166 " ideal model delta sigma weight residual 1.523 1.538 -0.015 1.56e-02 4.11e+03 9.20e-01 ... (remaining 4278 not shown) Histogram of bond angle deviations from ideal: 100.32 - 107.06: 128 107.06 - 113.79: 2269 113.79 - 120.52: 1831 120.52 - 127.25: 1555 127.25 - 133.99: 58 Bond angle restraints: 5841 Sorted by residual: angle pdb=" C17 W5F A 701 " pdb=" C14 W5F A 701 " pdb=" O02 W5F A 701 " ideal model delta sigma weight residual 109.31 119.90 -10.59 3.00e+00 1.11e-01 1.25e+01 angle pdb=" C18 W5F A 701 " pdb=" C14 W5F A 701 " pdb=" O02 W5F A 701 " ideal model delta sigma weight residual 129.39 120.24 9.15 3.00e+00 1.11e-01 9.29e+00 angle pdb=" N CYS A 175 " pdb=" CA CYS A 175 " pdb=" C CYS A 175 " ideal model delta sigma weight residual 109.40 113.89 -4.49 1.63e+00 3.76e-01 7.60e+00 angle pdb=" CB MET A 91 " pdb=" CG MET A 91 " pdb=" SD MET A 91 " ideal model delta sigma weight residual 112.70 119.73 -7.03 3.00e+00 1.11e-01 5.49e+00 angle pdb=" CA ASN A 171 " pdb=" CB ASN A 171 " pdb=" CG ASN A 171 " ideal model delta sigma weight residual 112.60 114.66 -2.06 1.00e+00 1.00e+00 4.25e+00 ... (remaining 5836 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 15.78: 1961 15.78 - 31.56: 293 31.56 - 47.34: 105 47.34 - 63.12: 35 63.12 - 78.90: 2 Dihedral angle restraints: 2396 sinusoidal: 902 harmonic: 1494 Sorted by residual: dihedral pdb=" CB CYS A 166 " pdb=" SG CYS A 166 " pdb=" SG CYS A 175 " pdb=" CB CYS A 175 " ideal model delta sinusoidal sigma weight residual -86.00 -116.76 30.76 1 1.00e+01 1.00e-02 1.35e+01 dihedral pdb=" CA PHE A 524 " pdb=" C PHE A 524 " pdb=" N VAL A 525 " pdb=" CA VAL A 525 " ideal model delta harmonic sigma weight residual 180.00 -164.71 -15.29 0 5.00e+00 4.00e-02 9.35e+00 dihedral pdb=" CA ILE A 252 " pdb=" CB ILE A 252 " pdb=" CG1 ILE A 252 " pdb=" CD1 ILE A 252 " ideal model delta sinusoidal sigma weight residual 60.00 113.55 -53.55 3 1.50e+01 4.44e-03 9.21e+00 ... (remaining 2393 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.038: 459 0.038 - 0.075: 143 0.075 - 0.112: 36 0.112 - 0.150: 3 0.150 - 0.187: 1 Chirality restraints: 642 Sorted by residual: chirality pdb=" CB ILE A 399 " pdb=" CA ILE A 399 " pdb=" CG1 ILE A 399 " pdb=" CG2 ILE A 399 " both_signs ideal model delta sigma weight residual False 2.64 2.46 0.19 2.00e-01 2.50e+01 8.77e-01 chirality pdb=" CA VAL A 434 " pdb=" N VAL A 434 " pdb=" C VAL A 434 " pdb=" CB VAL A 434 " both_signs ideal model delta sigma weight residual False 2.44 2.58 -0.14 2.00e-01 2.50e+01 5.01e-01 chirality pdb=" CB THR A 348 " pdb=" CA THR A 348 " pdb=" OG1 THR A 348 " pdb=" CG2 THR A 348 " both_signs ideal model delta sigma weight residual False 2.55 2.42 0.14 2.00e-01 2.50e+01 4.60e-01 ... (remaining 639 not shown) Planarity restraints: 715 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C SER A 526 " 0.035 5.00e-02 4.00e+02 5.34e-02 4.56e+00 pdb=" N PRO A 527 " -0.092 5.00e-02 4.00e+02 pdb=" CA PRO A 527 " 0.027 5.00e-02 4.00e+02 pdb=" CD PRO A 527 " 0.030 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C SER A 209 " 0.018 5.00e-02 4.00e+02 2.79e-02 1.24e+00 pdb=" N PRO A 210 " -0.048 5.00e-02 4.00e+02 pdb=" CA PRO A 210 " 0.014 5.00e-02 4.00e+02 pdb=" CD PRO A 210 " 0.016 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CB TRP A 170 " -0.008 2.00e-02 2.50e+03 6.91e-03 1.19e+00 pdb=" CG TRP A 170 " 0.019 2.00e-02 2.50e+03 pdb=" CD1 TRP A 170 " -0.008 2.00e-02 2.50e+03 pdb=" CD2 TRP A 170 " 0.000 2.00e-02 2.50e+03 pdb=" NE1 TRP A 170 " 0.000 2.00e-02 2.50e+03 pdb=" CE2 TRP A 170 " 0.000 2.00e-02 2.50e+03 pdb=" CE3 TRP A 170 " 0.000 2.00e-02 2.50e+03 pdb=" CZ2 TRP A 170 " -0.000 2.00e-02 2.50e+03 pdb=" CZ3 TRP A 170 " -0.002 2.00e-02 2.50e+03 pdb=" CH2 TRP A 170 " -0.000 2.00e-02 2.50e+03 ... (remaining 712 not shown) Histogram of nonbonded interaction distances: 2.25 - 2.78: 1005 2.78 - 3.31: 3900 3.31 - 3.84: 6899 3.84 - 4.37: 7602 4.37 - 4.90: 13569 Nonbonded interactions: 32975 Sorted by model distance: nonbonded pdb=" OH TYR A 77 " pdb=" O VAL A 375 " model vdw 2.248 2.440 nonbonded pdb=" O PRO A 460 " pdb=" OG SER A 463 " model vdw 2.264 2.440 nonbonded pdb=" OH TYR A 495 " pdb=" O ARG A 523 " model vdw 2.272 2.440 nonbonded pdb=" O ILE A 301 " pdb=" NE1 TRP A 307 " model vdw 2.278 2.520 nonbonded pdb=" O ASP A 309 " pdb=" OG SER A 312 " model vdw 2.286 2.440 ... (remaining 32970 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.970 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: 3.760 Check model and map are aligned: 0.050 Set scattering table: 0.040 Process input model: 16.060 Find NCS groups from input model: 0.120 Set up NCS constraints: 0.010 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.880 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 23.910 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7746 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 0.033 4283 Z= 0.170 Angle : 0.564 10.592 5841 Z= 0.281 Chirality : 0.039 0.187 642 Planarity : 0.004 0.053 715 Dihedral : 17.682 78.903 1447 Min Nonbonded Distance : 2.248 Molprobity Statistics. All-atom Clashscore : 9.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.84 % Favored : 93.16 % Rotamer: Outliers : 0.00 % Allowed : 30.73 % Favored : 69.27 % 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: 0.04 (0.39), residues: 512 helix: 1.11 (0.29), residues: 338 sheet: None (None), residues: 0 loop : -2.22 (0.47), residues: 174 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP A 170 HIS 0.008 0.001 HIS A 173 PHE 0.009 0.001 PHE A 408 TYR 0.014 0.001 TYR A 74 ARG 0.005 0.000 ARG A 580 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1024 Ramachandran restraints generated. 512 Oldfield, 0 Emsley, 512 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1024 Ramachandran restraints generated. 512 Oldfield, 0 Emsley, 512 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 65 residues out of total 440 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 65 time to evaluate : 0.457 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 65 average time/residue: 0.1667 time to fit residues: 13.7971 Evaluate side-chains 64 residues out of total 440 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 64 time to evaluate : 0.447 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 51 random chunks: chunk 43 optimal weight: 3.9990 chunk 38 optimal weight: 6.9990 chunk 21 optimal weight: 7.9990 chunk 13 optimal weight: 8.9990 chunk 26 optimal weight: 4.9990 chunk 20 optimal weight: 0.9990 chunk 39 optimal weight: 2.9990 chunk 15 optimal weight: 3.9990 chunk 24 optimal weight: 0.5980 chunk 29 optimal weight: 0.0670 chunk 46 optimal weight: 4.9990 overall best weight: 1.7324 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 171 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7833 moved from start: 0.0975 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.050 4283 Z= 0.296 Angle : 0.578 5.974 5841 Z= 0.298 Chirality : 0.042 0.197 642 Planarity : 0.004 0.033 715 Dihedral : 4.752 45.424 571 Min Nonbonded Distance : 2.133 Molprobity Statistics. All-atom Clashscore : 7.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.42 % Favored : 92.58 % Rotamer: Outliers : 5.28 % Allowed : 28.44 % Favored : 66.28 % 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: 0.10 (0.39), residues: 512 helix: 1.24 (0.29), residues: 344 sheet: None (None), residues: 0 loop : -2.53 (0.45), residues: 168 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 170 HIS 0.004 0.001 HIS A 370 PHE 0.019 0.002 PHE A 109 TYR 0.019 0.002 TYR A 74 ARG 0.004 0.001 ARG A 580 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1024 Ramachandran restraints generated. 512 Oldfield, 0 Emsley, 512 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1024 Ramachandran restraints generated. 512 Oldfield, 0 Emsley, 512 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 89 residues out of total 440 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 66 time to evaluate : 0.425 Fit side-chains revert: symmetry clash REVERT: A 358 PHE cc_start: 0.7603 (OUTLIER) cc_final: 0.6923 (t80) REVERT: A 507 GLN cc_start: 0.7366 (OUTLIER) cc_final: 0.7149 (tm-30) outliers start: 23 outliers final: 14 residues processed: 83 average time/residue: 0.1324 time to fit residues: 14.4888 Evaluate side-chains 78 residues out of total 440 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 62 time to evaluate : 0.451 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 74 TYR Chi-restraints excluded: chain A residue 134 VAL Chi-restraints excluded: chain A residue 143 ASN Chi-restraints excluded: chain A residue 172 THR Chi-restraints excluded: chain A residue 275 ILE Chi-restraints excluded: chain A residue 297 GLN Chi-restraints excluded: chain A residue 358 PHE Chi-restraints excluded: chain A residue 370 HIS Chi-restraints excluded: chain A residue 376 SER Chi-restraints excluded: chain A residue 446 VAL Chi-restraints excluded: chain A residue 467 ILE Chi-restraints excluded: chain A residue 494 MET Chi-restraints excluded: chain A residue 507 GLN Chi-restraints excluded: chain A residue 516 LEU Chi-restraints excluded: chain A residue 560 PHE Chi-restraints excluded: chain A residue 599 ASP Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 51 random chunks: chunk 25 optimal weight: 0.0370 chunk 14 optimal weight: 2.9990 chunk 38 optimal weight: 3.9990 chunk 31 optimal weight: 4.9990 chunk 12 optimal weight: 9.9990 chunk 46 optimal weight: 1.9990 chunk 50 optimal weight: 0.9980 chunk 41 optimal weight: 3.9990 chunk 15 optimal weight: 0.6980 chunk 37 optimal weight: 0.6980 chunk 45 optimal weight: 0.6980 overall best weight: 0.6258 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 171 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7784 moved from start: 0.1112 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 4283 Z= 0.169 Angle : 0.505 5.661 5841 Z= 0.257 Chirality : 0.039 0.186 642 Planarity : 0.004 0.032 715 Dihedral : 4.630 45.679 571 Min Nonbonded Distance : 2.076 Molprobity Statistics. All-atom Clashscore : 6.81 Ramachandran Plot: Outliers : 0.20 % Allowed : 5.66 % Favored : 94.14 % Rotamer: Outliers : 4.36 % Allowed : 29.13 % Favored : 66.51 % 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: 0.27 (0.39), residues: 512 helix: 1.39 (0.29), residues: 342 sheet: None (None), residues: 0 loop : -2.46 (0.45), residues: 170 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 554 HIS 0.003 0.001 HIS A 370 PHE 0.009 0.001 PHE A 408 TYR 0.014 0.001 TYR A 74 ARG 0.004 0.000 ARG A 580 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1024 Ramachandran restraints generated. 512 Oldfield, 0 Emsley, 512 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1024 Ramachandran restraints generated. 512 Oldfield, 0 Emsley, 512 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 86 residues out of total 440 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 67 time to evaluate : 0.419 Fit side-chains REVERT: A 358 PHE cc_start: 0.7608 (OUTLIER) cc_final: 0.6864 (t80) outliers start: 19 outliers final: 11 residues processed: 78 average time/residue: 0.1143 time to fit residues: 11.9294 Evaluate side-chains 76 residues out of total 440 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 64 time to evaluate : 0.385 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 74 TYR Chi-restraints excluded: chain A residue 172 THR Chi-restraints excluded: chain A residue 275 ILE Chi-restraints excluded: chain A residue 297 GLN Chi-restraints excluded: chain A residue 358 PHE Chi-restraints excluded: chain A residue 370 HIS Chi-restraints excluded: chain A residue 376 SER Chi-restraints excluded: chain A residue 446 VAL Chi-restraints excluded: chain A residue 467 ILE Chi-restraints excluded: chain A residue 486 SER Chi-restraints excluded: chain A residue 560 PHE Chi-restraints excluded: chain A residue 599 ASP Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 51 random chunks: chunk 34 optimal weight: 0.0670 chunk 24 optimal weight: 0.7980 chunk 5 optimal weight: 0.7980 chunk 22 optimal weight: 3.9990 chunk 31 optimal weight: 1.9990 chunk 46 optimal weight: 3.9990 chunk 49 optimal weight: 0.9980 chunk 44 optimal weight: 0.8980 chunk 13 optimal weight: 8.9990 chunk 41 optimal weight: 2.9990 chunk 27 optimal weight: 0.6980 overall best weight: 0.6518 ------------------------------------------------------------------------------- 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: 0.7780 moved from start: 0.1279 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 4283 Z= 0.167 Angle : 0.498 5.574 5841 Z= 0.251 Chirality : 0.039 0.185 642 Planarity : 0.004 0.033 715 Dihedral : 4.676 51.039 571 Min Nonbonded Distance : 2.150 Molprobity Statistics. All-atom Clashscore : 7.06 Ramachandran Plot: Outliers : 0.20 % Allowed : 6.05 % Favored : 93.75 % Rotamer: Outliers : 5.50 % Allowed : 28.44 % Favored : 66.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.39 (0.39), residues: 512 helix: 1.45 (0.29), residues: 346 sheet: None (None), residues: 0 loop : -2.43 (0.46), residues: 166 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 554 HIS 0.003 0.001 HIS A 370 PHE 0.009 0.001 PHE A 408 TYR 0.014 0.001 TYR A 74 ARG 0.004 0.000 ARG A 580 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1024 Ramachandran restraints generated. 512 Oldfield, 0 Emsley, 512 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1024 Ramachandran restraints generated. 512 Oldfield, 0 Emsley, 512 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 92 residues out of total 440 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 68 time to evaluate : 0.470 Fit side-chains REVERT: A 231 GLU cc_start: 0.7409 (OUTLIER) cc_final: 0.7109 (tt0) REVERT: A 358 PHE cc_start: 0.7609 (OUTLIER) cc_final: 0.6840 (t80) REVERT: A 510 LEU cc_start: 0.6852 (OUTLIER) cc_final: 0.6292 (mt) REVERT: A 546 TYR cc_start: 0.6957 (OUTLIER) cc_final: 0.5778 (t80) REVERT: A 590 LEU cc_start: 0.6055 (OUTLIER) cc_final: 0.5853 (tp) outliers start: 24 outliers final: 11 residues processed: 82 average time/residue: 0.1371 time to fit residues: 15.0183 Evaluate side-chains 82 residues out of total 440 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 66 time to evaluate : 0.471 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 74 TYR Chi-restraints excluded: chain A residue 172 THR Chi-restraints excluded: chain A residue 179 LEU Chi-restraints excluded: chain A residue 231 GLU Chi-restraints excluded: chain A residue 297 GLN Chi-restraints excluded: chain A residue 358 PHE Chi-restraints excluded: chain A residue 370 HIS Chi-restraints excluded: chain A residue 376 SER Chi-restraints excluded: chain A residue 446 VAL Chi-restraints excluded: chain A residue 467 ILE Chi-restraints excluded: chain A residue 486 SER Chi-restraints excluded: chain A residue 510 LEU Chi-restraints excluded: chain A residue 546 TYR Chi-restraints excluded: chain A residue 560 PHE Chi-restraints excluded: chain A residue 590 LEU Chi-restraints excluded: chain A residue 599 ASP Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 51 random chunks: chunk 0 optimal weight: 10.0000 chunk 36 optimal weight: 3.9990 chunk 20 optimal weight: 2.9990 chunk 42 optimal weight: 3.9990 chunk 34 optimal weight: 1.9990 chunk 25 optimal weight: 0.9990 chunk 44 optimal weight: 0.9990 chunk 12 optimal weight: 9.9990 chunk 16 optimal weight: 0.9980 chunk 9 optimal weight: 0.5980 chunk 28 optimal weight: 0.6980 overall best weight: 0.8584 ------------------------------------------------------------------------------- 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: 0.7794 moved from start: 0.1411 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 4283 Z= 0.187 Angle : 0.529 7.019 5841 Z= 0.265 Chirality : 0.039 0.185 642 Planarity : 0.004 0.032 715 Dihedral : 4.769 51.094 571 Min Nonbonded Distance : 2.182 Molprobity Statistics. All-atom Clashscore : 6.81 Ramachandran Plot: Outliers : 0.20 % Allowed : 6.45 % Favored : 93.36 % Rotamer: Outliers : 6.19 % Allowed : 28.44 % Favored : 65.37 % 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: 0.31 (0.38), residues: 512 helix: 1.42 (0.29), residues: 346 sheet: None (None), residues: 0 loop : -2.55 (0.44), residues: 166 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 554 HIS 0.003 0.001 HIS A 370 PHE 0.010 0.001 PHE A 408 TYR 0.016 0.001 TYR A 74 ARG 0.003 0.000 ARG A 580 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1024 Ramachandran restraints generated. 512 Oldfield, 0 Emsley, 512 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1024 Ramachandran restraints generated. 512 Oldfield, 0 Emsley, 512 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 94 residues out of total 440 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 67 time to evaluate : 0.448 Fit side-chains REVERT: A 231 GLU cc_start: 0.7408 (OUTLIER) cc_final: 0.7095 (tt0) REVERT: A 358 PHE cc_start: 0.7662 (OUTLIER) cc_final: 0.6886 (t80) REVERT: A 510 LEU cc_start: 0.6840 (OUTLIER) cc_final: 0.6273 (mt) REVERT: A 546 TYR cc_start: 0.7035 (OUTLIER) cc_final: 0.5821 (t80) outliers start: 27 outliers final: 16 residues processed: 85 average time/residue: 0.1465 time to fit residues: 16.3810 Evaluate side-chains 86 residues out of total 440 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 66 time to evaluate : 0.414 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 74 TYR Chi-restraints excluded: chain A residue 93 ILE Chi-restraints excluded: chain A residue 172 THR Chi-restraints excluded: chain A residue 179 LEU Chi-restraints excluded: chain A residue 231 GLU Chi-restraints excluded: chain A residue 275 ILE Chi-restraints excluded: chain A residue 297 GLN Chi-restraints excluded: chain A residue 358 PHE Chi-restraints excluded: chain A residue 370 HIS Chi-restraints excluded: chain A residue 376 SER Chi-restraints excluded: chain A residue 446 VAL Chi-restraints excluded: chain A residue 467 ILE Chi-restraints excluded: chain A residue 480 PHE Chi-restraints excluded: chain A residue 486 SER Chi-restraints excluded: chain A residue 494 MET Chi-restraints excluded: chain A residue 510 LEU Chi-restraints excluded: chain A residue 516 LEU Chi-restraints excluded: chain A residue 546 TYR Chi-restraints excluded: chain A residue 560 PHE Chi-restraints excluded: chain A residue 599 ASP Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 51 random chunks: chunk 12 optimal weight: 9.9990 chunk 49 optimal weight: 0.8980 chunk 40 optimal weight: 0.9990 chunk 22 optimal weight: 6.9990 chunk 4 optimal weight: 1.9990 chunk 16 optimal weight: 4.9990 chunk 25 optimal weight: 0.6980 chunk 47 optimal weight: 0.8980 chunk 5 optimal weight: 0.7980 chunk 28 optimal weight: 3.9990 chunk 36 optimal weight: 1.9990 overall best weight: 0.8582 ------------------------------------------------------------------------------- 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: 0.7796 moved from start: 0.1497 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 4283 Z= 0.186 Angle : 0.543 8.271 5841 Z= 0.262 Chirality : 0.040 0.245 642 Planarity : 0.004 0.077 715 Dihedral : 4.771 49.359 571 Min Nonbonded Distance : 2.188 Molprobity Statistics. All-atom Clashscore : 7.18 Ramachandran Plot: Outliers : 0.20 % Allowed : 6.84 % Favored : 92.97 % Rotamer: Outliers : 5.73 % Allowed : 28.90 % Favored : 65.37 % 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: 0.31 (0.39), residues: 512 helix: 1.41 (0.29), residues: 347 sheet: None (None), residues: 0 loop : -2.54 (0.44), residues: 165 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 554 HIS 0.004 0.001 HIS A 370 PHE 0.010 0.001 PHE A 408 TYR 0.017 0.001 TYR A 497 ARG 0.002 0.000 ARG A 580 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1024 Ramachandran restraints generated. 512 Oldfield, 0 Emsley, 512 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1024 Ramachandran restraints generated. 512 Oldfield, 0 Emsley, 512 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 90 residues out of total 440 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 65 time to evaluate : 0.421 Fit side-chains REVERT: A 91 MET cc_start: 0.7881 (mmm) cc_final: 0.7644 (mmm) REVERT: A 231 GLU cc_start: 0.7410 (OUTLIER) cc_final: 0.7085 (tt0) REVERT: A 358 PHE cc_start: 0.7692 (OUTLIER) cc_final: 0.6905 (t80) REVERT: A 510 LEU cc_start: 0.6833 (OUTLIER) cc_final: 0.6262 (mt) REVERT: A 546 TYR cc_start: 0.7015 (OUTLIER) cc_final: 0.5820 (t80) outliers start: 25 outliers final: 19 residues processed: 83 average time/residue: 0.1364 time to fit residues: 14.9472 Evaluate side-chains 89 residues out of total 440 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 66 time to evaluate : 0.464 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 74 TYR Chi-restraints excluded: chain A residue 105 SER Chi-restraints excluded: chain A residue 155 SER Chi-restraints excluded: chain A residue 172 THR Chi-restraints excluded: chain A residue 179 LEU Chi-restraints excluded: chain A residue 231 GLU Chi-restraints excluded: chain A residue 251 LEU Chi-restraints excluded: chain A residue 275 ILE Chi-restraints excluded: chain A residue 297 GLN Chi-restraints excluded: chain A residue 358 PHE Chi-restraints excluded: chain A residue 370 HIS Chi-restraints excluded: chain A residue 376 SER Chi-restraints excluded: chain A residue 446 VAL Chi-restraints excluded: chain A residue 467 ILE Chi-restraints excluded: chain A residue 480 PHE Chi-restraints excluded: chain A residue 486 SER Chi-restraints excluded: chain A residue 494 MET Chi-restraints excluded: chain A residue 510 LEU Chi-restraints excluded: chain A residue 516 LEU Chi-restraints excluded: chain A residue 546 TYR Chi-restraints excluded: chain A residue 560 PHE Chi-restraints excluded: chain A residue 566 SER Chi-restraints excluded: chain A residue 599 ASP Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 51 random chunks: chunk 27 optimal weight: 3.9990 chunk 41 optimal weight: 2.9990 chunk 49 optimal weight: 1.9990 chunk 30 optimal weight: 0.6980 chunk 29 optimal weight: 6.9990 chunk 22 optimal weight: 6.9990 chunk 19 optimal weight: 1.9990 chunk 14 optimal weight: 4.9990 chunk 9 optimal weight: 0.7980 chunk 31 optimal weight: 1.9990 chunk 33 optimal weight: 0.8980 overall best weight: 1.2784 ------------------------------------------------------------------------------- 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: 0.7842 moved from start: 0.1683 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 4283 Z= 0.236 Angle : 0.568 8.873 5841 Z= 0.278 Chirality : 0.040 0.180 642 Planarity : 0.004 0.064 715 Dihedral : 4.936 47.781 571 Min Nonbonded Distance : 2.155 Molprobity Statistics. All-atom Clashscore : 7.06 Ramachandran Plot: Outliers : 0.20 % Allowed : 7.42 % Favored : 92.38 % Rotamer: Outliers : 6.65 % Allowed : 28.90 % Favored : 64.45 % 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: 0.12 (0.38), residues: 512 helix: 1.28 (0.29), residues: 346 sheet: None (None), residues: 0 loop : -2.64 (0.43), residues: 166 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 554 HIS 0.004 0.001 HIS A 370 PHE 0.012 0.001 PHE A 94 TYR 0.018 0.001 TYR A 74 ARG 0.002 0.000 ARG A 589 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1024 Ramachandran restraints generated. 512 Oldfield, 0 Emsley, 512 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1024 Ramachandran restraints generated. 512 Oldfield, 0 Emsley, 512 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 97 residues out of total 440 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 68 time to evaluate : 0.459 Fit side-chains REVERT: A 231 GLU cc_start: 0.7443 (OUTLIER) cc_final: 0.7041 (tt0) REVERT: A 358 PHE cc_start: 0.7744 (OUTLIER) cc_final: 0.6937 (t80) REVERT: A 546 TYR cc_start: 0.7076 (OUTLIER) cc_final: 0.5921 (t80) outliers start: 29 outliers final: 23 residues processed: 89 average time/residue: 0.1368 time to fit residues: 16.3046 Evaluate side-chains 90 residues out of total 440 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 64 time to evaluate : 0.381 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 66 LEU Chi-restraints excluded: chain A residue 74 TYR Chi-restraints excluded: chain A residue 134 VAL Chi-restraints excluded: chain A residue 140 ILE Chi-restraints excluded: chain A residue 143 ASN Chi-restraints excluded: chain A residue 155 SER Chi-restraints excluded: chain A residue 172 THR Chi-restraints excluded: chain A residue 179 LEU Chi-restraints excluded: chain A residue 231 GLU Chi-restraints excluded: chain A residue 251 LEU Chi-restraints excluded: chain A residue 275 ILE Chi-restraints excluded: chain A residue 297 GLN Chi-restraints excluded: chain A residue 358 PHE Chi-restraints excluded: chain A residue 370 HIS Chi-restraints excluded: chain A residue 376 SER Chi-restraints excluded: chain A residue 446 VAL Chi-restraints excluded: chain A residue 467 ILE Chi-restraints excluded: chain A residue 480 PHE Chi-restraints excluded: chain A residue 486 SER Chi-restraints excluded: chain A residue 494 MET Chi-restraints excluded: chain A residue 510 LEU Chi-restraints excluded: chain A residue 516 LEU Chi-restraints excluded: chain A residue 546 TYR Chi-restraints excluded: chain A residue 560 PHE Chi-restraints excluded: chain A residue 566 SER Chi-restraints excluded: chain A residue 599 ASP Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 51 random chunks: chunk 24 optimal weight: 0.5980 chunk 4 optimal weight: 0.9990 chunk 38 optimal weight: 0.9980 chunk 44 optimal weight: 0.9990 chunk 47 optimal weight: 0.9990 chunk 42 optimal weight: 0.6980 chunk 45 optimal weight: 0.9980 chunk 27 optimal weight: 3.9990 chunk 19 optimal weight: 0.8980 chunk 35 optimal weight: 0.0670 chunk 14 optimal weight: 3.9990 overall best weight: 0.6518 ------------------------------------------------------------------------------- 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: 0.7797 moved from start: 0.1710 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 4283 Z= 0.179 Angle : 0.554 9.020 5841 Z= 0.269 Chirality : 0.039 0.182 642 Planarity : 0.004 0.059 715 Dihedral : 4.910 47.706 571 Min Nonbonded Distance : 2.191 Molprobity Statistics. All-atom Clashscore : 7.18 Ramachandran Plot: Outliers : 0.20 % Allowed : 6.05 % Favored : 93.75 % Rotamer: Outliers : 5.73 % Allowed : 30.28 % Favored : 63.99 % 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: 0.19 (0.38), residues: 512 helix: 1.32 (0.29), residues: 350 sheet: None (None), residues: 0 loop : -2.67 (0.44), residues: 162 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A 298 HIS 0.004 0.001 HIS A 370 PHE 0.009 0.001 PHE A 408 TYR 0.024 0.001 TYR A 497 ARG 0.002 0.000 ARG A 580 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1024 Ramachandran restraints generated. 512 Oldfield, 0 Emsley, 512 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1024 Ramachandran restraints generated. 512 Oldfield, 0 Emsley, 512 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 90 residues out of total 440 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 65 time to evaluate : 0.462 Fit side-chains REVERT: A 231 GLU cc_start: 0.7407 (OUTLIER) cc_final: 0.7055 (tt0) REVERT: A 358 PHE cc_start: 0.7679 (OUTLIER) cc_final: 0.6847 (t80) REVERT: A 546 TYR cc_start: 0.6973 (OUTLIER) cc_final: 0.5768 (t80) outliers start: 25 outliers final: 19 residues processed: 81 average time/residue: 0.1456 time to fit residues: 15.3941 Evaluate side-chains 86 residues out of total 440 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 64 time to evaluate : 0.446 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 74 TYR Chi-restraints excluded: chain A residue 143 ASN Chi-restraints excluded: chain A residue 155 SER Chi-restraints excluded: chain A residue 172 THR Chi-restraints excluded: chain A residue 175 CYS Chi-restraints excluded: chain A residue 179 LEU Chi-restraints excluded: chain A residue 231 GLU Chi-restraints excluded: chain A residue 251 LEU Chi-restraints excluded: chain A residue 275 ILE Chi-restraints excluded: chain A residue 297 GLN Chi-restraints excluded: chain A residue 358 PHE Chi-restraints excluded: chain A residue 370 HIS Chi-restraints excluded: chain A residue 376 SER Chi-restraints excluded: chain A residue 446 VAL Chi-restraints excluded: chain A residue 480 PHE Chi-restraints excluded: chain A residue 486 SER Chi-restraints excluded: chain A residue 510 LEU Chi-restraints excluded: chain A residue 516 LEU Chi-restraints excluded: chain A residue 546 TYR Chi-restraints excluded: chain A residue 560 PHE Chi-restraints excluded: chain A residue 590 LEU Chi-restraints excluded: chain A residue 599 ASP Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 51 random chunks: chunk 41 optimal weight: 1.9990 chunk 43 optimal weight: 0.0040 chunk 45 optimal weight: 0.4980 chunk 30 optimal weight: 0.9980 chunk 48 optimal weight: 0.8980 chunk 29 optimal weight: 6.9990 chunk 22 optimal weight: 3.9990 chunk 33 optimal weight: 1.9990 chunk 50 optimal weight: 6.9990 chunk 46 optimal weight: 0.6980 chunk 40 optimal weight: 0.8980 overall best weight: 0.5992 ------------------------------------------------------------------------------- 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: 0.7780 moved from start: 0.1783 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 4283 Z= 0.169 Angle : 0.536 8.755 5841 Z= 0.259 Chirality : 0.039 0.173 642 Planarity : 0.004 0.057 715 Dihedral : 4.834 48.788 571 Min Nonbonded Distance : 2.197 Molprobity Statistics. All-atom Clashscore : 6.33 Ramachandran Plot: Outliers : 0.20 % Allowed : 6.84 % Favored : 92.97 % Rotamer: Outliers : 5.73 % Allowed : 29.36 % Favored : 64.91 % 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: 0.27 (0.39), residues: 512 helix: 1.39 (0.29), residues: 350 sheet: None (None), residues: 0 loop : -2.66 (0.44), residues: 162 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 554 HIS 0.004 0.001 HIS A 370 PHE 0.008 0.001 PHE A 408 TYR 0.019 0.001 TYR A 497 ARG 0.002 0.000 ARG A 580 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1024 Ramachandran restraints generated. 512 Oldfield, 0 Emsley, 512 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1024 Ramachandran restraints generated. 512 Oldfield, 0 Emsley, 512 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 91 residues out of total 440 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 66 time to evaluate : 0.410 Fit side-chains REVERT: A 231 GLU cc_start: 0.7415 (OUTLIER) cc_final: 0.7052 (tt0) REVERT: A 273 LEU cc_start: 0.8267 (OUTLIER) cc_final: 0.8060 (mm) REVERT: A 358 PHE cc_start: 0.7659 (OUTLIER) cc_final: 0.6839 (t80) REVERT: A 546 TYR cc_start: 0.6949 (OUTLIER) cc_final: 0.5765 (t80) outliers start: 25 outliers final: 19 residues processed: 84 average time/residue: 0.1288 time to fit residues: 14.2614 Evaluate side-chains 85 residues out of total 440 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 62 time to evaluate : 0.404 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 74 TYR Chi-restraints excluded: chain A residue 155 SER Chi-restraints excluded: chain A residue 172 THR Chi-restraints excluded: chain A residue 175 CYS Chi-restraints excluded: chain A residue 179 LEU Chi-restraints excluded: chain A residue 231 GLU Chi-restraints excluded: chain A residue 251 LEU Chi-restraints excluded: chain A residue 273 LEU Chi-restraints excluded: chain A residue 275 ILE Chi-restraints excluded: chain A residue 297 GLN Chi-restraints excluded: chain A residue 358 PHE Chi-restraints excluded: chain A residue 370 HIS Chi-restraints excluded: chain A residue 376 SER Chi-restraints excluded: chain A residue 446 VAL Chi-restraints excluded: chain A residue 480 PHE Chi-restraints excluded: chain A residue 486 SER Chi-restraints excluded: chain A residue 510 LEU Chi-restraints excluded: chain A residue 516 LEU Chi-restraints excluded: chain A residue 546 TYR Chi-restraints excluded: chain A residue 560 PHE Chi-restraints excluded: chain A residue 566 SER Chi-restraints excluded: chain A residue 590 LEU Chi-restraints excluded: chain A residue 599 ASP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 51 random chunks: chunk 4 optimal weight: 0.9990 chunk 31 optimal weight: 0.0000 chunk 24 optimal weight: 4.9990 chunk 32 optimal weight: 0.5980 chunk 43 optimal weight: 0.1980 chunk 12 optimal weight: 7.9990 chunk 37 optimal weight: 0.0770 chunk 5 optimal weight: 0.9990 chunk 11 optimal weight: 2.9990 chunk 40 optimal weight: 0.7980 chunk 16 optimal weight: 1.9990 overall best weight: 0.3342 ------------------------------------------------------------------------------- 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: 0.7736 moved from start: 0.1837 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.029 4283 Z= 0.141 Angle : 0.519 8.287 5841 Z= 0.250 Chirality : 0.038 0.164 642 Planarity : 0.004 0.055 715 Dihedral : 4.725 49.103 571 Min Nonbonded Distance : 2.195 Molprobity Statistics. All-atom Clashscore : 6.45 Ramachandran Plot: Outliers : 0.20 % Allowed : 5.08 % Favored : 94.73 % Rotamer: Outliers : 4.59 % Allowed : 29.82 % Favored : 65.60 % 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: 0.42 (0.39), residues: 512 helix: 1.51 (0.29), residues: 345 sheet: None (None), residues: 0 loop : -2.49 (0.44), residues: 167 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 554 HIS 0.003 0.001 HIS A 370 PHE 0.007 0.001 PHE A 408 TYR 0.017 0.001 TYR A 497 ARG 0.002 0.000 ARG A 580 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1024 Ramachandran restraints generated. 512 Oldfield, 0 Emsley, 512 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1024 Ramachandran restraints generated. 512 Oldfield, 0 Emsley, 512 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 87 residues out of total 440 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 67 time to evaluate : 0.449 Fit side-chains REVERT: A 358 PHE cc_start: 0.7606 (OUTLIER) cc_final: 0.6800 (t80) REVERT: A 510 LEU cc_start: 0.6431 (OUTLIER) cc_final: 0.5714 (mt) REVERT: A 546 TYR cc_start: 0.6846 (OUTLIER) cc_final: 0.5649 (t80) outliers start: 20 outliers final: 15 residues processed: 81 average time/residue: 0.1354 time to fit residues: 14.7641 Evaluate side-chains 84 residues out of total 440 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 66 time to evaluate : 0.458 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 74 TYR Chi-restraints excluded: chain A residue 155 SER Chi-restraints excluded: chain A residue 172 THR Chi-restraints excluded: chain A residue 175 CYS Chi-restraints excluded: chain A residue 179 LEU Chi-restraints excluded: chain A residue 251 LEU Chi-restraints excluded: chain A residue 297 GLN Chi-restraints excluded: chain A residue 358 PHE Chi-restraints excluded: chain A residue 370 HIS Chi-restraints excluded: chain A residue 446 VAL Chi-restraints excluded: chain A residue 480 PHE Chi-restraints excluded: chain A residue 486 SER Chi-restraints excluded: chain A residue 510 LEU Chi-restraints excluded: chain A residue 516 LEU Chi-restraints excluded: chain A residue 546 TYR Chi-restraints excluded: chain A residue 560 PHE Chi-restraints excluded: chain A residue 590 LEU Chi-restraints excluded: chain A residue 599 ASP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 51 random chunks: chunk 41 optimal weight: 0.6980 chunk 5 optimal weight: 1.9990 chunk 7 optimal weight: 5.9990 chunk 35 optimal weight: 0.9990 chunk 2 optimal weight: 3.9990 chunk 29 optimal weight: 0.0060 chunk 46 optimal weight: 6.9990 chunk 27 optimal weight: 2.9990 chunk 34 optimal weight: 0.6980 chunk 1 optimal weight: 1.9990 chunk 32 optimal weight: 0.7980 overall best weight: 0.6398 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3812 r_free = 0.3812 target = 0.169099 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3638 r_free = 0.3638 target = 0.151708 restraints weight = 5636.761| |-----------------------------------------------------------------------------| r_work (start): 0.3652 rms_B_bonded: 2.56 r_work: 0.3551 rms_B_bonded: 3.19 restraints_weight: 0.5000 r_work (final): 0.3551 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7648 moved from start: 0.1856 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 4283 Z= 0.164 Angle : 0.538 8.760 5841 Z= 0.260 Chirality : 0.039 0.166 642 Planarity : 0.004 0.057 715 Dihedral : 4.751 49.034 571 Min Nonbonded Distance : 2.201 Molprobity Statistics. All-atom Clashscore : 6.57 Ramachandran Plot: Outliers : 0.20 % Allowed : 5.86 % Favored : 93.95 % Rotamer: Outliers : 4.13 % Allowed : 30.50 % Favored : 65.37 % 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: 0.43 (0.39), residues: 512 helix: 1.52 (0.29), residues: 344 sheet: None (None), residues: 0 loop : -2.46 (0.44), residues: 168 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 554 HIS 0.003 0.001 HIS A 370 PHE 0.008 0.001 PHE A 408 TYR 0.017 0.001 TYR A 497 ARG 0.002 0.000 ARG A 580 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1247.11 seconds wall clock time: 24 minutes 22.72 seconds (1462.72 seconds total)