Starting phenix.real_space_refine (version: dev) on Tue Nov 29 13:06:56 2022 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7fil_31602/11_2022/7fil_31602.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7fil_31602/11_2022/7fil_31602.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.0 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7fil_31602/11_2022/7fil_31602.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7fil_31602/11_2022/7fil_31602.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7fil_31602/11_2022/7fil_31602.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7fil_31602/11_2022/7fil_31602.pdb" } resolution = 3.0 write_initial_geo_file = False refinement { macro_cycles = 10 } 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 ------------------------------------------------------------------------------- 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 Convert atoms to be neutral Process input model Symmetric amino acids flipped Residue "A PHE 259": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 274": "OD1" <-> "OD2" Residue "A ASP 277": "OD1" <-> "OD2" Residue "A PHE 282": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 284": "OE1" <-> "OE2" Residue "A GLU 305": "OE1" <-> "OE2" Residue "A TYR 323": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 345": "OE1" <-> "OE2" Residue "A PHE 368": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 374": "OE1" <-> "OE2" Residue "A PHE 388": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 390": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 391": "OE1" <-> "OE2" Residue "A ASP 392": "OD1" <-> "OD2" Residue "A TYR 408": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 410": "OE1" <-> "OE2" Residue "A ASP 415": "OD1" <-> "OD2" Residue "A ARG 428": "NH1" <-> "NH2" Residue "A ARG 454": "NH1" <-> "NH2" Residue "A PHE 461": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 463": "NH1" <-> "NH2" Residue "A GLU 467": "OE1" <-> "OE2" Residue "A GLU 477": "OE1" <-> "OE2" Residue "A GLU 485": "OE1" <-> "OE2" Residue "A PHE 487": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 501": "OD1" <-> "OD2" Residue "A ARG 510": "NH1" <-> "NH2" Residue "A ARG 526": "NH1" <-> "NH2" Residue "A ASP 532": "OD1" <-> "OD2" Residue "A ARG 551": "NH1" <-> "NH2" Residue "A ARG 562": "NH1" <-> "NH2" Residue "A PHE 591": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 596": "OE1" <-> "OE2" Residue "A TYR 597": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 626": "OD1" <-> "OD2" Residue "A PHE 632": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 636": "OD1" <-> "OD2" Residue "A ASP 644": "OD1" <-> "OD2" Residue "A GLU 646": "OE1" <-> "OE2" Residue "A ASP 660": "OD1" <-> "OD2" Residue "A ASP 665": "OD1" <-> "OD2" Residue "A GLU 671": "OE1" <-> "OE2" Residue "A GLU 691": "OE1" <-> "OE2" Residue "A GLU 692": "OE1" <-> "OE2" Residue "A ASP 696": "OD1" <-> "OD2" Residue "A GLU 705": "OE1" <-> "OE2" Residue "A ASP 722": "OD1" <-> "OD2" Time to flip residues: 0.01s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-4778/modules/chem_data/mon_lib" Total number of atoms: 3993 Number of models: 1 Model: "" Number of chains: 1 Chain: "A" Number of atoms: 3993 Number of conformers: 1 Conformer: "" Number of residues, atoms: 504, 3993 Classifications: {'peptide': 504} Incomplete info: {'truncation_to_alanine': 22} Link IDs: {'PTRANS': 22, 'TRANS': 481} Chain breaks: 3 Unresolved chain link angles: 3 Unresolved non-hydrogen bonds: 74 Unresolved non-hydrogen angles: 92 Unresolved non-hydrogen dihedrals: 64 Unresolved non-hydrogen chiralities: 6 Planarities with less than four sites: {'PHE:plan': 1, 'GLU:plan': 1, 'ARG:plan': 2, 'TYR:plan': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 30 Time building chain proxies: 2.77, per 1000 atoms: 0.69 Number of scatterers: 3993 At special positions: 0 Unit cell: (76.285, 77.672, 102.638, 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 22 16.00 O 747 8.00 N 673 7.00 C 2551 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 1.63 Conformation dependent library (CDL) restraints added in 725.8 milliseconds 992 Ramachandran restraints generated. 496 Oldfield, 0 Emsley, 496 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 972 Finding SS restraints... Secondary structure from input PDB file: 20 helices and 0 sheets defined 67.7% alpha, 0.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.12 Creating SS restraints... Processing helix chain 'A' and resid 222 through 243 removed outlier: 4.095A pdb=" N LYS A 230 " --> pdb=" O ARG A 226 " (cutoff:3.500A) removed outlier: 3.788A pdb=" N GLU A 231 " --> pdb=" O MET A 227 " (cutoff:3.500A) Processing helix chain 'A' and resid 249 through 270 removed outlier: 3.565A pdb=" N LYS A 253 " --> pdb=" O VAL A 249 " (cutoff:3.500A) removed outlier: 4.051A pdb=" N ALA A 255 " --> pdb=" O LYS A 251 " (cutoff:3.500A) Processing helix chain 'A' and resid 276 through 305 removed outlier: 4.452A pdb=" N VAL A 280 " --> pdb=" O SER A 276 " (cutoff:3.500A) Processing helix chain 'A' and resid 312 through 325 removed outlier: 3.654A pdb=" N ALA A 322 " --> pdb=" O CYS A 318 " (cutoff:3.500A) Processing helix chain 'A' and resid 340 through 362 Processing helix chain 'A' and resid 366 through 375 removed outlier: 3.800A pdb=" N SER A 370 " --> pdb=" O GLN A 366 " (cutoff:3.500A) Processing helix chain 'A' and resid 379 through 390 removed outlier: 4.342A pdb=" N PHE A 388 " --> pdb=" O ILE A 384 " (cutoff:3.500A) removed outlier: 4.186A pdb=" N LEU A 389 " --> pdb=" O LEU A 385 " (cutoff:3.500A) Processing helix chain 'A' and resid 415 through 427 removed outlier: 3.880A pdb=" N SER A 420 " --> pdb=" O LEU A 416 " (cutoff:3.500A) Processing helix chain 'A' and resid 433 through 447 Processing helix chain 'A' and resid 452 through 461 removed outlier: 3.683A pdb=" N TRP A 456 " --> pdb=" O PRO A 452 " (cutoff:3.500A) Processing helix chain 'A' and resid 480 through 502 removed outlier: 3.536A pdb=" N LEU A 484 " --> pdb=" O CYS A 480 " (cutoff:3.500A) Processing helix chain 'A' and resid 524 through 539 Processing helix chain 'A' and resid 551 through 562 Processing helix chain 'A' and resid 570 through 588 removed outlier: 3.940A pdb=" N LEU A 574 " --> pdb=" O GLN A 570 " (cutoff:3.500A) removed outlier: 3.751A pdb=" N LEU A 588 " --> pdb=" O THR A 584 " (cutoff:3.500A) Processing helix chain 'A' and resid 590 through 614 removed outlier: 4.195A pdb=" N GLU A 596 " --> pdb=" O TYR A 592 " (cutoff:3.500A) Proline residue: A 610 - end of helix removed outlier: 3.555A pdb=" N LEU A 614 " --> pdb=" O PRO A 610 " (cutoff:3.500A) Processing helix chain 'A' and resid 641 through 659 Processing helix chain 'A' and resid 662 through 671 removed outlier: 3.511A pdb=" N ILE A 667 " --> pdb=" O THR A 663 " (cutoff:3.500A) Processing helix chain 'A' and resid 675 through 690 removed outlier: 3.508A pdb=" N TYR A 679 " --> pdb=" O ASN A 675 " (cutoff:3.500A) Processing helix chain 'A' and resid 697 through 713 removed outlier: 3.824A pdb=" N GLU A 701 " --> pdb=" O CYS A 697 " (cutoff:3.500A) Processing helix chain 'A' and resid 722 through 734 removed outlier: 3.683A pdb=" N ALA A 726 " --> pdb=" O ASP A 722 " (cutoff:3.500A) Proline residue: A 728 - end of helix 235 hydrogen bonds defined for protein. 705 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 0.87 Time building geometry restraints manager: 1.78 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 1056 1.33 - 1.45: 701 1.45 - 1.57: 2286 1.57 - 1.69: 1 1.69 - 1.82: 31 Bond restraints: 4075 Sorted by residual: bond pdb=" N PRO A 314 " pdb=" CA PRO A 314 " ideal model delta sigma weight residual 1.469 1.692 -0.223 1.28e-02 6.10e+03 3.05e+02 bond pdb=" C LYS A 327 " pdb=" N PRO A 328 " ideal model delta sigma weight residual 1.333 1.499 -0.167 1.17e-02 7.31e+03 2.03e+02 bond pdb=" C VAL A 325 " pdb=" N PRO A 326 " ideal model delta sigma weight residual 1.332 1.509 -0.177 1.32e-02 5.74e+03 1.80e+02 bond pdb=" C GLU A 313 " pdb=" N PRO A 314 " ideal model delta sigma weight residual 1.334 1.450 -0.116 2.34e-02 1.83e+03 2.48e+01 bond pdb=" N LYS A 365 " pdb=" CA LYS A 365 " ideal model delta sigma weight residual 1.453 1.492 -0.039 1.31e-02 5.83e+03 9.02e+00 ... (remaining 4070 not shown) Histogram of bond angle deviations from ideal: 97.38 - 105.30: 71 105.30 - 113.22: 2301 113.22 - 121.14: 2168 121.14 - 129.06: 943 129.06 - 136.98: 38 Bond angle restraints: 5521 Sorted by residual: angle pdb=" C LYS A 327 " pdb=" N PRO A 328 " pdb=" CA PRO A 328 " ideal model delta sigma weight residual 119.90 136.48 -16.58 1.05e+00 9.07e-01 2.49e+02 angle pdb=" C VAL A 325 " pdb=" N PRO A 326 " pdb=" CA PRO A 326 " ideal model delta sigma weight residual 119.76 134.51 -14.75 1.00e+00 1.00e+00 2.18e+02 angle pdb=" C GLU A 313 " pdb=" N PRO A 314 " pdb=" CA PRO A 314 " ideal model delta sigma weight residual 119.84 136.98 -17.14 1.25e+00 6.40e-01 1.88e+02 angle pdb=" N PRO A 314 " pdb=" CA PRO A 314 " pdb=" C PRO A 314 " ideal model delta sigma weight residual 112.47 97.38 15.09 2.06e+00 2.36e-01 5.37e+01 angle pdb=" CA PRO A 314 " pdb=" N PRO A 314 " pdb=" CD PRO A 314 " ideal model delta sigma weight residual 112.00 101.88 10.12 1.40e+00 5.10e-01 5.23e+01 ... (remaining 5516 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.76: 2098 17.76 - 35.52: 261 35.52 - 53.28: 80 53.28 - 71.04: 23 71.04 - 88.80: 7 Dihedral angle restraints: 2469 sinusoidal: 982 harmonic: 1487 Sorted by residual: dihedral pdb=" CA GLN A 564 " pdb=" C GLN A 564 " pdb=" N GLU A 565 " pdb=" CA GLU A 565 " ideal model delta harmonic sigma weight residual -180.00 -153.32 -26.68 0 5.00e+00 4.00e-02 2.85e+01 dihedral pdb=" C TYR A 597 " pdb=" N TYR A 597 " pdb=" CA TYR A 597 " pdb=" CB TYR A 597 " ideal model delta harmonic sigma weight residual -122.60 -133.07 10.47 0 2.50e+00 1.60e-01 1.76e+01 dihedral pdb=" CA PRO A 462 " pdb=" C PRO A 462 " pdb=" N ARG A 463 " pdb=" CA ARG A 463 " ideal model delta harmonic sigma weight residual -180.00 -159.69 -20.31 0 5.00e+00 4.00e-02 1.65e+01 ... (remaining 2466 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.128: 607 0.128 - 0.257: 15 0.257 - 0.385: 3 0.385 - 0.513: 0 0.513 - 0.641: 1 Chirality restraints: 626 Sorted by residual: chirality pdb=" CA PRO A 314 " pdb=" N PRO A 314 " pdb=" C PRO A 314 " pdb=" CB PRO A 314 " both_signs ideal model delta sigma weight residual False 2.72 3.36 -0.64 2.00e-01 2.50e+01 1.03e+01 chirality pdb=" CA TYR A 597 " pdb=" N TYR A 597 " pdb=" C TYR A 597 " pdb=" CB TYR A 597 " both_signs ideal model delta sigma weight residual False 2.51 2.21 0.30 2.00e-01 2.50e+01 2.31e+00 chirality pdb=" CA LYS A 327 " pdb=" N LYS A 327 " pdb=" C LYS A 327 " pdb=" CB LYS A 327 " both_signs ideal model delta sigma weight residual False 2.51 2.80 -0.29 2.00e-01 2.50e+01 2.09e+00 ... (remaining 623 not shown) Planarity restraints: 705 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA ALA A 322 " 0.012 2.00e-02 2.50e+03 2.50e-02 6.27e+00 pdb=" C ALA A 322 " -0.043 2.00e-02 2.50e+03 pdb=" O ALA A 322 " 0.016 2.00e-02 2.50e+03 pdb=" N TYR A 323 " 0.015 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA THR A 360 " 0.011 2.00e-02 2.50e+03 2.13e-02 4.55e+00 pdb=" C THR A 360 " -0.037 2.00e-02 2.50e+03 pdb=" O THR A 360 " 0.014 2.00e-02 2.50e+03 pdb=" N LEU A 361 " 0.012 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA PRO A 314 " -0.010 2.00e-02 2.50e+03 2.13e-02 4.55e+00 pdb=" C PRO A 314 " 0.037 2.00e-02 2.50e+03 pdb=" O PRO A 314 " -0.014 2.00e-02 2.50e+03 pdb=" N ALA A 315 " -0.012 2.00e-02 2.50e+03 ... (remaining 702 not shown) Histogram of nonbonded interaction distances: 2.21 - 2.75: 597 2.75 - 3.29: 4096 3.29 - 3.83: 6537 3.83 - 4.36: 7249 4.36 - 4.90: 12045 Nonbonded interactions: 30524 Sorted by model distance: nonbonded pdb=" O PHE A 632 " pdb=" N ASN A 634 " model vdw 2.213 2.520 nonbonded pdb=" O SER A 478 " pdb=" OG SER A 478 " model vdw 2.218 2.440 nonbonded pdb=" OG SER A 352 " pdb=" OD1 ASP A 423 " model vdw 2.224 2.440 nonbonded pdb=" ND2 ASN A 474 " pdb=" OG1 THR A 559 " model vdw 2.237 2.520 nonbonded pdb=" OE1 GLN A 324 " pdb=" NH1 ARG A 412 " model vdw 2.253 2.520 ... (remaining 30519 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 Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 22 5.16 5 C 2551 2.51 5 N 673 2.21 5 O 747 1.98 5 sf(0) = scattering factor at diffraction angle 0. 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: 0.330 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: 2.320 Check model and map are aligned: 0.060 Convert atoms to be neutral: 0.040 Process input model: 15.350 Find NCS groups from input model: 0.090 Set up NCS constraints: 0.010 Set refine NCS operators: 0.000 Set scattering table: 0.010 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:12.500 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 30.720 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7457 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 : 0.008 0.223 4075 Z= 0.513 Angle : 1.046 17.138 5521 Z= 0.706 Chirality : 0.062 0.641 626 Planarity : 0.005 0.040 705 Dihedral : 18.460 88.802 1497 Min Nonbonded Distance : 2.213 Molprobity Statistics. All-atom Clashscore : 19.35 Ramachandran Plot: Outliers : 1.21 % Allowed : 7.66 % Favored : 91.13 % Rotamer Outliers : 8.76 % Cbeta Deviations : 0.41 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.82 (0.36), residues: 496 helix: -0.21 (0.27), residues: 318 sheet: None (None), residues: 0 loop : -3.06 (0.43), residues: 178 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 992 Ramachandran restraints generated. 496 Oldfield, 0 Emsley, 496 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 992 Ramachandran restraints generated. 496 Oldfield, 0 Emsley, 496 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 108 residues out of total 456 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 38 poor density : 70 time to evaluate : 0.520 Fit side-chains revert: symmetry clash outliers start: 38 outliers final: 15 residues processed: 106 average time/residue: 0.8847 time to fit residues: 97.7267 Evaluate side-chains 72 residues out of total 456 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 57 time to evaluate : 0.504 Switching outliers to nearest non-outliers outliers start: 15 outliers final: 14 residues processed: 1 average time/residue: 0.2035 time to fit residues: 0.9215 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 50 random chunks: chunk 42 optimal weight: 3.9990 chunk 37 optimal weight: 0.7980 chunk 21 optimal weight: 1.9990 chunk 12 optimal weight: 0.6980 chunk 25 optimal weight: 0.6980 chunk 20 optimal weight: 5.9990 chunk 39 optimal weight: 2.9990 chunk 15 optimal weight: 0.9980 chunk 23 optimal weight: 3.9990 chunk 29 optimal weight: 0.0980 chunk 45 optimal weight: 0.9980 overall best weight: 0.6580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 367 ASN A 378 ASN A 393 ASN A 430 HIS A 436 HIS A 466 GLN A 500 GLN A 555 GLN A 556 HIS A 695 ASN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7402 moved from start: 0.2162 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.032 4075 Z= 0.216 Angle : 0.692 9.891 5521 Z= 0.351 Chirality : 0.041 0.183 626 Planarity : 0.005 0.054 705 Dihedral : 4.719 22.555 531 Min Nonbonded Distance : 2.236 Molprobity Statistics. All-atom Clashscore : 12.64 Ramachandran Plot: Outliers : 0.20 % Allowed : 7.06 % Favored : 92.74 % Rotamer Outliers : 10.37 % 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: -0.04 (0.39), residues: 496 helix: 1.15 (0.29), residues: 321 sheet: None (None), residues: 0 loop : -2.35 (0.49), residues: 175 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 992 Ramachandran restraints generated. 496 Oldfield, 0 Emsley, 496 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 992 Ramachandran restraints generated. 496 Oldfield, 0 Emsley, 496 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 108 residues out of total 456 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 45 poor density : 63 time to evaluate : 0.531 Fit side-chains outliers start: 45 outliers final: 16 residues processed: 95 average time/residue: 0.8252 time to fit residues: 82.1339 Evaluate side-chains 76 residues out of total 456 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 60 time to evaluate : 0.508 Switching outliers to nearest non-outliers outliers start: 16 outliers final: 14 residues processed: 2 average time/residue: 0.1268 time to fit residues: 1.0438 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 50 random chunks: chunk 25 optimal weight: 0.8980 chunk 14 optimal weight: 0.2980 chunk 37 optimal weight: 1.9990 chunk 30 optimal weight: 1.9990 chunk 12 optimal weight: 4.9990 chunk 45 optimal weight: 0.9980 chunk 49 optimal weight: 0.3980 chunk 40 optimal weight: 2.9990 chunk 15 optimal weight: 3.9990 chunk 36 optimal weight: 2.9990 chunk 44 optimal weight: 0.6980 overall best weight: 0.6580 ------------------------------------------------------------------------------- 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: 0.7395 moved from start: 0.2778 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.030 4075 Z= 0.209 Angle : 0.687 10.630 5521 Z= 0.345 Chirality : 0.041 0.193 626 Planarity : 0.005 0.056 705 Dihedral : 4.566 20.322 531 Min Nonbonded Distance : 2.224 Molprobity Statistics. All-atom Clashscore : 11.51 Ramachandran Plot: Outliers : 0.20 % Allowed : 7.46 % Favored : 92.34 % Rotamer Outliers : 10.14 % 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: 0.44 (0.39), residues: 496 helix: 1.59 (0.29), residues: 323 sheet: None (None), residues: 0 loop : -2.37 (0.49), residues: 173 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 992 Ramachandran restraints generated. 496 Oldfield, 0 Emsley, 496 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 992 Ramachandran restraints generated. 496 Oldfield, 0 Emsley, 496 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 104 residues out of total 456 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 44 poor density : 60 time to evaluate : 0.511 Fit side-chains outliers start: 44 outliers final: 21 residues processed: 95 average time/residue: 0.7634 time to fit residues: 76.2033 Evaluate side-chains 75 residues out of total 456 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 54 time to evaluate : 0.508 Switching outliers to nearest non-outliers outliers start: 21 outliers final: 19 residues processed: 3 average time/residue: 0.9351 time to fit residues: 3.5842 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 50 random chunks: chunk 34 optimal weight: 2.9990 chunk 23 optimal weight: 0.6980 chunk 5 optimal weight: 0.9990 chunk 21 optimal weight: 0.9980 chunk 30 optimal weight: 1.9990 chunk 45 optimal weight: 0.9990 chunk 48 optimal weight: 0.0030 chunk 43 optimal weight: 0.9990 chunk 13 optimal weight: 0.9980 chunk 40 optimal weight: 4.9990 chunk 27 optimal weight: 0.9990 overall best weight: 0.7392 ------------------------------------------------------------------------------- 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: 0.7402 moved from start: 0.3136 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.028 4075 Z= 0.213 Angle : 0.670 12.213 5521 Z= 0.330 Chirality : 0.040 0.180 626 Planarity : 0.005 0.054 705 Dihedral : 4.396 18.754 531 Min Nonbonded Distance : 2.230 Molprobity Statistics. All-atom Clashscore : 9.48 Ramachandran Plot: Outliers : 0.20 % Allowed : 7.86 % Favored : 91.94 % Rotamer Outliers : 10.37 % 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: 0.84 (0.39), residues: 496 helix: 1.94 (0.28), residues: 325 sheet: None (None), residues: 0 loop : -2.34 (0.49), residues: 171 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 992 Ramachandran restraints generated. 496 Oldfield, 0 Emsley, 496 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 992 Ramachandran restraints generated. 496 Oldfield, 0 Emsley, 496 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 107 residues out of total 456 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 45 poor density : 62 time to evaluate : 0.504 Fit side-chains revert: symmetry clash outliers start: 45 outliers final: 24 residues processed: 98 average time/residue: 0.7225 time to fit residues: 74.4698 Evaluate side-chains 75 residues out of total 456 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 51 time to evaluate : 0.521 Switching outliers to nearest non-outliers outliers start: 24 outliers final: 21 residues processed: 3 average time/residue: 0.4328 time to fit residues: 2.0694 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 50 random chunks: chunk 0 optimal weight: 5.9990 chunk 35 optimal weight: 5.9990 chunk 19 optimal weight: 0.9990 chunk 41 optimal weight: 1.9990 chunk 33 optimal weight: 0.5980 chunk 24 optimal weight: 2.9990 chunk 43 optimal weight: 0.1980 chunk 12 optimal weight: 0.5980 chunk 16 optimal weight: 0.3980 chunk 9 optimal weight: 0.8980 chunk 28 optimal weight: 0.9980 overall best weight: 0.5380 ------------------------------------------------------------------------------- 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: 0.7377 moved from start: 0.3493 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.050 4075 Z= 0.201 Angle : 0.671 10.388 5521 Z= 0.325 Chirality : 0.040 0.178 626 Planarity : 0.004 0.053 705 Dihedral : 4.271 22.968 531 Min Nonbonded Distance : 2.201 Molprobity Statistics. All-atom Clashscore : 10.87 Ramachandran Plot: Outliers : 0.20 % Allowed : 7.06 % Favored : 92.74 % Rotamer Outliers : 8.06 % 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: 1.17 (0.39), residues: 496 helix: 2.20 (0.28), residues: 325 sheet: None (None), residues: 0 loop : -2.23 (0.49), residues: 171 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 992 Ramachandran restraints generated. 496 Oldfield, 0 Emsley, 496 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 992 Ramachandran restraints generated. 496 Oldfield, 0 Emsley, 496 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 92 residues out of total 456 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 35 poor density : 57 time to evaluate : 0.501 Fit side-chains outliers start: 35 outliers final: 23 residues processed: 86 average time/residue: 0.8065 time to fit residues: 72.7215 Evaluate side-chains 78 residues out of total 456 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 55 time to evaluate : 0.465 Switching outliers to nearest non-outliers revert: symmetry clash outliers start: 23 outliers final: 22 residues processed: 2 average time/residue: 0.6111 time to fit residues: 2.0003 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 50 random chunks: chunk 11 optimal weight: 2.9990 chunk 48 optimal weight: 4.9990 chunk 40 optimal weight: 2.9990 chunk 22 optimal weight: 0.0870 chunk 4 optimal weight: 0.9990 chunk 16 optimal weight: 1.9990 chunk 25 optimal weight: 2.9990 chunk 46 optimal weight: 4.9990 chunk 5 optimal weight: 0.0970 chunk 27 optimal weight: 1.9990 chunk 35 optimal weight: 3.9990 overall best weight: 1.0362 ------------------------------------------------------------------------------- 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: 0.7434 moved from start: 0.3571 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.055 4075 Z= 0.246 Angle : 0.678 9.613 5521 Z= 0.336 Chirality : 0.041 0.180 626 Planarity : 0.005 0.050 705 Dihedral : 4.359 21.504 531 Min Nonbonded Distance : 2.214 Molprobity Statistics. All-atom Clashscore : 12.14 Ramachandran Plot: Outliers : 0.20 % Allowed : 7.86 % Favored : 91.94 % Rotamer Outliers : 8.99 % 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: 1.03 (0.39), residues: 496 helix: 2.14 (0.28), residues: 324 sheet: None (None), residues: 0 loop : -2.36 (0.47), residues: 172 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 992 Ramachandran restraints generated. 496 Oldfield, 0 Emsley, 496 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 992 Ramachandran restraints generated. 496 Oldfield, 0 Emsley, 496 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 98 residues out of total 456 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 39 poor density : 59 time to evaluate : 0.522 Fit side-chains outliers start: 39 outliers final: 28 residues processed: 91 average time/residue: 0.7577 time to fit residues: 72.8331 Evaluate side-chains 89 residues out of total 456 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 61 time to evaluate : 0.502 Switching outliers to nearest non-outliers outliers start: 28 outliers final: 24 residues processed: 4 average time/residue: 0.3970 time to fit residues: 2.4460 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 50 random chunks: chunk 27 optimal weight: 0.7980 chunk 40 optimal weight: 2.9990 chunk 48 optimal weight: 5.9990 chunk 30 optimal weight: 1.9990 chunk 29 optimal weight: 0.0870 chunk 22 optimal weight: 0.5980 chunk 19 optimal weight: 0.8980 chunk 28 optimal weight: 3.9990 chunk 14 optimal weight: 1.9990 chunk 9 optimal weight: 2.9990 chunk 32 optimal weight: 0.9980 overall best weight: 0.6758 ------------------------------------------------------------------------------- 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: 0.7403 moved from start: 0.3757 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.044 4075 Z= 0.210 Angle : 0.651 9.582 5521 Z= 0.323 Chirality : 0.041 0.182 626 Planarity : 0.004 0.050 705 Dihedral : 4.254 21.721 531 Min Nonbonded Distance : 2.207 Molprobity Statistics. All-atom Clashscore : 11.25 Ramachandran Plot: Outliers : 0.20 % Allowed : 7.46 % Favored : 92.34 % Rotamer Outliers : 8.06 % 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: 1.24 (0.39), residues: 496 helix: 2.27 (0.28), residues: 325 sheet: None (None), residues: 0 loop : -2.23 (0.49), residues: 171 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 992 Ramachandran restraints generated. 496 Oldfield, 0 Emsley, 496 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 992 Ramachandran restraints generated. 496 Oldfield, 0 Emsley, 496 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 96 residues out of total 456 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 35 poor density : 61 time to evaluate : 0.528 Fit side-chains outliers start: 35 outliers final: 28 residues processed: 90 average time/residue: 0.8476 time to fit residues: 79.8187 Evaluate side-chains 85 residues out of total 456 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 57 time to evaluate : 0.501 Switching outliers to nearest non-outliers outliers start: 28 outliers final: 25 residues processed: 4 average time/residue: 0.3581 time to fit residues: 2.2642 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 50 random chunks: chunk 23 optimal weight: 0.9980 chunk 4 optimal weight: 0.5980 chunk 37 optimal weight: 0.6980 chunk 43 optimal weight: 3.9990 chunk 46 optimal weight: 0.6980 chunk 42 optimal weight: 0.9980 chunk 44 optimal weight: 2.9990 chunk 27 optimal weight: 2.9990 chunk 19 optimal weight: 0.8980 chunk 35 optimal weight: 0.5980 chunk 13 optimal weight: 5.9990 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 445 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7401 moved from start: 0.3919 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.042 4075 Z= 0.215 Angle : 0.676 8.875 5521 Z= 0.333 Chirality : 0.040 0.183 626 Planarity : 0.004 0.049 705 Dihedral : 4.171 16.663 531 Min Nonbonded Distance : 2.212 Molprobity Statistics. All-atom Clashscore : 11.89 Ramachandran Plot: Outliers : 0.20 % Allowed : 7.26 % Favored : 92.54 % Rotamer Outliers : 8.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.24 (0.39), residues: 496 helix: 2.31 (0.28), residues: 325 sheet: None (None), residues: 0 loop : -2.33 (0.47), residues: 171 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 992 Ramachandran restraints generated. 496 Oldfield, 0 Emsley, 496 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 992 Ramachandran restraints generated. 496 Oldfield, 0 Emsley, 496 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 96 residues out of total 456 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 36 poor density : 60 time to evaluate : 0.506 Fit side-chains outliers start: 36 outliers final: 29 residues processed: 88 average time/residue: 0.8611 time to fit residues: 79.2264 Evaluate side-chains 89 residues out of total 456 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 60 time to evaluate : 0.410 Switching outliers to nearest non-outliers outliers start: 29 outliers final: 24 residues processed: 6 average time/residue: 0.4575 time to fit residues: 3.5429 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 50 random chunks: chunk 40 optimal weight: 2.9990 chunk 42 optimal weight: 0.4980 chunk 44 optimal weight: 3.9990 chunk 29 optimal weight: 0.3980 chunk 47 optimal weight: 2.9990 chunk 28 optimal weight: 0.1980 chunk 22 optimal weight: 2.9990 chunk 33 optimal weight: 0.7980 chunk 49 optimal weight: 5.9990 chunk 45 optimal weight: 0.0870 chunk 39 optimal weight: 0.4980 overall best weight: 0.3358 ------------------------------------------------------------------------------- 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: 0.7345 moved from start: 0.4217 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.035 4075 Z= 0.198 Angle : 0.691 9.254 5521 Z= 0.334 Chirality : 0.039 0.183 626 Planarity : 0.004 0.049 705 Dihedral : 4.004 14.629 531 Min Nonbonded Distance : 2.201 Molprobity Statistics. All-atom Clashscore : 10.87 Ramachandran Plot: Outliers : 0.20 % Allowed : 6.45 % Favored : 93.35 % Rotamer Outliers : 7.37 % 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: 1.46 (0.39), residues: 496 helix: 2.47 (0.28), residues: 325 sheet: None (None), residues: 0 loop : -2.22 (0.47), residues: 171 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 992 Ramachandran restraints generated. 496 Oldfield, 0 Emsley, 496 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 992 Ramachandran restraints generated. 496 Oldfield, 0 Emsley, 496 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 99 residues out of total 456 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 67 time to evaluate : 0.511 Fit side-chains outliers start: 32 outliers final: 22 residues processed: 93 average time/residue: 0.8272 time to fit residues: 80.5481 Evaluate side-chains 77 residues out of total 456 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 55 time to evaluate : 0.502 Switching outliers to nearest non-outliers outliers start: 22 outliers final: 21 residues processed: 1 average time/residue: 0.1994 time to fit residues: 0.9050 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 50 random chunks: chunk 4 optimal weight: 0.8980 chunk 30 optimal weight: 1.9990 chunk 24 optimal weight: 0.6980 chunk 31 optimal weight: 1.9990 chunk 42 optimal weight: 4.9990 chunk 12 optimal weight: 0.7980 chunk 36 optimal weight: 1.9990 chunk 5 optimal weight: 0.5980 chunk 11 optimal weight: 1.9990 chunk 39 optimal weight: 0.8980 chunk 16 optimal weight: 0.8980 overall best weight: 0.7780 ------------------------------------------------------------------------------- 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: 0.7384 moved from start: 0.4316 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.041 4075 Z= 0.237 Angle : 0.724 9.802 5521 Z= 0.350 Chirality : 0.041 0.178 626 Planarity : 0.004 0.050 705 Dihedral : 4.127 14.971 531 Min Nonbonded Distance : 2.221 Molprobity Statistics. All-atom Clashscore : 11.25 Ramachandran Plot: Outliers : 0.20 % Allowed : 7.26 % Favored : 92.54 % Rotamer Outliers : 6.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.20 (0.39), residues: 496 helix: 2.27 (0.28), residues: 326 sheet: None (None), residues: 0 loop : -2.34 (0.46), residues: 170 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 992 Ramachandran restraints generated. 496 Oldfield, 0 Emsley, 496 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 992 Ramachandran restraints generated. 496 Oldfield, 0 Emsley, 496 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 87 residues out of total 456 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 60 time to evaluate : 0.518 Fit side-chains revert: symmetry clash outliers start: 27 outliers final: 22 residues processed: 84 average time/residue: 0.8348 time to fit residues: 73.5100 Evaluate side-chains 82 residues out of total 456 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 60 time to evaluate : 0.512 Switching outliers to nearest non-outliers outliers start: 22 outliers final: 21 residues processed: 1 average time/residue: 0.0385 time to fit residues: 0.7519 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 50 random chunks: chunk 40 optimal weight: 0.9980 chunk 5 optimal weight: 0.0980 chunk 7 optimal weight: 0.7980 chunk 34 optimal weight: 2.9990 chunk 2 optimal weight: 1.9990 chunk 28 optimal weight: 1.9990 chunk 45 optimal weight: 0.0070 chunk 26 optimal weight: 2.9990 chunk 1 optimal weight: 0.8980 chunk 31 optimal weight: 0.0070 chunk 30 optimal weight: 0.8980 overall best weight: 0.3616 ------------------------------------------------------------------------------- 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 = 0.4323 r_free = 0.4323 target = 0.156316 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.4078 r_free = 0.4078 target = 0.134126 restraints weight = 6411.812| |-----------------------------------------------------------------------------| r_work (start): 0.4033 rms_B_bonded: 3.01 r_work: 0.4024 rms_B_bonded: 2.81 restraints_weight: 0.5000 r_work: 0.4015 rms_B_bonded: 2.77 restraints_weight: 0.2500 r_work: 0.4006 rms_B_bonded: 2.80 restraints_weight: 0.1250 r_work: 0.3996 rms_B_bonded: 2.88 restraints_weight: 0.0625 r_work: 0.3985 rms_B_bonded: 2.99 restraints_weight: 0.0312 r_work: 0.3974 rms_B_bonded: 3.14 restraints_weight: 0.0156 r_work: 0.3962 rms_B_bonded: 3.31 restraints_weight: 0.0078 r_work: 0.3950 rms_B_bonded: 3.52 restraints_weight: 0.0039 r_work: 0.3937 rms_B_bonded: 3.75 restraints_weight: 0.0020 r_work: 0.3923 rms_B_bonded: 4.01 restraints_weight: 0.0010 r_work: 0.3909 rms_B_bonded: 4.31 restraints_weight: 0.0005 r_work: 0.3894 rms_B_bonded: 4.64 restraints_weight: 0.0002 r_work (final): 0.3894 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7537 moved from start: 0.4529 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.033 4075 Z= 0.204 Angle : 0.724 9.322 5521 Z= 0.347 Chirality : 0.041 0.180 626 Planarity : 0.004 0.050 705 Dihedral : 3.994 14.265 531 Min Nonbonded Distance : 2.217 Molprobity Statistics. All-atom Clashscore : 10.49 Ramachandran Plot: Outliers : 0.20 % Allowed : 6.85 % Favored : 92.94 % Rotamer Outliers : 5.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.46 (0.39), residues: 496 helix: 2.47 (0.28), residues: 326 sheet: None (None), residues: 0 loop : -2.26 (0.47), residues: 170 =============================================================================== Job complete usr+sys time: 1866.51 seconds wall clock time: 33 minutes 54.19 seconds (2034.19 seconds total)