Starting phenix.real_space_refine on Mon Sep 23 15:35:53 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7wxg_32878/09_2024/7wxg_32878.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7wxg_32878/09_2024/7wxg_32878.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.2 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7wxg_32878/09_2024/7wxg_32878.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7wxg_32878/09_2024/7wxg_32878.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7wxg_32878/09_2024/7wxg_32878.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7wxg_32878/09_2024/7wxg_32878.cif" } resolution = 4.2 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.005 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 P 3 5.49 5 S 15 5.16 5 C 2048 2.51 5 N 593 2.21 5 O 636 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 20 residue(s): 0.01s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5461/modules/chem_data/mon_lib" Total number of atoms: 3295 Number of models: 1 Model: "" Number of chains: 2 Chain: "A" Number of atoms: 3247 Number of conformers: 1 Conformer: "" Number of residues, atoms: 430, 3247 Classifications: {'peptide': 430} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 15, 'TRANS': 414} Chain: "A" Number of atoms: 48 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 48 Unusual residues: {'NAP': 1} Classifications: {'undetermined': 1} Time building chain proxies: 3.44, per 1000 atoms: 1.04 Number of scatterers: 3295 At special positions: 0 Unit cell: (80.56, 93.28, 60.42, 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 15 16.00 P 3 15.00 O 636 8.00 N 593 7.00 C 2048 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 - 3.00 Amino acid : True - 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: 0.92 Conformation dependent library (CDL) restraints added in 426.5 milliseconds 856 Ramachandran restraints generated. 428 Oldfield, 0 Emsley, 428 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 798 Finding SS restraints... Secondary structure from input PDB file: 18 helices and 5 sheets defined 49.5% alpha, 10.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.37 Creating SS restraints... Processing helix chain 'A' and resid 348 through 364 Processing helix chain 'A' and resid 366 through 384 removed outlier: 3.901A pdb=" N ARG A 370 " --> pdb=" O THR A 366 " (cutoff:3.500A) removed outlier: 3.676A pdb=" N SER A 372 " --> pdb=" O ALA A 368 " (cutoff:3.500A) Processing helix chain 'A' and resid 384 through 403 removed outlier: 3.814A pdb=" N ILE A 388 " --> pdb=" O ARG A 384 " (cutoff:3.500A) Processing helix chain 'A' and resid 405 through 413 Processing helix chain 'A' and resid 415 through 432 Processing helix chain 'A' and resid 471 through 484 removed outlier: 4.333A pdb=" N GLN A 475 " --> pdb=" O ASP A 471 " (cutoff:3.500A) Processing helix chain 'A' and resid 495 through 511 Processing helix chain 'A' and resid 524 through 534 removed outlier: 3.672A pdb=" N ILE A 528 " --> pdb=" O THR A 524 " (cutoff:3.500A) Processing helix chain 'A' and resid 546 through 557 Processing helix chain 'A' and resid 579 through 592 Processing helix chain 'A' and resid 609 through 611 No H-bonds generated for 'chain 'A' and resid 609 through 611' Processing helix chain 'A' and resid 614 through 626 removed outlier: 3.610A pdb=" N ASP A 618 " --> pdb=" O ALA A 614 " (cutoff:3.500A) Processing helix chain 'A' and resid 633 through 640 Processing helix chain 'A' and resid 666 through 678 Processing helix chain 'A' and resid 689 through 700 Processing helix chain 'A' and resid 716 through 720 Processing helix chain 'A' and resid 740 through 742 No H-bonds generated for 'chain 'A' and resid 740 through 742' Processing helix chain 'A' and resid 757 through 761 removed outlier: 3.557A pdb=" N PHE A 760 " --> pdb=" O ALA A 757 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 440 through 444 removed outlier: 7.232A pdb=" N VAL A 440 " --> pdb=" O THR A 456 " (cutoff:3.500A) removed outlier: 6.455A pdb=" N THR A 456 " --> pdb=" O VAL A 440 " (cutoff:3.500A) removed outlier: 3.906A pdb=" N ARG A 442 " --> pdb=" O GLN A 454 " (cutoff:3.500A) removed outlier: 3.527A pdb=" N GLU A 751 " --> pdb=" O GLU A 451 " (cutoff:3.500A) removed outlier: 3.650A pdb=" N ILE A 749 " --> pdb=" O LYS A 453 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 486 through 488 removed outlier: 6.258A pdb=" N LEU A 462 " --> pdb=" O LEU A 488 " (cutoff:3.500A) removed outlier: 7.280A pdb=" N VAL A 461 " --> pdb=" O LEU A 540 " (cutoff:3.500A) removed outlier: 8.498A pdb=" N ILE A 542 " --> pdb=" O VAL A 461 " (cutoff:3.500A) removed outlier: 7.425A pdb=" N LEU A 463 " --> pdb=" O ILE A 542 " (cutoff:3.500A) removed outlier: 7.555A pdb=" N ARG A 544 " --> pdb=" O LEU A 463 " (cutoff:3.500A) removed outlier: 7.438A pdb=" N ILE A 465 " --> pdb=" O ARG A 544 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA2 Processing sheet with id=AA3, first strand: chain 'A' and resid 604 through 607 removed outlier: 6.131A pdb=" N LEU A 604 " --> pdb=" O GLU A 662 " (cutoff:3.500A) removed outlier: 7.222A pdb=" N VAL A 664 " --> pdb=" O LEU A 604 " (cutoff:3.500A) removed outlier: 5.970A pdb=" N ILE A 606 " --> pdb=" O VAL A 664 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA3 Processing sheet with id=AA4, first strand: chain 'A' and resid 683 through 685 removed outlier: 6.862A pdb=" N ASP A 683 " --> pdb=" O PHE A 706 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA4 Processing sheet with id=AA5, first strand: chain 'A' and resid 727 through 728 149 hydrogen bonds defined for protein. 435 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: 0.88 Time building geometry restraints manager: 1.08 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.18 - 1.31: 571 1.31 - 1.43: 791 1.43 - 1.56: 1955 1.56 - 1.68: 8 1.68 - 1.81: 24 Bond restraints: 3349 Sorted by residual: bond pdb=" C1D NAP A 801 " pdb=" C2D NAP A 801 " ideal model delta sigma weight residual 1.533 1.271 0.262 2.00e-02 2.50e+03 1.72e+02 bond pdb=" C3D NAP A 801 " pdb=" C4D NAP A 801 " ideal model delta sigma weight residual 1.518 1.261 0.257 2.00e-02 2.50e+03 1.65e+02 bond pdb=" C3B NAP A 801 " pdb=" C4B NAP A 801 " ideal model delta sigma weight residual 1.543 1.294 0.249 2.00e-02 2.50e+03 1.56e+02 bond pdb=" C4B NAP A 801 " pdb=" O4B NAP A 801 " ideal model delta sigma weight residual 1.426 1.623 -0.197 2.00e-02 2.50e+03 9.67e+01 bond pdb=" C1D NAP A 801 " pdb=" O4D NAP A 801 " ideal model delta sigma weight residual 1.375 1.550 -0.175 2.00e-02 2.50e+03 7.65e+01 ... (remaining 3344 not shown) Histogram of bond angle deviations from ideal: 0.00 - 3.97: 4500 3.97 - 7.94: 33 7.94 - 11.90: 5 11.90 - 15.87: 3 15.87 - 19.84: 3 Bond angle restraints: 4544 Sorted by residual: angle pdb=" N1A NAP A 801 " pdb=" C6A NAP A 801 " pdb=" N6A NAP A 801 " ideal model delta sigma weight residual 119.30 99.46 19.84 3.00e+00 1.11e-01 4.37e+01 angle pdb=" C1B NAP A 801 " pdb=" N9A NAP A 801 " pdb=" C4A NAP A 801 " ideal model delta sigma weight residual 124.31 107.08 17.23 3.00e+00 1.11e-01 3.30e+01 angle pdb=" C5A NAP A 801 " pdb=" C6A NAP A 801 " pdb=" N6A NAP A 801 " ideal model delta sigma weight residual 122.73 139.91 -17.18 3.00e+00 1.11e-01 3.28e+01 angle pdb=" C1B NAP A 801 " pdb=" N9A NAP A 801 " pdb=" C8A NAP A 801 " ideal model delta sigma weight residual 129.84 145.62 -15.78 3.00e+00 1.11e-01 2.77e+01 angle pdb=" O1N NAP A 801 " pdb=" PN NAP A 801 " pdb=" O2N NAP A 801 " ideal model delta sigma weight residual 122.51 109.58 12.93 3.00e+00 1.11e-01 1.86e+01 ... (remaining 4539 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 14.77: 1765 14.77 - 29.54: 216 29.54 - 44.30: 84 44.30 - 59.07: 15 59.07 - 73.84: 5 Dihedral angle restraints: 2085 sinusoidal: 853 harmonic: 1232 Sorted by residual: dihedral pdb=" CA PHE A 642 " pdb=" C PHE A 642 " pdb=" N GLY A 643 " pdb=" CA GLY A 643 " ideal model delta harmonic sigma weight residual 180.00 158.98 21.02 0 5.00e+00 4.00e-02 1.77e+01 dihedral pdb=" CA CYS A 598 " pdb=" C CYS A 598 " pdb=" N ASN A 599 " pdb=" CA ASN A 599 " ideal model delta harmonic sigma weight residual -180.00 -162.95 -17.05 0 5.00e+00 4.00e-02 1.16e+01 dihedral pdb=" CA ALA A 714 " pdb=" C ALA A 714 " pdb=" N ASP A 715 " pdb=" CA ASP A 715 " ideal model delta harmonic sigma weight residual 180.00 164.01 15.99 0 5.00e+00 4.00e-02 1.02e+01 ... (remaining 2082 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.072: 466 0.072 - 0.144: 58 0.144 - 0.215: 5 0.215 - 0.287: 1 0.287 - 0.359: 1 Chirality restraints: 531 Sorted by residual: chirality pdb=" C3D NAP A 801 " pdb=" C2D NAP A 801 " pdb=" C4D NAP A 801 " pdb=" O3D NAP A 801 " both_signs ideal model delta sigma weight residual False -2.74 -2.38 -0.36 2.00e-01 2.50e+01 3.22e+00 chirality pdb=" C2B NAP A 801 " pdb=" C1B NAP A 801 " pdb=" C3B NAP A 801 " pdb=" O2B NAP A 801 " both_signs ideal model delta sigma weight residual False -2.75 -2.50 -0.26 2.00e-01 2.50e+01 1.64e+00 chirality pdb=" C2D NAP A 801 " pdb=" C1D NAP A 801 " pdb=" C3D NAP A 801 " pdb=" O2D NAP A 801 " both_signs ideal model delta sigma weight residual False -2.55 -2.37 -0.18 2.00e-01 2.50e+01 8.07e-01 ... (remaining 528 not shown) Planarity restraints: 588 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ILE A 560 " 0.022 5.00e-02 4.00e+02 3.34e-02 1.78e+00 pdb=" N PRO A 561 " -0.058 5.00e-02 4.00e+02 pdb=" CA PRO A 561 " 0.017 5.00e-02 4.00e+02 pdb=" CD PRO A 561 " 0.019 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C TYR A 594 " 0.022 5.00e-02 4.00e+02 3.25e-02 1.69e+00 pdb=" N PRO A 595 " -0.056 5.00e-02 4.00e+02 pdb=" CA PRO A 595 " 0.017 5.00e-02 4.00e+02 pdb=" CD PRO A 595 " 0.018 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ARG A 469 " 0.021 5.00e-02 4.00e+02 3.21e-02 1.65e+00 pdb=" N PRO A 470 " -0.055 5.00e-02 4.00e+02 pdb=" CA PRO A 470 " 0.016 5.00e-02 4.00e+02 pdb=" CD PRO A 470 " 0.018 5.00e-02 4.00e+02 ... (remaining 585 not shown) Histogram of nonbonded interaction distances: 2.18 - 2.73: 278 2.73 - 3.27: 3683 3.27 - 3.81: 5261 3.81 - 4.36: 5991 4.36 - 4.90: 10082 Nonbonded interactions: 25295 Sorted by model distance: nonbonded pdb=" O SER A 410 " pdb=" OG SER A 413 " model vdw 2.184 3.040 nonbonded pdb=" O CYS A 570 " pdb=" ND1 HIS A 571 " model vdw 2.185 3.120 nonbonded pdb=" O ASP A 530 " pdb=" OG SER A 533 " model vdw 2.254 3.040 nonbonded pdb=" O ALA A 399 " pdb=" OG SER A 402 " model vdw 2.257 3.040 nonbonded pdb=" NH1 ARG A 525 " pdb=" O4B NAP A 801 " model vdw 2.272 3.120 ... (remaining 25290 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 group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.490 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.150 Check model and map are aligned: 0.020 Set scattering table: 0.040 Process input model: 13.810 Find NCS groups from input model: 0.040 Set up NCS constraints: 0.010 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.750 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 18.320 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7931 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.012 0.262 3349 Z= 0.784 Angle : 1.073 19.838 4544 Z= 0.492 Chirality : 0.050 0.359 531 Planarity : 0.004 0.033 588 Dihedral : 15.420 73.837 1287 Min Nonbonded Distance : 2.184 Molprobity Statistics. All-atom Clashscore : 12.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.75 % Favored : 89.25 % Rotamer: Outliers : 0.29 % Allowed : 7.54 % Favored : 92.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -5.16 (0.29), residues: 428 helix: -2.48 (0.29), residues: 186 sheet: -4.14 (0.44), residues: 61 loop : -4.14 (0.33), residues: 181 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.003 TRP A 768 HIS 0.003 0.001 HIS A 681 PHE 0.021 0.002 PHE A 642 TYR 0.010 0.002 TYR A 573 ARG 0.002 0.000 ARG A 370 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 856 Ramachandran restraints generated. 428 Oldfield, 0 Emsley, 428 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 856 Ramachandran restraints generated. 428 Oldfield, 0 Emsley, 428 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 85 residues out of total 345 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 84 time to evaluate : 0.395 Fit side-chains revert: symmetry clash REVERT: A 362 MET cc_start: 0.8692 (mtp) cc_final: 0.8466 (mtp) REVERT: A 497 HIS cc_start: 0.8544 (m90) cc_final: 0.8323 (m90) REVERT: A 521 LEU cc_start: 0.8997 (mt) cc_final: 0.8744 (mp) REVERT: A 536 ASN cc_start: 0.8874 (t0) cc_final: 0.8492 (t0) REVERT: A 594 TYR cc_start: 0.8507 (m-10) cc_final: 0.8192 (m-80) REVERT: A 602 GLU cc_start: 0.8841 (pt0) cc_final: 0.8314 (mt-10) REVERT: A 651 LYS cc_start: 0.9059 (mttt) cc_final: 0.8254 (tptt) REVERT: A 652 HIS cc_start: 0.7686 (t-90) cc_final: 0.7388 (t-90) REVERT: A 668 ASP cc_start: 0.7950 (t0) cc_final: 0.7628 (t0) outliers start: 1 outliers final: 0 residues processed: 85 average time/residue: 0.1873 time to fit residues: 18.7283 Evaluate side-chains 63 residues out of total 345 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 63 time to evaluate : 0.348 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 43 random chunks: chunk 36 optimal weight: 0.2980 chunk 32 optimal weight: 6.9990 chunk 18 optimal weight: 1.9990 chunk 11 optimal weight: 3.9990 chunk 21 optimal weight: 6.9990 chunk 17 optimal weight: 3.9990 chunk 33 optimal weight: 0.8980 chunk 13 optimal weight: 0.6980 chunk 20 optimal weight: 1.9990 chunk 25 optimal weight: 0.7980 chunk 39 optimal weight: 0.0060 overall best weight: 0.5396 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 375 ASN A 392 ASN A 434 HIS A 536 ASN A 607 HIS A 672 ASN A 681 HIS Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7813 moved from start: 0.2153 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.021 3349 Z= 0.162 Angle : 0.639 6.304 4544 Z= 0.320 Chirality : 0.045 0.151 531 Planarity : 0.005 0.044 588 Dihedral : 9.325 46.948 526 Min Nonbonded Distance : 2.496 Molprobity Statistics. All-atom Clashscore : 9.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.84 % Favored : 94.16 % Rotamer: Outliers : 0.58 % Allowed : 4.64 % Favored : 94.78 % 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: -2.94 (0.37), residues: 428 helix: -0.62 (0.35), residues: 191 sheet: -3.35 (0.49), residues: 60 loop : -2.89 (0.42), residues: 177 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.002 TRP A 748 HIS 0.004 0.001 HIS A 673 PHE 0.012 0.001 PHE A 616 TYR 0.007 0.001 TYR A 631 ARG 0.003 0.000 ARG A 712 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 856 Ramachandran restraints generated. 428 Oldfield, 0 Emsley, 428 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 856 Ramachandran restraints generated. 428 Oldfield, 0 Emsley, 428 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 93 residues out of total 345 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 91 time to evaluate : 0.397 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 351 MET cc_start: 0.8967 (mtp) cc_final: 0.8754 (mtt) REVERT: A 428 GLN cc_start: 0.8712 (mt0) cc_final: 0.8375 (tm-30) REVERT: A 481 MET cc_start: 0.7783 (ttm) cc_final: 0.7581 (ptm) REVERT: A 489 LEU cc_start: 0.9230 (mm) cc_final: 0.8940 (mm) REVERT: A 497 HIS cc_start: 0.8448 (m90) cc_final: 0.8102 (t70) REVERT: A 504 GLU cc_start: 0.8056 (tm-30) cc_final: 0.7855 (tm-30) REVERT: A 536 ASN cc_start: 0.8693 (t0) cc_final: 0.8369 (t0) REVERT: A 556 GLN cc_start: 0.8024 (mt0) cc_final: 0.7771 (tt0) REVERT: A 601 MET cc_start: 0.7816 (tmm) cc_final: 0.7610 (tmm) REVERT: A 651 LYS cc_start: 0.8925 (mttt) cc_final: 0.8055 (tptt) REVERT: A 668 ASP cc_start: 0.7878 (t0) cc_final: 0.7556 (t0) REVERT: A 712 ARG cc_start: 0.8194 (tpp80) cc_final: 0.7642 (ttp-170) outliers start: 2 outliers final: 0 residues processed: 92 average time/residue: 0.1659 time to fit residues: 18.5700 Evaluate side-chains 63 residues out of total 345 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 63 time to evaluate : 0.357 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 43 random chunks: chunk 21 optimal weight: 1.9990 chunk 12 optimal weight: 4.9990 chunk 32 optimal weight: 5.9990 chunk 26 optimal weight: 0.3980 chunk 10 optimal weight: 6.9990 chunk 39 optimal weight: 2.9990 chunk 42 optimal weight: 7.9990 chunk 34 optimal weight: 4.9990 chunk 38 optimal weight: 2.9990 chunk 13 optimal weight: 0.9990 chunk 31 optimal weight: 3.9990 overall best weight: 1.8788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 652 HIS A 689 ASN A 695 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7889 moved from start: 0.2316 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 3349 Z= 0.264 Angle : 0.646 7.079 4544 Z= 0.327 Chirality : 0.045 0.198 531 Planarity : 0.005 0.046 588 Dihedral : 8.928 48.953 526 Min Nonbonded Distance : 2.468 Molprobity Statistics. All-atom Clashscore : 10.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.78 % Favored : 93.22 % Rotamer: Outliers : 0.29 % Allowed : 5.51 % Favored : 94.20 % 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: -2.27 (0.38), residues: 428 helix: 0.01 (0.36), residues: 190 sheet: -3.00 (0.54), residues: 58 loop : -2.66 (0.43), residues: 180 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP A 768 HIS 0.002 0.001 HIS A 681 PHE 0.017 0.002 PHE A 642 TYR 0.005 0.001 TYR A 654 ARG 0.004 0.000 ARG A 544 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 856 Ramachandran restraints generated. 428 Oldfield, 0 Emsley, 428 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 856 Ramachandran restraints generated. 428 Oldfield, 0 Emsley, 428 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 83 residues out of total 345 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 82 time to evaluate : 0.568 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 497 HIS cc_start: 0.8481 (m90) cc_final: 0.8129 (t70) REVERT: A 536 ASN cc_start: 0.8677 (t0) cc_final: 0.8230 (t0) REVERT: A 556 GLN cc_start: 0.8026 (mt0) cc_final: 0.7560 (tt0) REVERT: A 601 MET cc_start: 0.7777 (tmm) cc_final: 0.7552 (tmm) REVERT: A 602 GLU cc_start: 0.8971 (pt0) cc_final: 0.8270 (mt-10) REVERT: A 651 LYS cc_start: 0.8960 (mttt) cc_final: 0.8098 (tptt) REVERT: A 652 HIS cc_start: 0.7881 (t-90) cc_final: 0.7215 (t-90) REVERT: A 668 ASP cc_start: 0.7985 (t0) cc_final: 0.7576 (t0) REVERT: A 684 VAL cc_start: 0.9627 (t) cc_final: 0.9396 (p) REVERT: A 712 ARG cc_start: 0.8297 (tpp80) cc_final: 0.7665 (ttp-170) outliers start: 1 outliers final: 0 residues processed: 83 average time/residue: 0.1612 time to fit residues: 16.8465 Evaluate side-chains 57 residues out of total 345 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 57 time to evaluate : 0.379 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 43 random chunks: chunk 38 optimal weight: 0.9990 chunk 29 optimal weight: 1.9990 chunk 20 optimal weight: 1.9990 chunk 4 optimal weight: 1.9990 chunk 18 optimal weight: 5.9990 chunk 26 optimal weight: 0.4980 chunk 39 optimal weight: 0.7980 chunk 41 optimal weight: 0.9990 chunk 37 optimal weight: 0.9990 chunk 11 optimal weight: 1.9990 chunk 34 optimal weight: 2.9990 overall best weight: 0.8586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 392 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7808 moved from start: 0.2985 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.020 3349 Z= 0.173 Angle : 0.620 10.053 4544 Z= 0.303 Chirality : 0.044 0.153 531 Planarity : 0.004 0.047 588 Dihedral : 8.286 50.398 526 Min Nonbonded Distance : 2.506 Molprobity Statistics. All-atom Clashscore : 8.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.78 % Favored : 93.22 % Rotamer: Outliers : 0.29 % Allowed : 4.06 % Favored : 95.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.55 (0.40), residues: 428 helix: 0.39 (0.37), residues: 197 sheet: -2.60 (0.55), residues: 63 loop : -2.05 (0.47), residues: 168 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.002 TRP A 768 HIS 0.004 0.001 HIS A 673 PHE 0.008 0.001 PHE A 642 TYR 0.013 0.002 TYR A 573 ARG 0.004 0.000 ARG A 544 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 856 Ramachandran restraints generated. 428 Oldfield, 0 Emsley, 428 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 856 Ramachandran restraints generated. 428 Oldfield, 0 Emsley, 428 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 91 residues out of total 345 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 90 time to evaluate : 0.377 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 481 MET cc_start: 0.7439 (ttp) cc_final: 0.7126 (ptm) REVERT: A 497 HIS cc_start: 0.8416 (m90) cc_final: 0.8064 (t70) REVERT: A 536 ASN cc_start: 0.8542 (t0) cc_final: 0.8058 (t0) REVERT: A 556 GLN cc_start: 0.8066 (mt0) cc_final: 0.7692 (tt0) REVERT: A 651 LYS cc_start: 0.8803 (mttt) cc_final: 0.7951 (tptt) REVERT: A 652 HIS cc_start: 0.7802 (t-90) cc_final: 0.7228 (t70) REVERT: A 668 ASP cc_start: 0.7910 (t0) cc_final: 0.7460 (t0) REVERT: A 712 ARG cc_start: 0.8153 (tpp80) cc_final: 0.7607 (ttp-170) outliers start: 1 outliers final: 0 residues processed: 91 average time/residue: 0.1537 time to fit residues: 17.0055 Evaluate side-chains 63 residues out of total 345 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 63 time to evaluate : 0.392 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 43 random chunks: chunk 23 optimal weight: 8.9990 chunk 0 optimal weight: 9.9990 chunk 30 optimal weight: 4.9990 chunk 17 optimal weight: 8.9990 chunk 35 optimal weight: 2.9990 chunk 28 optimal weight: 0.9980 chunk 21 optimal weight: 9.9990 chunk 37 optimal weight: 1.9990 chunk 10 optimal weight: 0.8980 chunk 13 optimal weight: 0.8980 chunk 8 optimal weight: 1.9990 overall best weight: 1.3584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 392 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7833 moved from start: 0.3082 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 3349 Z= 0.225 Angle : 0.641 8.736 4544 Z= 0.321 Chirality : 0.044 0.185 531 Planarity : 0.004 0.046 588 Dihedral : 8.165 53.192 526 Min Nonbonded Distance : 2.394 Molprobity Statistics. All-atom Clashscore : 9.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.31 % Favored : 93.69 % Rotamer: Outliers : 0.00 % Allowed : 2.90 % Favored : 97.10 % 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: -1.49 (0.40), residues: 428 helix: 0.45 (0.37), residues: 197 sheet: -2.44 (0.53), residues: 68 loop : -2.07 (0.48), residues: 163 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.002 TRP A 768 HIS 0.003 0.001 HIS A 565 PHE 0.009 0.002 PHE A 642 TYR 0.004 0.001 TYR A 631 ARG 0.003 0.000 ARG A 411 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 856 Ramachandran restraints generated. 428 Oldfield, 0 Emsley, 428 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 856 Ramachandran restraints generated. 428 Oldfield, 0 Emsley, 428 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 85 residues out of total 345 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 85 time to evaluate : 0.383 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 375 ASN cc_start: 0.8791 (m-40) cc_final: 0.8443 (m-40) REVERT: A 428 GLN cc_start: 0.8111 (tm-30) cc_final: 0.7748 (tm-30) REVERT: A 497 HIS cc_start: 0.8463 (m90) cc_final: 0.8131 (t70) REVERT: A 536 ASN cc_start: 0.8609 (t0) cc_final: 0.8150 (t0) REVERT: A 556 GLN cc_start: 0.8118 (mt0) cc_final: 0.7657 (tt0) REVERT: A 565 HIS cc_start: 0.6990 (p-80) cc_final: 0.6222 (p90) REVERT: A 602 GLU cc_start: 0.8865 (pt0) cc_final: 0.8253 (mt-10) REVERT: A 629 LYS cc_start: 0.8461 (pptt) cc_final: 0.8058 (pptt) REVERT: A 651 LYS cc_start: 0.8804 (mttt) cc_final: 0.8171 (ptpp) REVERT: A 652 HIS cc_start: 0.7571 (t-90) cc_final: 0.7112 (t-90) REVERT: A 668 ASP cc_start: 0.7922 (t0) cc_final: 0.7456 (t0) REVERT: A 712 ARG cc_start: 0.8166 (tpp80) cc_final: 0.7526 (ttp80) outliers start: 0 outliers final: 0 residues processed: 85 average time/residue: 0.1443 time to fit residues: 15.1104 Evaluate side-chains 65 residues out of total 345 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 65 time to evaluate : 0.357 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 43 random chunks: chunk 24 optimal weight: 0.7980 chunk 10 optimal weight: 1.9990 chunk 41 optimal weight: 0.8980 chunk 34 optimal weight: 2.9990 chunk 19 optimal weight: 0.0970 chunk 3 optimal weight: 0.9990 chunk 13 optimal weight: 0.9980 chunk 21 optimal weight: 7.9990 chunk 40 optimal weight: 5.9990 chunk 4 optimal weight: 0.8980 chunk 23 optimal weight: 0.9980 overall best weight: 0.7378 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 392 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7780 moved from start: 0.3423 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 3349 Z= 0.171 Angle : 0.605 7.675 4544 Z= 0.302 Chirality : 0.043 0.154 531 Planarity : 0.004 0.045 588 Dihedral : 7.890 52.270 526 Min Nonbonded Distance : 2.468 Molprobity Statistics. All-atom Clashscore : 7.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.54 % Favored : 93.46 % Rotamer: Outliers : 0.00 % Allowed : 3.19 % Favored : 96.81 % 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: -1.12 (0.41), residues: 428 helix: 0.64 (0.37), residues: 197 sheet: -2.22 (0.56), residues: 71 loop : -1.70 (0.50), residues: 160 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.002 TRP A 768 HIS 0.004 0.001 HIS A 673 PHE 0.007 0.001 PHE A 616 TYR 0.006 0.001 TYR A 654 ARG 0.003 0.000 ARG A 544 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 856 Ramachandran restraints generated. 428 Oldfield, 0 Emsley, 428 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 856 Ramachandran restraints generated. 428 Oldfield, 0 Emsley, 428 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 92 residues out of total 345 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 92 time to evaluate : 0.379 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 419 LEU cc_start: 0.8881 (mm) cc_final: 0.8659 (mm) REVERT: A 428 GLN cc_start: 0.8177 (tm-30) cc_final: 0.7780 (tm-30) REVERT: A 497 HIS cc_start: 0.8456 (m90) cc_final: 0.8122 (t70) REVERT: A 536 ASN cc_start: 0.8654 (t0) cc_final: 0.8162 (t0) REVERT: A 556 GLN cc_start: 0.8080 (mt0) cc_final: 0.7798 (tt0) REVERT: A 565 HIS cc_start: 0.6724 (p-80) cc_final: 0.6016 (p90) REVERT: A 651 LYS cc_start: 0.8752 (mttt) cc_final: 0.8177 (ptpp) REVERT: A 652 HIS cc_start: 0.7730 (t-90) cc_final: 0.7331 (t70) REVERT: A 668 ASP cc_start: 0.7917 (t0) cc_final: 0.7462 (t0) REVERT: A 669 GLU cc_start: 0.7630 (tp30) cc_final: 0.7390 (tp30) REVERT: A 712 ARG cc_start: 0.8044 (tpp80) cc_final: 0.7465 (ttp80) outliers start: 0 outliers final: 0 residues processed: 92 average time/residue: 0.1685 time to fit residues: 18.9023 Evaluate side-chains 65 residues out of total 345 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 65 time to evaluate : 0.395 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 43 random chunks: chunk 30 optimal weight: 0.4980 chunk 23 optimal weight: 0.0270 chunk 35 optimal weight: 0.0980 chunk 41 optimal weight: 0.0980 chunk 25 optimal weight: 1.9990 chunk 19 optimal weight: 0.6980 chunk 16 optimal weight: 0.8980 chunk 24 optimal weight: 3.9990 chunk 12 optimal weight: 1.9990 chunk 8 optimal weight: 0.8980 chunk 26 optimal weight: 0.7980 overall best weight: 0.2838 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 392 ASN A 607 HIS A 770 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7719 moved from start: 0.3899 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.027 3349 Z= 0.153 Angle : 0.611 7.796 4544 Z= 0.301 Chirality : 0.043 0.140 531 Planarity : 0.004 0.045 588 Dihedral : 7.707 51.479 526 Min Nonbonded Distance : 2.410 Molprobity Statistics. All-atom Clashscore : 8.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.31 % Favored : 93.69 % Rotamer: Outliers : 0.29 % Allowed : 1.74 % Favored : 97.97 % 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: -0.90 (0.41), residues: 428 helix: 0.76 (0.38), residues: 198 sheet: -1.85 (0.57), residues: 69 loop : -1.67 (0.49), residues: 161 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 748 HIS 0.004 0.001 HIS A 565 PHE 0.009 0.001 PHE A 719 TYR 0.007 0.001 TYR A 631 ARG 0.003 0.000 ARG A 712 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 856 Ramachandran restraints generated. 428 Oldfield, 0 Emsley, 428 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 856 Ramachandran restraints generated. 428 Oldfield, 0 Emsley, 428 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 97 residues out of total 345 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 96 time to evaluate : 0.397 Fit side-chains REVERT: A 375 ASN cc_start: 0.8800 (m-40) cc_final: 0.8525 (m110) REVERT: A 419 LEU cc_start: 0.8893 (mm) cc_final: 0.8648 (mm) REVERT: A 497 HIS cc_start: 0.8404 (m90) cc_final: 0.8175 (m90) REVERT: A 536 ASN cc_start: 0.8498 (t0) cc_final: 0.8156 (t0) REVERT: A 555 GLN cc_start: 0.8816 (mp10) cc_final: 0.8501 (pp30) REVERT: A 651 LYS cc_start: 0.8691 (mttt) cc_final: 0.8070 (ptpp) REVERT: A 668 ASP cc_start: 0.7878 (t0) cc_final: 0.7443 (t0) REVERT: A 727 ILE cc_start: 0.8390 (mt) cc_final: 0.8072 (tt) REVERT: A 750 LEU cc_start: 0.8776 (tp) cc_final: 0.7456 (pt) REVERT: A 760 PHE cc_start: 0.9157 (m-80) cc_final: 0.8957 (m-80) outliers start: 1 outliers final: 0 residues processed: 96 average time/residue: 0.1362 time to fit residues: 16.3631 Evaluate side-chains 67 residues out of total 345 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 67 time to evaluate : 0.390 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 43 random chunks: chunk 28 optimal weight: 0.6980 chunk 20 optimal weight: 0.7980 chunk 3 optimal weight: 3.9990 chunk 32 optimal weight: 0.0770 chunk 37 optimal weight: 0.0030 chunk 39 optimal weight: 0.7980 chunk 36 optimal weight: 0.9990 chunk 38 optimal weight: 2.9990 chunk 23 optimal weight: 2.9990 chunk 16 optimal weight: 0.9990 chunk 30 optimal weight: 4.9990 overall best weight: 0.4748 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 392 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7711 moved from start: 0.4121 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.023 3349 Z= 0.162 Angle : 0.601 8.301 4544 Z= 0.299 Chirality : 0.042 0.138 531 Planarity : 0.004 0.044 588 Dihedral : 7.645 51.637 526 Min Nonbonded Distance : 2.375 Molprobity Statistics. All-atom Clashscore : 9.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.84 % Favored : 94.16 % Rotamer: Outliers : 0.00 % Allowed : 0.58 % Favored : 99.42 % 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: -0.57 (0.41), residues: 428 helix: 0.97 (0.38), residues: 198 sheet: -1.45 (0.59), residues: 68 loop : -1.55 (0.48), residues: 162 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A 748 HIS 0.006 0.001 HIS A 565 PHE 0.016 0.002 PHE A 387 TYR 0.010 0.001 TYR A 631 ARG 0.003 0.000 ARG A 718 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 856 Ramachandran restraints generated. 428 Oldfield, 0 Emsley, 428 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 856 Ramachandran restraints generated. 428 Oldfield, 0 Emsley, 428 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 100 residues out of total 345 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 100 time to evaluate : 0.379 Fit side-chains revert: symmetry clash REVERT: A 375 ASN cc_start: 0.8833 (m-40) cc_final: 0.8557 (m110) REVERT: A 387 PHE cc_start: 0.8318 (t80) cc_final: 0.8094 (t80) REVERT: A 419 LEU cc_start: 0.8907 (mm) cc_final: 0.8679 (mm) REVERT: A 497 HIS cc_start: 0.8435 (m90) cc_final: 0.8155 (m90) REVERT: A 536 ASN cc_start: 0.8509 (t0) cc_final: 0.8160 (t0) REVERT: A 555 GLN cc_start: 0.8832 (mp10) cc_final: 0.8468 (pp30) REVERT: A 629 LYS cc_start: 0.8204 (pptt) cc_final: 0.7712 (pptt) REVERT: A 651 LYS cc_start: 0.8713 (mttt) cc_final: 0.8088 (ptpp) REVERT: A 668 ASP cc_start: 0.7903 (t0) cc_final: 0.7420 (t0) REVERT: A 669 GLU cc_start: 0.7618 (tp30) cc_final: 0.7386 (tp30) REVERT: A 727 ILE cc_start: 0.8513 (mt) cc_final: 0.8182 (tt) REVERT: A 750 LEU cc_start: 0.8791 (tp) cc_final: 0.7561 (pt) outliers start: 0 outliers final: 0 residues processed: 100 average time/residue: 0.1460 time to fit residues: 17.8736 Evaluate side-chains 69 residues out of total 345 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 69 time to evaluate : 0.373 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 43 random chunks: chunk 11 optimal weight: 0.6980 chunk 34 optimal weight: 3.9990 chunk 36 optimal weight: 2.9990 chunk 38 optimal weight: 4.9990 chunk 25 optimal weight: 1.9990 chunk 40 optimal weight: 3.9990 chunk 24 optimal weight: 0.9980 chunk 19 optimal weight: 2.9990 chunk 28 optimal weight: 2.9990 chunk 42 optimal weight: 7.9990 chunk 39 optimal weight: 2.9990 overall best weight: 1.9386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 392 ASN A 637 ASN A 652 HIS A 770 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7840 moved from start: 0.3700 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.046 3349 Z= 0.295 Angle : 0.678 9.333 4544 Z= 0.343 Chirality : 0.045 0.169 531 Planarity : 0.004 0.039 588 Dihedral : 8.095 52.770 526 Min Nonbonded Distance : 2.353 Molprobity Statistics. All-atom Clashscore : 9.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.54 % Favored : 93.46 % Rotamer: Outliers : 0.00 % Allowed : 0.87 % Favored : 99.13 % 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: -0.94 (0.40), residues: 428 helix: 0.93 (0.37), residues: 190 sheet: -1.60 (0.58), residues: 73 loop : -2.00 (0.47), residues: 165 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP A 768 HIS 0.005 0.001 HIS A 565 PHE 0.013 0.002 PHE A 387 TYR 0.006 0.001 TYR A 631 ARG 0.004 0.000 ARG A 718 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 856 Ramachandran restraints generated. 428 Oldfield, 0 Emsley, 428 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 856 Ramachandran restraints generated. 428 Oldfield, 0 Emsley, 428 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 85 residues out of total 345 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 85 time to evaluate : 0.366 Fit side-chains revert: symmetry clash REVERT: A 375 ASN cc_start: 0.8862 (m-40) cc_final: 0.8600 (m-40) REVERT: A 401 LYS cc_start: 0.8186 (mttt) cc_final: 0.7780 (ptpt) REVERT: A 497 HIS cc_start: 0.8450 (m90) cc_final: 0.8158 (m90) REVERT: A 536 ASN cc_start: 0.8731 (t0) cc_final: 0.8226 (t0) REVERT: A 555 GLN cc_start: 0.8869 (mp10) cc_final: 0.8575 (pp30) REVERT: A 651 LYS cc_start: 0.8805 (mttt) cc_final: 0.8208 (ptpp) REVERT: A 652 HIS cc_start: 0.7691 (t-90) cc_final: 0.7483 (t-90) REVERT: A 668 ASP cc_start: 0.7910 (t0) cc_final: 0.7441 (t0) REVERT: A 669 GLU cc_start: 0.7752 (tp30) cc_final: 0.7524 (tp30) REVERT: A 724 GLU cc_start: 0.9149 (pp20) cc_final: 0.8865 (pp20) outliers start: 0 outliers final: 0 residues processed: 85 average time/residue: 0.1425 time to fit residues: 15.0493 Evaluate side-chains 60 residues out of total 345 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 60 time to evaluate : 0.384 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 43 random chunks: chunk 34 optimal weight: 0.9990 chunk 3 optimal weight: 5.9990 chunk 26 optimal weight: 0.6980 chunk 20 optimal weight: 3.9990 chunk 27 optimal weight: 1.9990 chunk 36 optimal weight: 0.8980 chunk 10 optimal weight: 1.9990 chunk 31 optimal weight: 0.6980 chunk 5 optimal weight: 5.9990 chunk 9 optimal weight: 0.9990 chunk 14 optimal weight: 0.9990 overall best weight: 0.8584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 392 ASN A 607 HIS A 770 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7775 moved from start: 0.4046 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 3349 Z= 0.182 Angle : 0.626 9.511 4544 Z= 0.311 Chirality : 0.044 0.163 531 Planarity : 0.004 0.042 588 Dihedral : 7.913 53.415 526 Min Nonbonded Distance : 2.350 Molprobity Statistics. All-atom Clashscore : 9.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.78 % Favored : 93.22 % Rotamer: Outliers : 0.00 % Allowed : 0.58 % Favored : 99.42 % 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: -0.63 (0.41), residues: 428 helix: 0.95 (0.38), residues: 198 sheet: -1.42 (0.60), residues: 69 loop : -1.65 (0.49), residues: 161 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.002 TRP A 768 HIS 0.003 0.001 HIS A 673 PHE 0.020 0.002 PHE A 387 TYR 0.007 0.001 TYR A 631 ARG 0.002 0.000 ARG A 712 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 856 Ramachandran restraints generated. 428 Oldfield, 0 Emsley, 428 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 856 Ramachandran restraints generated. 428 Oldfield, 0 Emsley, 428 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 88 residues out of total 345 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 88 time to evaluate : 0.398 Fit side-chains revert: symmetry clash REVERT: A 375 ASN cc_start: 0.8818 (m-40) cc_final: 0.8547 (m-40) REVERT: A 497 HIS cc_start: 0.8422 (m90) cc_final: 0.8205 (t70) REVERT: A 528 ILE cc_start: 0.9022 (mm) cc_final: 0.8765 (mm) REVERT: A 536 ASN cc_start: 0.8667 (t0) cc_final: 0.8118 (t0) REVERT: A 555 GLN cc_start: 0.8839 (mp10) cc_final: 0.8515 (pp30) REVERT: A 651 LYS cc_start: 0.8789 (mttt) cc_final: 0.8190 (ptpp) REVERT: A 652 HIS cc_start: 0.7790 (t-90) cc_final: 0.7413 (t70) REVERT: A 668 ASP cc_start: 0.7913 (t0) cc_final: 0.7485 (t0) REVERT: A 712 ARG cc_start: 0.5893 (ttp-170) cc_final: 0.4830 (ttp80) outliers start: 0 outliers final: 0 residues processed: 88 average time/residue: 0.1411 time to fit residues: 15.4112 Evaluate side-chains 67 residues out of total 345 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 67 time to evaluate : 0.381 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 43 random chunks: chunk 35 optimal weight: 0.9980 chunk 4 optimal weight: 0.9980 chunk 6 optimal weight: 0.8980 chunk 29 optimal weight: 1.9990 chunk 1 optimal weight: 2.9990 chunk 24 optimal weight: 1.9990 chunk 39 optimal weight: 0.0060 chunk 22 optimal weight: 2.9990 chunk 27 optimal weight: 2.9990 chunk 26 optimal weight: 3.9990 chunk 16 optimal weight: 4.9990 overall best weight: 0.9798 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 392 ASN A 607 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3694 r_free = 0.3694 target = 0.127883 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3318 r_free = 0.3318 target = 0.102133 restraints weight = 6467.711| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3369 r_free = 0.3369 target = 0.105652 restraints weight = 4040.373| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 40)----------------| | r_work = 0.3413 r_free = 0.3413 target = 0.108346 restraints weight = 2922.938| |-----------------------------------------------------------------------------| r_work (final): 0.3410 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7836 moved from start: 0.4156 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 3349 Z= 0.204 Angle : 0.656 9.415 4544 Z= 0.329 Chirality : 0.043 0.140 531 Planarity : 0.004 0.042 588 Dihedral : 7.860 53.295 526 Min Nonbonded Distance : 2.359 Molprobity Statistics. All-atom Clashscore : 8.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.31 % Favored : 93.69 % Rotamer: Outliers : 0.00 % Allowed : 0.87 % Favored : 99.13 % 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: -0.61 (0.41), residues: 428 helix: 0.95 (0.37), residues: 198 sheet: -1.31 (0.60), residues: 69 loop : -1.67 (0.49), residues: 161 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 768 HIS 0.003 0.001 HIS A 673 PHE 0.009 0.001 PHE A 466 TYR 0.015 0.001 TYR A 573 ARG 0.002 0.000 ARG A 360 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1190.61 seconds wall clock time: 21 minutes 44.71 seconds (1304.71 seconds total)