Starting phenix.real_space_refine on Sun Mar 10 16:24:38 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7wxg_32878/03_2024/7wxg_32878_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7wxg_32878/03_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_32878/03_2024/7wxg_32878.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7wxg_32878/03_2024/7wxg_32878.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7wxg_32878/03_2024/7wxg_32878_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7wxg_32878/03_2024/7wxg_32878_updated.pdb" } 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 Residue "A ARG 356": "NH1" <-> "NH2" Residue "A ARG 384": "NH1" <-> "NH2" Residue "A ASP 390": "OD1" <-> "OD2" Residue "A ARG 439": "NH1" <-> "NH2" Residue "A ARG 469": "NH1" <-> "NH2" Residue "A ARG 525": "NH1" <-> "NH2" Residue "A GLU 527": "OE1" <-> "OE2" Residue "A ASP 530": "OD1" <-> "OD2" Residue "A ASP 548": "OD1" <-> "OD2" Residue "A ARG 551": "NH1" <-> "NH2" Residue "A TYR 573": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 576": "NH1" <-> "NH2" Residue "A ASP 609": "OD1" <-> "OD2" Residue "A ARG 625": "NH1" <-> "NH2" Residue "A ASP 668": "OD1" <-> "OD2" Residue "A ASP 683": "OD1" <-> "OD2" Residue "A ASP 690": "OD1" <-> "OD2" Residue "A ARG 694": "NH1" <-> "NH2" Residue "A PHE 760": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 766": "NH1" <-> "NH2" Time to flip residues: 0.01s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 3295 Number of models: 1 Model: "" Number of chains: 1 Chain: "A" Number of atoms: 3295 Number of conformers: 1 Conformer: "" Number of residues, atoms: 431, 3295 Unusual residues: {'NAP': 1} Inner-chain residues flagged as termini: ['pdbres="ASP A 776 "'] Classifications: {'peptide': 430, 'undetermined': 1} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 15, 'TRANS': 414, None: 1} Not linked: pdbres="ASP A 776 " pdbres="NAP A 801 " Time building chain proxies: 2.32, per 1000 atoms: 0.70 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 - 3.50 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: 1.21 Conformation dependent library (CDL) restraints added in 1.0 seconds 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... running ksdssp... Secondary structure from input PDB file: 17 helices and 4 sheets defined 43.0% alpha, 9.5% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.65 Creating SS restraints... Processing helix chain 'A' and resid 349 through 364 Processing helix chain 'A' and resid 367 through 402 removed outlier: 3.676A pdb=" N SER A 372 " --> pdb=" O ALA A 368 " (cutoff:3.500A) removed outlier: 3.707A pdb=" N GLU A 385 " --> pdb=" O LEU A 381 " (cutoff:3.500A) removed outlier: 5.512A pdb=" N LYS A 386 " --> pdb=" O VAL A 382 " (cutoff:3.500A) removed outlier: 6.040A pdb=" N PHE A 387 " --> pdb=" O SER A 383 " (cutoff:3.500A) removed outlier: 3.814A pdb=" N ILE A 388 " --> pdb=" O ARG A 384 " (cutoff:3.500A) Processing helix chain 'A' and resid 406 through 412 Processing helix chain 'A' and resid 416 through 431 Processing helix chain 'A' and resid 472 through 483 Processing helix chain 'A' and resid 496 through 512 removed outlier: 4.468A pdb=" N THR A 512 " --> pdb=" O GLU A 508 " (cutoff:3.500A) Processing helix chain 'A' and resid 525 through 533 Processing helix chain 'A' and resid 547 through 556 Processing helix chain 'A' and resid 580 through 591 Processing helix chain 'A' and resid 608 through 610 No H-bonds generated for 'chain 'A' and resid 608 through 610' Processing helix chain 'A' and resid 615 through 625 Processing helix chain 'A' and resid 634 through 639 Processing helix chain 'A' and resid 667 through 677 Processing helix chain 'A' and resid 690 through 699 Processing helix chain 'A' and resid 717 through 719 No H-bonds generated for 'chain 'A' and resid 717 through 719' Processing helix chain 'A' and resid 741 through 743 No H-bonds generated for 'chain 'A' and resid 741 through 743' Processing helix chain 'A' and resid 758 through 760 No H-bonds generated for 'chain 'A' and resid 758 through 760' Processing sheet with id= A, first strand: chain 'A' and resid 744 through 752 removed outlier: 3.650A pdb=" N ILE A 749 " --> pdb=" O LYS A 453 " (cutoff:3.500A) removed outlier: 3.527A pdb=" N GLU A 751 " --> pdb=" O GLU A 451 " (cutoff:3.500A) removed outlier: 3.906A pdb=" N ARG A 442 " --> pdb=" O GLN A 454 " (cutoff:3.500A) removed outlier: 6.455A pdb=" N THR A 456 " --> pdb=" O VAL A 440 " (cutoff:3.500A) removed outlier: 7.232A pdb=" N VAL A 440 " --> pdb=" O THR A 456 " (cutoff:3.500A) Processing sheet with id= B, first strand: chain 'A' and resid 486 through 488 removed outlier: 6.545A pdb=" N LEU A 540 " --> pdb=" O LEU A 463 " (cutoff:3.500A) removed outlier: 7.667A pdb=" N ILE A 465 " --> pdb=" O LEU A 540 " (cutoff:3.500A) removed outlier: 5.712A pdb=" N ILE A 542 " --> pdb=" O ILE A 465 " (cutoff:3.500A) Processing sheet with id= C, first strand: chain 'A' and resid 604 through 607 Processing sheet with id= D, first strand: chain 'A' and resid 683 through 685 132 hydrogen bonds defined for protein. 396 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: 0.78 Time building geometry restraints manager: 1.31 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: 99.46 - 108.69: 214 108.69 - 117.92: 2411 117.92 - 127.15: 1886 127.15 - 136.39: 31 136.39 - 145.62: 2 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: 282 2.73 - 3.27: 3698 3.27 - 3.81: 5285 3.81 - 4.36: 6013 4.36 - 4.90: 10085 Nonbonded interactions: 25363 Sorted by model distance: nonbonded pdb=" O SER A 410 " pdb=" OG SER A 413 " model vdw 2.184 2.440 nonbonded pdb=" O CYS A 570 " pdb=" ND1 HIS A 571 " model vdw 2.185 2.520 nonbonded pdb=" O ASP A 530 " pdb=" OG SER A 533 " model vdw 2.254 2.440 nonbonded pdb=" O ALA A 399 " pdb=" OG SER A 402 " model vdw 2.257 2.440 nonbonded pdb=" NH1 ARG A 525 " pdb=" O4B NAP A 801 " model vdw 2.272 2.520 ... (remaining 25358 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: 1.240 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.000 Extract box with map and model: 5.480 Check model and map are aligned: 0.050 Set scattering table: 0.030 Process input model: 13.800 Find NCS groups from input model: 0.080 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:3.570 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 24.270 ------------------------------------------------------------------------------- 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= 0.741 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 : 0.370 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: 0.1893 time to fit residues: 18.8811 Evaluate side-chains 63 residues out of total 345 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 63 time to evaluate : 0.366 ------------------------------------------------------------------------------- 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: 0.0370 chunk 32 optimal weight: 5.9990 chunk 18 optimal weight: 1.9990 chunk 11 optimal weight: 0.9980 chunk 21 optimal weight: 0.4980 chunk 17 optimal weight: 1.9990 chunk 33 optimal weight: 0.9980 chunk 13 optimal weight: 0.7980 chunk 20 optimal weight: 10.0000 chunk 25 optimal weight: 0.7980 chunk 39 optimal weight: 0.9980 overall best weight: 0.6258 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 375 ASN A 434 HIS A 536 ASN A 607 HIS A 672 ASN A 673 HIS A 681 HIS Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7829 moved from start: 0.1851 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= 0.157 Angle : 0.613 6.403 4544 Z= 0.304 Chirality : 0.044 0.151 531 Planarity : 0.004 0.044 588 Dihedral : 9.469 44.174 526 Min Nonbonded Distance : 2.214 Molprobity Statistics. All-atom Clashscore : 9.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.31 % Favored : 93.69 % 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: -3.11 (0.36), residues: 428 helix: -0.78 (0.35), residues: 187 sheet: -3.34 (0.49), residues: 60 loop : -2.95 (0.41), residues: 181 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.002 TRP A 748 HIS 0.004 0.001 HIS A 673 PHE 0.011 0.002 PHE A 616 TYR 0.007 0.001 TYR A 631 ARG 0.002 0.000 ARG A 544 *********************** 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 90 residues out of total 345 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 89 time to evaluate : 0.280 Fit side-chains revert: symmetry clash REVERT: A 428 GLN cc_start: 0.8747 (mt0) cc_final: 0.8370 (tm-30) REVERT: A 481 MET cc_start: 0.7846 (ttm) cc_final: 0.7609 (ptm) REVERT: A 497 HIS cc_start: 0.8450 (m90) cc_final: 0.8123 (t70) REVERT: A 504 GLU cc_start: 0.7998 (tm-30) cc_final: 0.7768 (tm-30) REVERT: A 536 ASN cc_start: 0.8718 (t0) cc_final: 0.8373 (t0) REVERT: A 556 GLN cc_start: 0.8047 (mt0) cc_final: 0.7811 (tt0) REVERT: A 602 GLU cc_start: 0.8816 (pt0) cc_final: 0.8014 (mt-10) REVERT: A 651 LYS cc_start: 0.8936 (mttt) cc_final: 0.8097 (tptt) REVERT: A 652 HIS cc_start: 0.7723 (t-90) cc_final: 0.7438 (t70) REVERT: A 668 ASP cc_start: 0.7811 (t0) cc_final: 0.7441 (t0) REVERT: A 712 ARG cc_start: 0.8169 (tpp80) cc_final: 0.7579 (ttp-170) REVERT: A 727 ILE cc_start: 0.8696 (mt) cc_final: 0.8259 (tt) outliers start: 1 outliers final: 0 residues processed: 89 average time/residue: 0.1554 time to fit residues: 16.8254 Evaluate side-chains 66 residues out of total 345 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 66 time to evaluate : 0.364 ------------------------------------------------------------------------------- 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: 0.8980 chunk 12 optimal weight: 0.9980 chunk 32 optimal weight: 0.9980 chunk 26 optimal weight: 2.9990 chunk 10 optimal weight: 0.7980 chunk 39 optimal weight: 0.3980 chunk 42 optimal weight: 9.9990 chunk 34 optimal weight: 5.9990 chunk 38 optimal weight: 1.9990 chunk 13 optimal weight: 2.9990 chunk 31 optimal weight: 3.9990 overall best weight: 0.8180 ------------------------------------------------------------------------------- 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 695 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7825 moved from start: 0.2301 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.022 3349 Z= 0.160 Angle : 0.581 6.882 4544 Z= 0.287 Chirality : 0.043 0.158 531 Planarity : 0.004 0.048 588 Dihedral : 8.366 44.795 526 Min Nonbonded Distance : 2.261 Molprobity Statistics. All-atom Clashscore : 9.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.14 % Favored : 94.86 % Rotamer: Outliers : 0.29 % Allowed : 2.90 % 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: -2.11 (0.38), residues: 428 helix: -0.01 (0.36), residues: 193 sheet: -2.88 (0.51), residues: 61 loop : -2.40 (0.44), residues: 174 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.002 TRP A 768 HIS 0.002 0.001 HIS A 673 PHE 0.010 0.001 PHE A 642 TYR 0.011 0.001 TYR A 573 ARG 0.003 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 92 residues out of total 345 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 91 time to evaluate : 0.377 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 497 HIS cc_start: 0.8459 (m90) cc_final: 0.8128 (t70) REVERT: A 536 ASN cc_start: 0.8705 (t0) cc_final: 0.8346 (t0) REVERT: A 602 GLU cc_start: 0.8962 (pt0) cc_final: 0.8060 (mt-10) REVERT: A 651 LYS cc_start: 0.8928 (mttt) cc_final: 0.7978 (tptt) REVERT: A 652 HIS cc_start: 0.7726 (t-90) cc_final: 0.7378 (t-90) REVERT: A 668 ASP cc_start: 0.7753 (t0) cc_final: 0.7360 (t0) REVERT: A 712 ARG cc_start: 0.8075 (tpp80) cc_final: 0.7762 (tpp80) REVERT: A 727 ILE cc_start: 0.8615 (mt) cc_final: 0.8262 (tt) outliers start: 1 outliers final: 0 residues processed: 92 average time/residue: 0.1416 time to fit residues: 16.0577 Evaluate side-chains 61 residues out of total 345 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 61 time to evaluate : 0.375 ------------------------------------------------------------------------------- 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: 0.3980 chunk 29 optimal weight: 3.9990 chunk 20 optimal weight: 0.8980 chunk 4 optimal weight: 1.9990 chunk 18 optimal weight: 0.8980 chunk 26 optimal weight: 0.7980 chunk 39 optimal weight: 0.9990 chunk 41 optimal weight: 0.0030 chunk 37 optimal weight: 2.9990 chunk 11 optimal weight: 0.7980 chunk 34 optimal weight: 0.7980 overall best weight: 0.5590 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 392 ASN A 556 GLN A 770 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7791 moved from start: 0.2817 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.017 3349 Z= 0.142 Angle : 0.588 8.249 4544 Z= 0.281 Chirality : 0.043 0.147 531 Planarity : 0.004 0.046 588 Dihedral : 7.843 46.301 526 Min Nonbonded Distance : 2.309 Molprobity Statistics. All-atom Clashscore : 9.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.61 % Favored : 94.39 % Rotamer: Outliers : 0.29 % Allowed : 5.22 % Favored : 94.49 % 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: -1.40 (0.40), residues: 428 helix: 0.58 (0.38), residues: 193 sheet: -2.46 (0.54), residues: 61 loop : -2.05 (0.46), residues: 174 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 768 HIS 0.002 0.000 HIS A 607 PHE 0.008 0.001 PHE A 616 TYR 0.004 0.001 TYR A 631 ARG 0.002 0.000 ARG A 712 *********************** 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 94 residues out of total 345 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 93 time to evaluate : 0.346 Fit side-chains revert: symmetry clash REVERT: A 392 ASN cc_start: 0.7495 (OUTLIER) cc_final: 0.7221 (t0) REVERT: A 428 GLN cc_start: 0.7896 (tm-30) cc_final: 0.7629 (tm-30) REVERT: A 497 HIS cc_start: 0.8484 (m90) cc_final: 0.8173 (t70) REVERT: A 503 MET cc_start: 0.9197 (mmp) cc_final: 0.8975 (mmm) REVERT: A 536 ASN cc_start: 0.8626 (t0) cc_final: 0.8312 (t0) REVERT: A 555 GLN cc_start: 0.8894 (mp10) cc_final: 0.8626 (pp30) REVERT: A 651 LYS cc_start: 0.8810 (mttt) cc_final: 0.8255 (ptpp) REVERT: A 668 ASP cc_start: 0.7732 (t0) cc_final: 0.7345 (t0) REVERT: A 712 ARG cc_start: 0.7934 (tpp80) cc_final: 0.7692 (tpp80) REVERT: A 727 ILE cc_start: 0.8589 (mt) cc_final: 0.8231 (tt) outliers start: 1 outliers final: 0 residues processed: 94 average time/residue: 0.1387 time to fit residues: 16.0706 Evaluate side-chains 62 residues out of total 345 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 61 time to evaluate : 0.672 ------------------------------------------------------------------------------- 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: 0.0970 chunk 0 optimal weight: 9.9990 chunk 30 optimal weight: 5.9990 chunk 17 optimal weight: 0.0980 chunk 35 optimal weight: 0.0050 chunk 28 optimal weight: 3.9990 chunk 21 optimal weight: 0.2980 chunk 37 optimal weight: 0.0980 chunk 10 optimal weight: 3.9990 chunk 13 optimal weight: 0.9980 chunk 8 optimal weight: 4.9990 overall best weight: 0.1192 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 652 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7723 moved from start: 0.3388 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.020 3349 Z= 0.128 Angle : 0.585 6.940 4544 Z= 0.281 Chirality : 0.042 0.145 531 Planarity : 0.004 0.044 588 Dihedral : 7.446 44.501 526 Min Nonbonded Distance : 2.328 Molprobity Statistics. All-atom Clashscore : 9.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.84 % Favored : 94.16 % Rotamer: Outliers : 0.00 % Allowed : 1.16 % Favored : 98.84 % 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: -0.93 (0.41), residues: 428 helix: 0.96 (0.39), residues: 192 sheet: -2.07 (0.55), residues: 62 loop : -1.85 (0.46), residues: 174 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A 748 HIS 0.003 0.000 HIS A 607 PHE 0.009 0.001 PHE A 616 TYR 0.014 0.001 TYR A 573 ARG 0.002 0.000 ARG A 718 *********************** 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 95 residues out of total 345 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 95 time to evaluate : 0.379 Fit side-chains revert: symmetry clash REVERT: A 497 HIS cc_start: 0.8510 (m90) cc_final: 0.8188 (t70) REVERT: A 503 MET cc_start: 0.9004 (mmp) cc_final: 0.8723 (mmm) REVERT: A 536 ASN cc_start: 0.8524 (t0) cc_final: 0.8191 (t0) REVERT: A 555 GLN cc_start: 0.8846 (mp10) cc_final: 0.8594 (pp30) REVERT: A 651 LYS cc_start: 0.8866 (mttt) cc_final: 0.7923 (mmtt) REVERT: A 658 GLU cc_start: 0.7973 (mp0) cc_final: 0.7749 (mp0) REVERT: A 668 ASP cc_start: 0.7711 (t0) cc_final: 0.7310 (t0) REVERT: A 727 ILE cc_start: 0.8528 (mt) cc_final: 0.8228 (tt) outliers start: 0 outliers final: 0 residues processed: 95 average time/residue: 0.1376 time to fit residues: 16.3071 Evaluate side-chains 65 residues out of total 345 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 65 time to evaluate : 0.378 ------------------------------------------------------------------------------- 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: 3.9990 chunk 10 optimal weight: 0.7980 chunk 41 optimal weight: 9.9990 chunk 34 optimal weight: 9.9990 chunk 19 optimal weight: 0.4980 chunk 3 optimal weight: 3.9990 chunk 13 optimal weight: 0.0670 chunk 21 optimal weight: 3.9990 chunk 40 optimal weight: 10.0000 chunk 4 optimal weight: 0.9990 chunk 23 optimal weight: 1.9990 overall best weight: 0.8722 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 375 ASN A 637 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7780 moved from start: 0.3316 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.022 3349 Z= 0.162 Angle : 0.589 6.615 4544 Z= 0.286 Chirality : 0.042 0.172 531 Planarity : 0.004 0.041 588 Dihedral : 7.350 45.138 526 Min Nonbonded Distance : 2.289 Molprobity Statistics. All-atom Clashscore : 10.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.84 % Favored : 94.16 % Rotamer: Outliers : 0.00 % Allowed : 2.32 % Favored : 97.68 % 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: -0.69 (0.42), residues: 428 helix: 1.18 (0.39), residues: 192 sheet: -1.91 (0.57), residues: 63 loop : -1.76 (0.47), residues: 173 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 768 HIS 0.002 0.001 HIS A 607 PHE 0.006 0.001 PHE A 616 TYR 0.002 0.001 TYR A 677 ARG 0.001 0.000 ARG A 718 *********************** 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 90 residues out of total 345 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 90 time to evaluate : 0.412 Fit side-chains revert: symmetry clash REVERT: A 497 HIS cc_start: 0.8531 (m90) cc_final: 0.8207 (t70) REVERT: A 536 ASN cc_start: 0.8597 (t0) cc_final: 0.8281 (t0) REVERT: A 555 GLN cc_start: 0.8901 (mp10) cc_final: 0.8576 (pp30) REVERT: A 651 LYS cc_start: 0.8864 (mttt) cc_final: 0.7986 (mmtt) REVERT: A 668 ASP cc_start: 0.7744 (t0) cc_final: 0.7333 (t0) REVERT: A 727 ILE cc_start: 0.8617 (mt) cc_final: 0.8279 (tt) REVERT: A 750 LEU cc_start: 0.8684 (tp) cc_final: 0.7270 (pt) outliers start: 0 outliers final: 0 residues processed: 90 average time/residue: 0.1460 time to fit residues: 16.2698 Evaluate side-chains 64 residues out of total 345 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 64 time to evaluate : 0.371 ------------------------------------------------------------------------------- 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: 2.9990 chunk 23 optimal weight: 0.8980 chunk 35 optimal weight: 0.3980 chunk 41 optimal weight: 9.9990 chunk 25 optimal weight: 1.9990 chunk 19 optimal weight: 2.9990 chunk 16 optimal weight: 3.9990 chunk 24 optimal weight: 0.8980 chunk 12 optimal weight: 5.9990 chunk 8 optimal weight: 1.9990 chunk 26 optimal weight: 0.9980 overall best weight: 1.0382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7797 moved from start: 0.3328 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 3349 Z= 0.180 Angle : 0.596 7.755 4544 Z= 0.291 Chirality : 0.042 0.149 531 Planarity : 0.004 0.042 588 Dihedral : 7.466 49.477 526 Min Nonbonded Distance : 2.288 Molprobity Statistics. All-atom Clashscore : 10.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.54 % Favored : 93.46 % Rotamer: Outliers : 0.00 % Allowed : 2.32 % Favored : 97.68 % 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: -0.69 (0.42), residues: 428 helix: 1.08 (0.39), residues: 193 sheet: -1.86 (0.56), residues: 63 loop : -1.67 (0.48), residues: 172 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.002 TRP A 768 HIS 0.002 0.001 HIS A 673 PHE 0.006 0.001 PHE A 616 TYR 0.004 0.001 TYR A 631 ARG 0.001 0.000 ARG A 551 *********************** 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 94 residues out of total 345 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 94 time to evaluate : 0.380 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 497 HIS cc_start: 0.8529 (m90) cc_final: 0.8221 (t70) REVERT: A 503 MET cc_start: 0.9200 (mmp) cc_final: 0.8977 (mmm) REVERT: A 536 ASN cc_start: 0.8657 (t0) cc_final: 0.8310 (t0) REVERT: A 555 GLN cc_start: 0.8988 (mp10) cc_final: 0.8719 (pp30) REVERT: A 602 GLU cc_start: 0.8882 (pt0) cc_final: 0.7941 (mt-10) REVERT: A 651 LYS cc_start: 0.8833 (mttt) cc_final: 0.7982 (mmtt) REVERT: A 652 HIS cc_start: 0.7677 (t-90) cc_final: 0.7272 (t-90) REVERT: A 668 ASP cc_start: 0.7722 (t0) cc_final: 0.7341 (t0) REVERT: A 727 ILE cc_start: 0.8643 (mt) cc_final: 0.8316 (tt) REVERT: A 750 LEU cc_start: 0.8758 (tp) cc_final: 0.7397 (pt) outliers start: 0 outliers final: 0 residues processed: 94 average time/residue: 0.1399 time to fit residues: 16.2421 Evaluate side-chains 64 residues out of total 345 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 64 time to evaluate : 0.359 ------------------------------------------------------------------------------- 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: 0.1980 chunk 20 optimal weight: 0.9990 chunk 3 optimal weight: 6.9990 chunk 32 optimal weight: 1.9990 chunk 37 optimal weight: 4.9990 chunk 39 optimal weight: 2.9990 chunk 36 optimal weight: 0.0870 chunk 38 optimal weight: 1.9990 chunk 23 optimal weight: 0.5980 chunk 16 optimal weight: 4.9990 chunk 30 optimal weight: 4.9990 overall best weight: 0.7762 ------------------------------------------------------------------------------- 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: 0.7775 moved from start: 0.3521 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.025 3349 Z= 0.160 Angle : 0.592 7.708 4544 Z= 0.290 Chirality : 0.042 0.138 531 Planarity : 0.004 0.041 588 Dihedral : 7.420 51.491 526 Min Nonbonded Distance : 2.304 Molprobity Statistics. All-atom Clashscore : 9.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.31 % Favored : 93.69 % Rotamer: Outliers : 0.00 % Allowed : 1.16 % Favored : 98.84 % 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: -0.56 (0.42), residues: 428 helix: 1.18 (0.39), residues: 193 sheet: -1.61 (0.57), residues: 62 loop : -1.69 (0.47), residues: 173 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 768 HIS 0.002 0.001 HIS A 607 PHE 0.009 0.001 PHE A 719 TYR 0.014 0.001 TYR A 573 ARG 0.001 0.000 ARG A 525 *********************** 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 89 residues out of total 345 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 89 time to evaluate : 0.399 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 497 HIS cc_start: 0.8512 (m90) cc_final: 0.8190 (t70) REVERT: A 503 MET cc_start: 0.9204 (mmp) cc_final: 0.8962 (mmm) REVERT: A 536 ASN cc_start: 0.8661 (t0) cc_final: 0.8313 (t0) REVERT: A 555 GLN cc_start: 0.8943 (mp10) cc_final: 0.8626 (pp30) REVERT: A 651 LYS cc_start: 0.8850 (mttt) cc_final: 0.7974 (mmtt) REVERT: A 652 HIS cc_start: 0.7805 (t-90) cc_final: 0.7439 (t70) REVERT: A 668 ASP cc_start: 0.7744 (t0) cc_final: 0.7332 (t0) REVERT: A 727 ILE cc_start: 0.8613 (mt) cc_final: 0.8194 (tt) REVERT: A 750 LEU cc_start: 0.8786 (tp) cc_final: 0.7520 (pt) outliers start: 0 outliers final: 0 residues processed: 89 average time/residue: 0.1452 time to fit residues: 16.1316 Evaluate side-chains 68 residues out of total 345 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 68 time to evaluate : 0.382 ------------------------------------------------------------------------------- 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: 0.8980 chunk 34 optimal weight: 2.9990 chunk 36 optimal weight: 0.9990 chunk 38 optimal weight: 6.9990 chunk 25 optimal weight: 5.9990 chunk 40 optimal weight: 2.9990 chunk 24 optimal weight: 0.9980 chunk 19 optimal weight: 0.0670 chunk 28 optimal weight: 0.7980 chunk 42 optimal weight: 0.0770 chunk 39 optimal weight: 0.2980 overall best weight: 0.4276 ------------------------------------------------------------------------------- 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: 0.7739 moved from start: 0.3748 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.026 3349 Z= 0.140 Angle : 0.578 8.213 4544 Z= 0.280 Chirality : 0.042 0.134 531 Planarity : 0.004 0.041 588 Dihedral : 7.235 53.122 526 Min Nonbonded Distance : 2.331 Molprobity Statistics. All-atom Clashscore : 9.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.61 % Favored : 94.39 % Rotamer: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % 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: -0.32 (0.42), residues: 428 helix: 1.30 (0.40), residues: 194 sheet: -1.36 (0.59), residues: 62 loop : -1.54 (0.48), residues: 172 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A 748 HIS 0.001 0.000 HIS A 565 PHE 0.009 0.001 PHE A 616 TYR 0.007 0.001 TYR A 631 ARG 0.003 0.000 ARG A 712 *********************** 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 90 residues out of total 345 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 90 time to evaluate : 0.367 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 497 HIS cc_start: 0.8506 (m90) cc_final: 0.8185 (t70) REVERT: A 503 MET cc_start: 0.9194 (mmp) cc_final: 0.8969 (mmm) REVERT: A 536 ASN cc_start: 0.8651 (t0) cc_final: 0.8278 (t0) REVERT: A 555 GLN cc_start: 0.8902 (mp10) cc_final: 0.8606 (pp30) REVERT: A 565 HIS cc_start: 0.6756 (p-80) cc_final: 0.5961 (p90) REVERT: A 651 LYS cc_start: 0.8864 (mttt) cc_final: 0.7904 (mmtt) REVERT: A 668 ASP cc_start: 0.7716 (t0) cc_final: 0.7297 (t0) REVERT: A 727 ILE cc_start: 0.8652 (mt) cc_final: 0.8388 (tt) REVERT: A 750 LEU cc_start: 0.8765 (tp) cc_final: 0.7567 (pt) outliers start: 0 outliers final: 0 residues processed: 90 average time/residue: 0.1255 time to fit residues: 14.2878 Evaluate side-chains 64 residues out of total 345 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 64 time to evaluate : 0.363 ------------------------------------------------------------------------------- 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: 9.9990 chunk 26 optimal weight: 2.9990 chunk 20 optimal weight: 7.9990 chunk 27 optimal weight: 5.9990 chunk 36 optimal weight: 0.0470 chunk 10 optimal weight: 1.9990 chunk 31 optimal weight: 0.9980 chunk 5 optimal weight: 0.8980 chunk 9 optimal weight: 2.9990 chunk 14 optimal weight: 2.9990 overall best weight: 0.9882 ------------------------------------------------------------------------------- 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: 0.7781 moved from start: 0.3703 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= 0.181 Angle : 0.613 8.821 4544 Z= 0.298 Chirality : 0.043 0.146 531 Planarity : 0.004 0.041 588 Dihedral : 7.275 55.198 526 Min Nonbonded Distance : 2.277 Molprobity Statistics. All-atom Clashscore : 10.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.84 % Favored : 94.16 % Rotamer: Outliers : 0.00 % Allowed : 0.29 % Favored : 99.71 % 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: -0.41 (0.42), residues: 428 helix: 1.19 (0.39), residues: 193 sheet: -1.28 (0.60), residues: 62 loop : -1.57 (0.48), residues: 173 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.002 TRP A 768 HIS 0.002 0.001 HIS A 565 PHE 0.006 0.001 PHE A 719 TYR 0.013 0.001 TYR A 573 ARG 0.001 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 : 0.393 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 497 HIS cc_start: 0.8487 (m90) cc_final: 0.8200 (t70) REVERT: A 536 ASN cc_start: 0.8689 (t0) cc_final: 0.8154 (t0) REVERT: A 555 GLN cc_start: 0.8909 (mp10) cc_final: 0.8615 (pp30) REVERT: A 651 LYS cc_start: 0.8875 (mttt) cc_final: 0.7959 (mmtt) REVERT: A 652 HIS cc_start: 0.7788 (t-90) cc_final: 0.7411 (t-90) REVERT: A 668 ASP cc_start: 0.7749 (t0) cc_final: 0.7314 (t0) REVERT: A 727 ILE cc_start: 0.8671 (mt) cc_final: 0.8283 (tt) REVERT: A 750 LEU cc_start: 0.8784 (tp) cc_final: 0.7586 (pt) outliers start: 0 outliers final: 0 residues processed: 88 average time/residue: 0.1272 time to fit residues: 14.2294 Evaluate side-chains 64 residues out of total 345 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 64 time to evaluate : 0.406 ------------------------------------------------------------------------------- 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: 0.8980 chunk 4 optimal weight: 0.6980 chunk 6 optimal weight: 4.9990 chunk 29 optimal weight: 2.9990 chunk 1 optimal weight: 4.9990 chunk 24 optimal weight: 3.9990 chunk 39 optimal weight: 0.9980 chunk 22 optimal weight: 0.9990 chunk 27 optimal weight: 1.9990 chunk 26 optimal weight: 0.9980 chunk 16 optimal weight: 1.9990 overall best weight: 0.9182 ------------------------------------------------------------------------------- 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 = 0.3676 r_free = 0.3676 target = 0.127629 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3317 r_free = 0.3317 target = 0.103079 restraints weight = 6549.479| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3374 r_free = 0.3374 target = 0.106877 restraints weight = 3907.710| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3414 r_free = 0.3414 target = 0.109570 restraints weight = 2719.711| |-----------------------------------------------------------------------------| r_work (final): 0.3411 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7801 moved from start: 0.3788 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 3349 Z= 0.182 Angle : 0.622 8.906 4544 Z= 0.301 Chirality : 0.043 0.138 531 Planarity : 0.004 0.041 588 Dihedral : 7.281 56.985 526 Min Nonbonded Distance : 2.247 Molprobity Statistics. All-atom Clashscore : 10.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.54 % Favored : 93.46 % Rotamer: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % 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 (0.42), residues: 428 helix: 1.18 (0.40), residues: 192 sheet: -1.35 (0.57), residues: 65 loop : -1.54 (0.49), residues: 171 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 768 HIS 0.002 0.001 HIS A 673 PHE 0.006 0.001 PHE A 719 TYR 0.010 0.001 TYR A 631 ARG 0.002 0.000 ARG A 712 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1187.02 seconds wall clock time: 21 minutes 52.96 seconds (1312.96 seconds total)