Starting phenix.real_space_refine on Thu Jul 18 20:54:14 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7wxg_32878/07_2024/7wxg_32878.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7wxg_32878/07_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_32878/07_2024/7wxg_32878.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7wxg_32878/07_2024/7wxg_32878.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7wxg_32878/07_2024/7wxg_32878.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7wxg_32878/07_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 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-5388/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: 2.87, per 1000 atoms: 0.87 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: 1.31 Conformation dependent library (CDL) restraints added in 580.3 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: 0.35 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: 0.81 Time building geometry restraints manager: 1.45 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: 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 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 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: 1.140 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: 0.150 Check model and map are aligned: 0.020 Set scattering table: 0.040 Process input model: 13.920 Find NCS groups from input model: 0.030 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:2.720 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 18.030 ------------------------------------------------------------------------------- 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 : 0.391 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: 0.1923 time to fit residues: 19.1878 Evaluate side-chains 63 residues out of total 345 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 63 time to evaluate : 0.378 ------------------------------------------------------------------------------- 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: 0.4980 chunk 32 optimal weight: 6.9990 chunk 18 optimal weight: 0.9980 chunk 11 optimal weight: 5.9990 chunk 21 optimal weight: 7.9990 chunk 17 optimal weight: 3.9990 chunk 33 optimal weight: 0.9980 chunk 13 optimal weight: 0.9990 chunk 20 optimal weight: 1.9990 chunk 25 optimal weight: 1.9990 chunk 39 optimal weight: 2.9990 overall best weight: 1.0984 ------------------------------------------------------------------------------- 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 681 HIS Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7860 moved from start: 0.1803 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.022 3349 Z= 0.194 Angle : 0.639 6.450 4544 Z= 0.320 Chirality : 0.045 0.164 531 Planarity : 0.004 0.042 588 Dihedral : 9.680 44.631 526 Min Nonbonded Distance : 2.187 Molprobity Statistics. All-atom Clashscore : 12.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.31 % Favored : 93.69 % Rotamer: Outliers : 0.29 % Allowed : 4.64 % Favored : 95.07 % 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: -3.20 (0.36), residues: 428 helix: -0.83 (0.35), residues: 191 sheet: -3.43 (0.49), residues: 62 loop : -3.04 (0.42), residues: 175 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.002 TRP A 748 HIS 0.004 0.001 HIS A 673 PHE 0.013 0.002 PHE A 642 TYR 0.006 0.001 TYR A 654 ARG 0.003 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 84 residues out of total 345 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 83 time to evaluate : 0.398 Fit side-chains revert: symmetry clash REVERT: A 351 MET cc_start: 0.8990 (mtp) cc_final: 0.8752 (mtt) REVERT: A 428 GLN cc_start: 0.8730 (mt0) cc_final: 0.8338 (tm-30) REVERT: A 481 MET cc_start: 0.7833 (ttm) cc_final: 0.7540 (ptm) REVERT: A 497 HIS cc_start: 0.8452 (m90) cc_final: 0.8111 (t70) REVERT: A 504 GLU cc_start: 0.8010 (tm-30) cc_final: 0.7788 (tm-30) REVERT: A 536 ASN cc_start: 0.8715 (t0) cc_final: 0.8289 (t0) REVERT: A 556 GLN cc_start: 0.7814 (mt0) cc_final: 0.7569 (tt0) REVERT: A 601 MET cc_start: 0.7796 (tmm) cc_final: 0.7573 (tmm) REVERT: A 602 GLU cc_start: 0.8878 (pt0) cc_final: 0.8102 (mt-10) REVERT: A 651 LYS cc_start: 0.8952 (mttt) cc_final: 0.8190 (tptt) REVERT: A 652 HIS cc_start: 0.7832 (t-90) cc_final: 0.7370 (t-90) REVERT: A 668 ASP cc_start: 0.7878 (t0) cc_final: 0.7527 (t0) REVERT: A 712 ARG cc_start: 0.8238 (tpp80) cc_final: 0.7615 (ttp-170) outliers start: 1 outliers final: 0 residues processed: 83 average time/residue: 0.1576 time to fit residues: 15.9273 Evaluate side-chains 64 residues out of total 345 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 64 time to evaluate : 0.377 ------------------------------------------------------------------------------- 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: 0.0170 chunk 12 optimal weight: 0.9990 chunk 32 optimal weight: 0.9990 chunk 26 optimal weight: 4.9990 chunk 10 optimal weight: 1.9990 chunk 39 optimal weight: 0.8980 chunk 42 optimal weight: 0.9980 chunk 34 optimal weight: 2.9990 chunk 38 optimal weight: 2.9990 chunk 13 optimal weight: 3.9990 chunk 31 optimal weight: 4.9990 overall best weight: 0.7822 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 689 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7828 moved from start: 0.2313 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= 0.158 Angle : 0.588 6.845 4544 Z= 0.294 Chirality : 0.044 0.156 531 Planarity : 0.004 0.047 588 Dihedral : 8.667 45.303 526 Min Nonbonded Distance : 2.263 Molprobity Statistics. All-atom Clashscore : 10.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.61 % Favored : 94.39 % Rotamer: Outliers : 0.00 % Allowed : 4.64 % Favored : 95.36 % 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: -2.01 (0.39), residues: 428 helix: 0.08 (0.37), residues: 196 sheet: -2.92 (0.51), residues: 63 loop : -2.34 (0.46), residues: 169 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 0.011 0.001 PHE A 642 TYR 0.012 0.001 TYR A 573 ARG 0.002 0.000 ARG A 694 *********************** 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 93 residues out of total 345 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 93 time to evaluate : 0.342 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 497 HIS cc_start: 0.8433 (m90) cc_final: 0.8083 (t70) REVERT: A 536 ASN cc_start: 0.8684 (t0) cc_final: 0.8187 (t0) REVERT: A 556 GLN cc_start: 0.7986 (mt0) cc_final: 0.7718 (tt0) REVERT: A 601 MET cc_start: 0.7663 (tmm) cc_final: 0.7346 (tmm) REVERT: A 602 GLU cc_start: 0.8964 (pt0) cc_final: 0.8088 (mt-10) REVERT: A 651 LYS cc_start: 0.8841 (mttt) cc_final: 0.7970 (tptt) REVERT: A 652 HIS cc_start: 0.7516 (t-90) cc_final: 0.7205 (t-90) REVERT: A 668 ASP cc_start: 0.7815 (t0) cc_final: 0.7402 (t0) REVERT: A 712 ARG cc_start: 0.8077 (tpp80) cc_final: 0.7808 (tpp80) outliers start: 0 outliers final: 0 residues processed: 93 average time/residue: 0.1394 time to fit residues: 16.0681 Evaluate side-chains 61 residues out of total 345 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 61 time to evaluate : 0.383 ------------------------------------------------------------------------------- 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: 7.9990 chunk 29 optimal weight: 0.6980 chunk 20 optimal weight: 4.9990 chunk 4 optimal weight: 1.9990 chunk 18 optimal weight: 4.9990 chunk 26 optimal weight: 1.9990 chunk 39 optimal weight: 0.9990 chunk 41 optimal weight: 0.9990 chunk 37 optimal weight: 0.9980 chunk 11 optimal weight: 0.8980 chunk 34 optimal weight: 2.9990 overall best weight: 0.9184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 695 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7817 moved from start: 0.2787 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.021 3349 Z= 0.170 Angle : 0.600 9.230 4544 Z= 0.296 Chirality : 0.044 0.159 531 Planarity : 0.004 0.047 588 Dihedral : 7.987 46.428 526 Min Nonbonded Distance : 2.289 Molprobity Statistics. All-atom Clashscore : 11.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.54 % Favored : 93.46 % Rotamer: Outliers : 0.00 % Allowed : 4.64 % Favored : 95.36 % 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: -1.50 (0.40), residues: 428 helix: 0.63 (0.38), residues: 190 sheet: -2.64 (0.53), residues: 63 loop : -2.18 (0.47), residues: 175 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 0.015 0.002 PHE A 696 TYR 0.006 0.001 TYR A 654 ARG 0.003 0.000 ARG A 718 *********************** 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 89 residues out of total 345 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 89 time to evaluate : 0.373 Fit side-chains revert: symmetry clash REVERT: A 428 GLN cc_start: 0.8035 (tm-30) cc_final: 0.7396 (tm-30) REVERT: A 536 ASN cc_start: 0.8683 (t0) cc_final: 0.8174 (t0) REVERT: A 651 LYS cc_start: 0.8834 (mttt) cc_final: 0.7970 (tptt) REVERT: A 652 HIS cc_start: 0.7699 (t-90) cc_final: 0.7366 (t-90) REVERT: A 668 ASP cc_start: 0.7761 (t0) cc_final: 0.7338 (t0) REVERT: A 712 ARG cc_start: 0.8043 (tpp80) cc_final: 0.7780 (tpp80) REVERT: A 760 PHE cc_start: 0.9218 (m-80) cc_final: 0.9004 (m-80) outliers start: 0 outliers final: 0 residues processed: 89 average time/residue: 0.1421 time to fit residues: 15.5960 Evaluate side-chains 59 residues out of total 345 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 59 time to evaluate : 0.367 ------------------------------------------------------------------------------- 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: 3.9990 chunk 0 optimal weight: 9.9990 chunk 30 optimal weight: 0.9990 chunk 17 optimal weight: 1.9990 chunk 35 optimal weight: 2.9990 chunk 28 optimal weight: 0.6980 chunk 21 optimal weight: 5.9990 chunk 37 optimal weight: 2.9990 chunk 10 optimal weight: 0.9990 chunk 13 optimal weight: 0.7980 chunk 8 optimal weight: 2.9990 overall best weight: 1.0986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 497 HIS A 556 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7819 moved from start: 0.3086 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.023 3349 Z= 0.190 Angle : 0.625 7.665 4544 Z= 0.309 Chirality : 0.044 0.185 531 Planarity : 0.004 0.046 588 Dihedral : 8.115 48.888 526 Min Nonbonded Distance : 2.286 Molprobity Statistics. All-atom Clashscore : 10.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.31 % Favored : 93.69 % Rotamer: Outliers : 0.00 % Allowed : 2.61 % Favored : 97.39 % 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: -1.26 (0.41), residues: 428 helix: 0.63 (0.37), residues: 196 sheet: -2.48 (0.53), residues: 63 loop : -1.89 (0.48), residues: 169 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.002 TRP A 768 HIS 0.003 0.001 HIS A 673 PHE 0.009 0.002 PHE A 696 TYR 0.011 0.001 TYR A 573 ARG 0.001 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 88 residues out of total 345 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 88 time to evaluate : 0.349 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 428 GLN cc_start: 0.8328 (tm-30) cc_final: 0.7922 (tm-30) REVERT: A 536 ASN cc_start: 0.8648 (t0) cc_final: 0.8320 (t0) REVERT: A 555 GLN cc_start: 0.8853 (mp10) cc_final: 0.8626 (pp30) REVERT: A 651 LYS cc_start: 0.8823 (mttt) cc_final: 0.8241 (ptpp) REVERT: A 668 ASP cc_start: 0.7696 (t0) cc_final: 0.7311 (t0) REVERT: A 760 PHE cc_start: 0.9231 (m-80) cc_final: 0.9016 (m-80) outliers start: 0 outliers final: 0 residues processed: 88 average time/residue: 0.1473 time to fit residues: 16.1463 Evaluate side-chains 58 residues out of total 345 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 58 time to evaluate : 0.388 ------------------------------------------------------------------------------- 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: 0.6980 chunk 10 optimal weight: 2.9990 chunk 41 optimal weight: 1.9990 chunk 34 optimal weight: 0.9980 chunk 19 optimal weight: 0.0170 chunk 3 optimal weight: 0.9980 chunk 13 optimal weight: 0.9990 chunk 21 optimal weight: 0.9990 chunk 40 optimal weight: 0.6980 chunk 4 optimal weight: 0.7980 chunk 23 optimal weight: 3.9990 overall best weight: 0.6418 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 497 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7770 moved from start: 0.3411 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.028 3349 Z= 0.170 Angle : 0.604 7.195 4544 Z= 0.299 Chirality : 0.043 0.153 531 Planarity : 0.004 0.046 588 Dihedral : 7.847 49.879 526 Min Nonbonded Distance : 2.278 Molprobity Statistics. All-atom Clashscore : 11.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.01 % Favored : 92.99 % Rotamer: Outliers : 0.00 % Allowed : 2.03 % 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: -0.96 (0.41), residues: 428 helix: 0.85 (0.38), residues: 196 sheet: -2.16 (0.56), residues: 63 loop : -1.77 (0.49), residues: 169 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 616 TYR 0.004 0.001 TYR A 654 ARG 0.003 0.000 ARG A 551 *********************** 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 : 0.374 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 497 HIS cc_start: 0.8365 (m-70) cc_final: 0.7978 (t70) REVERT: A 536 ASN cc_start: 0.8646 (t0) cc_final: 0.8295 (t0) REVERT: A 553 ILE cc_start: 0.8598 (mm) cc_final: 0.8383 (mm) REVERT: A 651 LYS cc_start: 0.8785 (mttt) cc_final: 0.8173 (ptpp) REVERT: A 668 ASP cc_start: 0.7728 (t0) cc_final: 0.7285 (t0) REVERT: A 760 PHE cc_start: 0.9230 (m-80) cc_final: 0.9010 (m-80) outliers start: 0 outliers final: 0 residues processed: 90 average time/residue: 0.1381 time to fit residues: 15.3447 Evaluate side-chains 58 residues out of total 345 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 58 time to evaluate : 0.372 ------------------------------------------------------------------------------- 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: 0.6980 chunk 23 optimal weight: 0.8980 chunk 35 optimal weight: 0.4980 chunk 41 optimal weight: 8.9990 chunk 25 optimal weight: 2.9990 chunk 19 optimal weight: 4.9990 chunk 16 optimal weight: 2.9990 chunk 24 optimal weight: 1.9990 chunk 12 optimal weight: 0.3980 chunk 8 optimal weight: 4.9990 chunk 26 optimal weight: 3.9990 overall best weight: 0.8982 ------------------------------------------------------------------------------- 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: 0.7784 moved from start: 0.3635 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= 0.192 Angle : 0.635 7.777 4544 Z= 0.316 Chirality : 0.043 0.156 531 Planarity : 0.004 0.045 588 Dihedral : 7.769 48.025 526 Min Nonbonded Distance : 2.299 Molprobity Statistics. All-atom Clashscore : 11.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.07 % Favored : 93.93 % Rotamer: Outliers : 0.00 % Allowed : 1.45 % Favored : 98.55 % 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: -0.83 (0.42), residues: 428 helix: 0.97 (0.38), residues: 195 sheet: -1.95 (0.57), residues: 63 loop : -1.76 (0.49), residues: 170 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.002 TRP A 768 HIS 0.003 0.001 HIS A 673 PHE 0.010 0.001 PHE A 719 TYR 0.013 0.001 TYR A 573 ARG 0.003 0.000 ARG A 718 *********************** 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 84 residues out of total 345 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 84 time to evaluate : 0.361 Fit side-chains REVERT: A 497 HIS cc_start: 0.8378 (m-70) cc_final: 0.8006 (t70) REVERT: A 536 ASN cc_start: 0.8653 (t0) cc_final: 0.8156 (t0) REVERT: A 553 ILE cc_start: 0.8597 (mm) cc_final: 0.8335 (mm) REVERT: A 572 VAL cc_start: 0.9461 (t) cc_final: 0.9251 (m) REVERT: A 651 LYS cc_start: 0.8777 (mttt) cc_final: 0.8227 (ptpp) REVERT: A 668 ASP cc_start: 0.7669 (t0) cc_final: 0.7271 (t0) REVERT: A 760 PHE cc_start: 0.9221 (m-80) cc_final: 0.9000 (m-80) outliers start: 0 outliers final: 0 residues processed: 84 average time/residue: 0.1275 time to fit residues: 13.5228 Evaluate side-chains 59 residues out of total 345 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 59 time to evaluate : 0.372 ------------------------------------------------------------------------------- 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: 4.9990 chunk 20 optimal weight: 3.9990 chunk 3 optimal weight: 8.9990 chunk 32 optimal weight: 0.9980 chunk 37 optimal weight: 3.9990 chunk 39 optimal weight: 1.9990 chunk 36 optimal weight: 0.9990 chunk 38 optimal weight: 0.8980 chunk 23 optimal weight: 0.4980 chunk 16 optimal weight: 6.9990 chunk 30 optimal weight: 3.9990 overall best weight: 1.0784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 555 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7796 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 0.030 3349 Z= 0.197 Angle : 0.622 8.368 4544 Z= 0.309 Chirality : 0.043 0.154 531 Planarity : 0.004 0.044 588 Dihedral : 7.832 49.222 526 Min Nonbonded Distance : 2.284 Molprobity Statistics. All-atom Clashscore : 11.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.01 % Favored : 92.99 % 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 (0.42), residues: 428 helix: 1.00 (0.39), residues: 196 sheet: -1.98 (0.55), residues: 66 loop : -1.96 (0.48), residues: 166 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.002 TRP A 768 HIS 0.003 0.001 HIS A 673 PHE 0.009 0.001 PHE A 387 TYR 0.004 0.001 TYR A 631 ARG 0.004 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 84 residues out of total 345 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 83 time to evaluate : 0.343 Fit side-chains revert: symmetry clash REVERT: A 497 HIS cc_start: 0.8367 (m-70) cc_final: 0.8019 (t70) REVERT: A 503 MET cc_start: 0.8720 (mmp) cc_final: 0.8471 (mmp) REVERT: A 536 ASN cc_start: 0.8705 (t0) cc_final: 0.8188 (t0) REVERT: A 553 ILE cc_start: 0.8661 (mm) cc_final: 0.8423 (mm) REVERT: A 572 VAL cc_start: 0.9459 (t) cc_final: 0.9212 (m) REVERT: A 651 LYS cc_start: 0.8775 (mttt) cc_final: 0.8233 (ptpp) REVERT: A 668 ASP cc_start: 0.7759 (t0) cc_final: 0.7357 (t0) outliers start: 1 outliers final: 0 residues processed: 84 average time/residue: 0.1468 time to fit residues: 15.2412 Evaluate side-chains 57 residues out of total 345 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 57 time to evaluate : 0.389 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Traceback (most recent call last): File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5388/build/../modules/phenix/phenix/command_line/real_space_refine.py", line 8, in run_program(real_space_refine.Program) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5388/modules/cctbx_project/iotbx/cli_parser.py", line 946, in run_program task.run() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5388/modules/phenix/phenix/programs/real_space_refine.py", line 200, in run log = self.logger) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5388/modules/phenix/phenix/refinement/rsr/wrappers.py", line 58, in __init__ log = log) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5388/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 306, in __init__ self.caller(self.refine_xyz) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5388/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 321, in caller func() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5388/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 702, in refine_xyz self.minimization_no_ncs() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5388/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 766, in minimization_no_ncs log = self.log) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5388/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 51, in __init__ gradients_method = gradients_method) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5388/modules/cctbx_project/mmtbx/refinement/real_space/weight.py", line 87, in __init__ rms_angles_limit = rms_angles_limit) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5388/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 368, in refine rms_angles_limit = rms_angles_limit) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5388/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 235, in __init__ weight = weight) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5388/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 112, in refine states_collector = self.states_accumulator) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5388/modules/cctbx_project/cctbx/maptbx/real_space_refinement_simple.py", line 174, in __init__ exception_handling_params=lbfgs_exception_handling_params) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5388/modules/cctbx_project/scitbx/lbfgs/__init__.py", line 278, in run line_search) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5388/modules/cctbx_project/scitbx/lbfgs/__init__.py", line 131, in run_c_plus_plus f, g = target_evaluator.compute_functional_and_gradients() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5388/modules/cctbx_project/cctbx/maptbx/real_space_refinement_simple.py", line 245, in compute_functional_and_gradients compute_gradients=True) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5388/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1477, in energies_sites flags=flags, sites_cart=sites_cart, site_labels=site_labels) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5388/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1379, in pair_proxies check_bonded_distance_cutoff(sites_frac=sites_frac) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5388/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1260, in check_bonded_distance_cutoff raise RuntimeError(msg) RuntimeError: Bond distance > max_reasonable_bond_distance: 53.0563 > 50: distance: 103 - 108: 12.974 distance: 108 - 109: 13.788 distance: 109 - 110: 8.367 distance: 109 - 112: 25.765 distance: 110 - 111: 17.387 distance: 110 - 119: 10.366 distance: 112 - 113: 5.504 distance: 113 - 114: 28.927 distance: 113 - 115: 15.072 distance: 114 - 116: 6.438 distance: 115 - 117: 3.338 distance: 116 - 118: 24.196 distance: 117 - 118: 13.773 distance: 120 - 121: 19.208 distance: 120 - 123: 8.410 distance: 121 - 122: 16.660 distance: 121 - 129: 17.504 distance: 123 - 124: 4.734 distance: 124 - 126: 27.641 distance: 125 - 127: 8.466 distance: 127 - 128: 17.651 distance: 129 - 130: 17.617 distance: 130 - 131: 24.771 distance: 130 - 133: 9.504 distance: 131 - 132: 17.368 distance: 131 - 137: 20.882 distance: 133 - 134: 13.319 distance: 134 - 135: 8.947 distance: 134 - 136: 4.605 distance: 137 - 138: 19.317 distance: 138 - 141: 26.847 distance: 139 - 140: 9.157 distance: 139 - 142: 13.579 distance: 142 - 143: 27.298 distance: 143 - 144: 12.212 distance: 144 - 145: 15.119 distance: 144 - 148: 25.430 distance: 146 - 147: 14.617 distance: 148 - 149: 17.189 distance: 149 - 150: 25.262 distance: 149 - 152: 19.512 distance: 150 - 154: 8.926 distance: 152 - 153: 7.550 distance: 154 - 155: 5.483 distance: 155 - 156: 4.308 distance: 155 - 158: 6.153 distance: 156 - 165: 12.830 distance: 158 - 159: 4.467 distance: 159 - 160: 12.612 distance: 160 - 161: 6.065 distance: 161 - 162: 12.152 distance: 162 - 163: 5.383 distance: 162 - 164: 9.073 distance: 165 - 166: 28.640 distance: 166 - 167: 8.439 distance: 166 - 169: 3.753 distance: 167 - 168: 23.171 distance: 167 - 176: 18.313 distance: 169 - 170: 25.464 distance: 170 - 171: 19.387 distance: 170 - 172: 11.723 distance: 171 - 173: 10.929 distance: 172 - 174: 18.354 distance: 173 - 175: 26.377 distance: 174 - 175: 13.551 distance: 176 - 177: 18.678 distance: 177 - 178: 13.151 distance: 177 - 180: 19.205 distance: 178 - 179: 41.357 distance: 178 - 181: 18.425 distance: 181 - 182: 20.243 distance: 182 - 183: 15.122 distance: 182 - 185: 10.137 distance: 183 - 184: 7.629 distance: 183 - 189: 9.854 distance: 185 - 186: 14.672 distance: 186 - 187: 13.964 distance: 186 - 188: 14.731