Starting phenix.real_space_refine on Mon Sep 23 17:51:50 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7yp2_33994/09_2024/7yp2_33994.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7yp2_33994/09_2024/7yp2_33994.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.52 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7yp2_33994/09_2024/7yp2_33994.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7yp2_33994/09_2024/7yp2_33994.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7yp2_33994/09_2024/7yp2_33994.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7yp2_33994/09_2024/7yp2_33994.cif" } resolution = 3.52 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= 0.014 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: 4 Type Number sf(0) Gaussians S 19 5.16 5 C 2699 2.51 5 N 709 2.21 5 O 821 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 6 residue(s): 0.01s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5461/modules/chem_data/mon_lib" Total number of atoms: 4248 Number of models: 1 Model: "" Number of chains: 3 Chain: "A" Number of atoms: 2450 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 314, 2443 Classifications: {'peptide': 314} Link IDs: {'PTRANS': 11, 'TRANS': 302} Conformer: "B" Number of residues, atoms: 314, 2443 Classifications: {'peptide': 314} Link IDs: {'PTRANS': 11, 'TRANS': 302} bond proxies already assigned to first conformer: 2479 Chain: "H" Number of atoms: 933 Number of conformers: 1 Conformer: "" Number of residues, atoms: 120, 933 Classifications: {'peptide': 120} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 5, 'TRANS': 114} Chain: "L" Number of atoms: 865 Number of conformers: 1 Conformer: "" Number of residues, atoms: 112, 865 Classifications: {'peptide': 112} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 4, 'TRANS': 106} Time building chain proxies: 5.61, per 1000 atoms: 1.32 Number of scatterers: 4248 At special positions: 0 Unit cell: (72.354, 80.134, 98.028, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 19 16.00 O 821 8.00 N 709 7.00 C 2699 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=5, symmetry=0 Simple disulfide: pdb=" SG CYS A 454 " - pdb=" SG CYS A 478 " distance=2.03 Simple disulfide: pdb=" SG CYS A 534 " - pdb=" SG CYS A 587 " distance=2.03 Simple disulfide: pdb=" SG CYS A 612 " - pdb=" SG CYS A 615 " distance=2.03 Simple disulfide: pdb=" SG CYS H 22 " - pdb=" SG CYS H 96 " distance=2.03 Simple disulfide: pdb=" SG CYS L 23 " - pdb=" SG CYS L 94 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 0.97 Conformation dependent library (CDL) restraints added in 754.8 milliseconds 1082 Ramachandran restraints generated. 541 Oldfield, 0 Emsley, 541 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1010 Finding SS restraints... Secondary structure from input PDB file: 15 helices and 8 sheets defined 24.2% alpha, 19.2% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.57 Creating SS restraints... Processing helix chain 'A' and resid 369 through 383 removed outlier: 3.701A pdb=" N GLU A 373 " --> pdb=" O THR A 369 " (cutoff:3.500A) removed outlier: 3.756A pdb=" N TYR A 374 " --> pdb=" O GLU A 370 " (cutoff:3.500A) removed outlier: 3.773A pdb=" N ALA A 375 " --> pdb=" O LYS A 371 " (cutoff:3.500A) removed outlier: 3.859A pdb=" N ALA A 379 " --> pdb=" O ALA A 375 " (cutoff:3.500A) removed outlier: 3.644A pdb=" N THR A 380 " --> pdb=" O LEU A 376 " (cutoff:3.500A) Processing helix chain 'A' and resid 389 through 391 No H-bonds generated for 'chain 'A' and resid 389 through 391' Processing helix chain 'A' and resid 392 through 405 removed outlier: 3.521A pdb=" N LEU A 400 " --> pdb=" O ALA A 396 " (cutoff:3.500A) removed outlier: 3.502A pdb=" N ASN A 405 " --> pdb=" O LEU A 401 " (cutoff:3.500A) Processing helix chain 'A' and resid 416 through 424 removed outlier: 3.508A pdb=" N GLY A 424 " --> pdb=" O THR A 420 " (cutoff:3.500A) Processing helix chain 'A' and resid 425 through 430 Processing helix chain 'A' and resid 440 through 453 Processing helix chain 'A' and resid 455 through 469 removed outlier: 3.537A pdb=" N GLY A 460 " --> pdb=" O ALA A 456 " (cutoff:3.500A) removed outlier: 3.533A pdb=" N GLU A 461 " --> pdb=" O LEU A 457 " (cutoff:3.500A) removed outlier: 3.836A pdb=" N ARG A 464 " --> pdb=" O GLY A 460 " (cutoff:3.500A) removed outlier: 3.501A pdb=" N ALA A 467 " --> pdb=" O LEU A 463 " (cutoff:3.500A) Processing helix chain 'A' and resid 476 through 480 removed outlier: 3.544A pdb=" N LEU A 480 " --> pdb=" O PRO A 477 " (cutoff:3.500A) Processing helix chain 'A' and resid 487 through 492 Processing helix chain 'A' and resid 502 through 517 removed outlier: 3.617A pdb=" N ASN A 508 " --> pdb=" O ALA A 504 " (cutoff:3.500A) Processing helix chain 'A' and resid 520 through 524 removed outlier: 3.672A pdb=" N ASP A 523 " --> pdb=" O GLU A 520 " (cutoff:3.500A) removed outlier: 3.857A pdb=" N ARG A 524 " --> pdb=" O ARG A 521 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 520 through 524' Processing helix chain 'A' and resid 529 through 534 removed outlier: 3.660A pdb=" N LYS A 533 " --> pdb=" O PRO A 530 " (cutoff:3.500A) Processing helix chain 'A' and resid 537 through 539 No H-bonds generated for 'chain 'A' and resid 537 through 539' Processing helix chain 'A' and resid 636 through 645 removed outlier: 3.554A pdb=" N SER A 642 " --> pdb=" O GLU A 638 " (cutoff:3.500A) Processing helix chain 'L' and resid 85 through 89 removed outlier: 4.355A pdb=" N LEU L 89 " --> pdb=" O ALA L 86 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 541 through 546 Processing sheet with id=AA2, first strand: chain 'A' and resid 566 through 567 Processing sheet with id=AA3, first strand: chain 'A' and resid 601 through 602 removed outlier: 4.454A pdb=" N TYR A 658 " --> pdb=" O ILE A 670 " (cutoff:3.500A) removed outlier: 5.972A pdb=" N ASP A 623 " --> pdb=" O LEU A 628 " (cutoff:3.500A) removed outlier: 4.269A pdb=" N LEU A 628 " --> pdb=" O ASP A 623 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'H' and resid 5 through 7 removed outlier: 3.568A pdb=" N LEU H 79 " --> pdb=" O CYS H 22 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'H' and resid 10 through 12 Processing sheet with id=AA6, first strand: chain 'H' and resid 58 through 60 removed outlier: 6.835A pdb=" N TRP H 36 " --> pdb=" O ILE H 48 " (cutoff:3.500A) removed outlier: 4.745A pdb=" N GLU H 50 " --> pdb=" O MET H 34 " (cutoff:3.500A) removed outlier: 7.010A pdb=" N MET H 34 " --> pdb=" O GLU H 50 " (cutoff:3.500A) removed outlier: 4.018A pdb=" N TRP H 33 " --> pdb=" O SER H 99 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'L' and resid 10 through 13 removed outlier: 6.579A pdb=" N TRP L 41 " --> pdb=" O LEU L 53 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'L' and resid 19 through 24 removed outlier: 3.599A pdb=" N THR L 80 " --> pdb=" O THR L 69 " (cutoff:3.500A) 130 hydrogen bonds defined for protein. 345 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 1.07 Time building geometry restraints manager: 1.16 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.14 - 1.28: 692 1.28 - 1.41: 1091 1.41 - 1.55: 2521 1.55 - 1.68: 5 1.68 - 1.82: 28 Bond restraints: 4337 Sorted by residual: bond pdb=" C THR L 75 " pdb=" O THR L 75 " ideal model delta sigma weight residual 1.236 1.147 0.089 1.15e-02 7.56e+03 6.04e+01 bond pdb=" C ASP L 76 " pdb=" O ASP L 76 " ideal model delta sigma weight residual 1.235 1.144 0.091 1.21e-02 6.83e+03 5.62e+01 bond pdb=" CA THR L 75 " pdb=" CB THR L 75 " ideal model delta sigma weight residual 1.529 1.428 0.101 1.55e-02 4.16e+03 4.27e+01 bond pdb=" CA ASP L 76 " pdb=" CB ASP L 76 " ideal model delta sigma weight residual 1.528 1.449 0.080 1.49e-02 4.50e+03 2.86e+01 bond pdb=" C GLY L 72 " pdb=" O GLY L 72 " ideal model delta sigma weight residual 1.235 1.166 0.069 1.35e-02 5.49e+03 2.58e+01 ... (remaining 4332 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.84: 5783 2.84 - 5.67: 83 5.67 - 8.51: 17 8.51 - 11.35: 2 11.35 - 14.18: 2 Bond angle restraints: 5887 Sorted by residual: angle pdb=" N THR L 75 " pdb=" CA THR L 75 " pdb=" C THR L 75 " ideal model delta sigma weight residual 111.07 125.25 -14.18 1.07e+00 8.73e-01 1.76e+02 angle pdb=" CA THR L 75 " pdb=" C THR L 75 " pdb=" N ASP L 76 " ideal model delta sigma weight residual 117.07 127.93 -10.86 1.14e+00 7.69e-01 9.07e+01 angle pdb=" O THR L 75 " pdb=" C THR L 75 " pdb=" N ASP L 76 " ideal model delta sigma weight residual 122.07 115.72 6.35 1.03e+00 9.43e-01 3.80e+01 angle pdb=" CA ASP L 76 " pdb=" C ASP L 76 " pdb=" N PHE L 77 " ideal model delta sigma weight residual 116.23 123.91 -7.68 1.30e+00 5.92e-01 3.49e+01 angle pdb=" N ASP L 76 " pdb=" CA ASP L 76 " pdb=" C ASP L 76 " ideal model delta sigma weight residual 109.76 118.93 -9.17 1.59e+00 3.96e-01 3.33e+01 ... (remaining 5882 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.54: 2281 16.54 - 33.07: 244 33.07 - 49.61: 62 49.61 - 66.14: 8 66.14 - 82.68: 6 Dihedral angle restraints: 2601 sinusoidal: 1017 harmonic: 1584 Sorted by residual: dihedral pdb=" CB CYS A 612 " pdb=" SG CYS A 612 " pdb=" SG CYS A 615 " pdb=" CB CYS A 615 " ideal model delta sinusoidal sigma weight residual 93.00 153.55 -60.55 1 1.00e+01 1.00e-02 4.88e+01 dihedral pdb=" CA ALA H 92 " pdb=" C ALA H 92 " pdb=" N LEU H 93 " pdb=" CA LEU H 93 " ideal model delta harmonic sigma weight residual 180.00 155.28 24.72 0 5.00e+00 4.00e-02 2.44e+01 dihedral pdb=" CA CYS A 612 " pdb=" C CYS A 612 " pdb=" N ILE A 613 " pdb=" CA ILE A 613 " ideal model delta harmonic sigma weight residual 180.00 156.94 23.06 0 5.00e+00 4.00e-02 2.13e+01 ... (remaining 2598 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.092: 611 0.092 - 0.184: 56 0.184 - 0.276: 2 0.276 - 0.368: 0 0.368 - 0.460: 1 Chirality restraints: 670 Sorted by residual: chirality pdb=" CA THR L 75 " pdb=" N THR L 75 " pdb=" C THR L 75 " pdb=" CB THR L 75 " both_signs ideal model delta sigma weight residual False 2.53 2.07 0.46 2.00e-01 2.50e+01 5.29e+00 chirality pdb=" CB VAL A 381 " pdb=" CA VAL A 381 " pdb=" CG1 VAL A 381 " pdb=" CG2 VAL A 381 " both_signs ideal model delta sigma weight residual False -2.63 -2.43 -0.20 2.00e-01 2.50e+01 9.81e-01 chirality pdb=" CA PRO H 53 " pdb=" N PRO H 53 " pdb=" C PRO H 53 " pdb=" CB PRO H 53 " both_signs ideal model delta sigma weight residual False 2.72 2.53 0.19 2.00e-01 2.50e+01 9.14e-01 ... (remaining 667 not shown) Planarity restraints: 748 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA ASP L 76 " 0.019 2.00e-02 2.50e+03 3.76e-02 1.41e+01 pdb=" C ASP L 76 " -0.065 2.00e-02 2.50e+03 pdb=" O ASP L 76 " 0.023 2.00e-02 2.50e+03 pdb=" N PHE L 77 " 0.023 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA GLY L 74 " 0.017 2.00e-02 2.50e+03 3.32e-02 1.10e+01 pdb=" C GLY L 74 " -0.058 2.00e-02 2.50e+03 pdb=" O GLY L 74 " 0.021 2.00e-02 2.50e+03 pdb=" N THR L 75 " 0.020 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C GLY A 440 " 0.049 5.00e-02 4.00e+02 7.35e-02 8.65e+00 pdb=" N PRO A 441 " -0.127 5.00e-02 4.00e+02 pdb=" CA PRO A 441 " 0.038 5.00e-02 4.00e+02 pdb=" CD PRO A 441 " 0.041 5.00e-02 4.00e+02 ... (remaining 745 not shown) Histogram of nonbonded interaction distances: 2.29 - 2.82: 1311 2.82 - 3.34: 3363 3.34 - 3.86: 6466 3.86 - 4.38: 7467 4.38 - 4.90: 13573 Nonbonded interactions: 32180 Sorted by model distance: nonbonded pdb=" N GLY L 72 " pdb=" O GLY L 72 " model vdw 2.294 2.496 nonbonded pdb=" O SER A 556 " pdb=" OG SER A 556 " model vdw 2.310 3.040 nonbonded pdb=" OD1 ASP H 28 " pdb=" OG SER H 30 " model vdw 2.320 3.040 nonbonded pdb=" OE2 GLU A 373 " pdb=" OG1 THR A 420 " model vdw 2.345 3.040 nonbonded pdb=" OD2 ASP A 650 " pdb=" OH TYR L 98 " model vdw 2.372 3.040 ... (remaining 32175 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 ========== 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=0.50 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: 5.330 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.000 Extract box with map and model: 0.200 Check model and map are aligned: 0.030 Set scattering table: 0.040 Process input model: 17.310 Find NCS groups from input model: 0.050 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: 0.010 Load rotamer database and sin/cos tables:3.270 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 26.260 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8421 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 : 0.007 0.101 4337 Z= 0.453 Angle : 0.934 14.183 5887 Z= 0.563 Chirality : 0.055 0.460 670 Planarity : 0.007 0.074 748 Dihedral : 14.655 82.677 1576 Min Nonbonded Distance : 2.294 Molprobity Statistics. All-atom Clashscore : 3.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.96 % Favored : 92.04 % Rotamer: Outliers : 0.00 % Allowed : 8.96 % Favored : 91.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.76 % 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: -4.80 (0.28), residues: 541 helix: -4.68 (0.16), residues: 109 sheet: -2.48 (0.37), residues: 166 loop : -2.92 (0.30), residues: 266 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP H 33 HIS 0.003 0.001 HIS A 655 PHE 0.019 0.002 PHE A 475 TYR 0.011 0.002 TYR L 38 ARG 0.003 0.000 ARG A 430 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1082 Ramachandran restraints generated. 541 Oldfield, 0 Emsley, 541 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1082 Ramachandran restraints generated. 541 Oldfield, 0 Emsley, 541 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 70 residues out of total 467 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 70 time to evaluate : 0.479 Fit side-chains REVERT: A 389 TYR cc_start: 0.7781 (t80) cc_final: 0.7560 (t80) REVERT: A 475 PHE cc_start: 0.8496 (t80) cc_final: 0.7865 (t80) REVERT: A 575 SER cc_start: 0.9076 (t) cc_final: 0.8728 (m) REVERT: A 650 ASP cc_start: 0.8309 (t0) cc_final: 0.8103 (t0) REVERT: H 3 LYS cc_start: 0.8732 (tttm) cc_final: 0.7997 (tmtt) REVERT: L 56 TRP cc_start: 0.8578 (m-10) cc_final: 0.7591 (m-10) REVERT: L 58 SER cc_start: 0.8674 (m) cc_final: 0.8362 (p) REVERT: L 88 ASP cc_start: 0.8542 (m-30) cc_final: 0.8311 (m-30) outliers start: 0 outliers final: 0 residues processed: 70 average time/residue: 0.1898 time to fit residues: 16.4099 Evaluate side-chains 54 residues out of total 467 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 54 time to evaluate : 0.473 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 54 random chunks: chunk 45 optimal weight: 0.8980 chunk 40 optimal weight: 0.5980 chunk 22 optimal weight: 1.9990 chunk 13 optimal weight: 0.6980 chunk 27 optimal weight: 0.5980 chunk 21 optimal weight: 0.8980 chunk 42 optimal weight: 0.9980 chunk 16 optimal weight: 3.9990 chunk 25 optimal weight: 1.9990 chunk 31 optimal weight: 1.9990 chunk 49 optimal weight: 0.0670 overall best weight: 0.5718 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 447 GLN A 604 ASN A 640 GLN H 39 GLN L 44 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8406 moved from start: 0.1420 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.102 4337 Z= 0.271 Angle : 0.583 5.909 5887 Z= 0.310 Chirality : 0.043 0.140 670 Planarity : 0.005 0.051 748 Dihedral : 5.461 68.426 601 Min Nonbonded Distance : 2.518 Molprobity Statistics. All-atom Clashscore : 4.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.93 % Favored : 94.07 % Rotamer: Outliers : 1.07 % Allowed : 13.22 % Favored : 85.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.76 % 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: -3.68 (0.31), residues: 541 helix: -2.75 (0.37), residues: 111 sheet: -1.93 (0.38), residues: 155 loop : -2.60 (0.32), residues: 275 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP H 47 HIS 0.002 0.001 HIS A 414 PHE 0.010 0.001 PHE A 475 TYR 0.011 0.001 TYR A 374 ARG 0.004 0.000 ARG H 38 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1082 Ramachandran restraints generated. 541 Oldfield, 0 Emsley, 541 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1082 Ramachandran restraints generated. 541 Oldfield, 0 Emsley, 541 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 64 residues out of total 467 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 59 time to evaluate : 0.474 Fit side-chains REVERT: A 389 TYR cc_start: 0.7832 (t80) cc_final: 0.7605 (t80) REVERT: A 474 LEU cc_start: 0.8791 (OUTLIER) cc_final: 0.8548 (tt) REVERT: A 650 ASP cc_start: 0.8417 (t0) cc_final: 0.8195 (t0) REVERT: A 668 MET cc_start: 0.8256 (mtp) cc_final: 0.8005 (mtm) REVERT: H 3 LYS cc_start: 0.8756 (tttm) cc_final: 0.8015 (tmtt) REVERT: L 56 TRP cc_start: 0.8700 (m-10) cc_final: 0.7628 (m-10) REVERT: L 87 GLU cc_start: 0.7471 (tm-30) cc_final: 0.7088 (tm-30) REVERT: L 88 ASP cc_start: 0.8636 (m-30) cc_final: 0.8229 (m-30) outliers start: 5 outliers final: 3 residues processed: 63 average time/residue: 0.1731 time to fit residues: 13.8496 Evaluate side-chains 55 residues out of total 467 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 51 time to evaluate : 0.418 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 474 LEU Chi-restraints excluded: chain A residue 604 ASN Chi-restraints excluded: chain H residue 12 VAL Chi-restraints excluded: chain L residue 3 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 54 random chunks: chunk 27 optimal weight: 1.9990 chunk 15 optimal weight: 0.6980 chunk 40 optimal weight: 0.0870 chunk 33 optimal weight: 0.9990 chunk 13 optimal weight: 0.8980 chunk 49 optimal weight: 0.9990 chunk 53 optimal weight: 0.0980 chunk 43 optimal weight: 0.0040 chunk 48 optimal weight: 0.5980 chunk 16 optimal weight: 0.3980 chunk 39 optimal weight: 0.6980 overall best weight: 0.2370 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: L 44 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8356 moved from start: 0.1739 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.113 4337 Z= 0.193 Angle : 0.494 6.212 5887 Z= 0.261 Chirality : 0.041 0.149 670 Planarity : 0.004 0.043 748 Dihedral : 4.849 61.421 601 Min Nonbonded Distance : 2.555 Molprobity Statistics. All-atom Clashscore : 4.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.56 % Favored : 94.44 % Rotamer: Outliers : 1.49 % Allowed : 13.86 % Favored : 84.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.76 % 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: -2.81 (0.33), residues: 541 helix: -1.41 (0.45), residues: 111 sheet: -1.24 (0.42), residues: 149 loop : -2.43 (0.32), residues: 281 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP H 47 HIS 0.001 0.000 HIS A 414 PHE 0.007 0.001 PHE A 475 TYR 0.018 0.001 TYR A 532 ARG 0.005 0.000 ARG H 87 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1082 Ramachandran restraints generated. 541 Oldfield, 0 Emsley, 541 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1082 Ramachandran restraints generated. 541 Oldfield, 0 Emsley, 541 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 62 residues out of total 467 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 55 time to evaluate : 0.489 Fit side-chains REVERT: A 389 TYR cc_start: 0.7779 (t80) cc_final: 0.7540 (t80) REVERT: A 650 ASP cc_start: 0.8397 (t0) cc_final: 0.8161 (t0) REVERT: H 3 LYS cc_start: 0.8719 (tttm) cc_final: 0.7906 (tmtt) REVERT: L 56 TRP cc_start: 0.8633 (m-10) cc_final: 0.7748 (m-10) REVERT: L 87 GLU cc_start: 0.7380 (tm-30) cc_final: 0.6956 (tm-30) outliers start: 7 outliers final: 3 residues processed: 61 average time/residue: 0.1826 time to fit residues: 14.0326 Evaluate side-chains 51 residues out of total 467 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 48 time to evaluate : 0.467 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 381 VAL Chi-restraints excluded: chain A residue 474 LEU Chi-restraints excluded: chain L residue 3 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 54 random chunks: chunk 48 optimal weight: 0.9990 chunk 36 optimal weight: 0.3980 chunk 25 optimal weight: 0.8980 chunk 5 optimal weight: 0.3980 chunk 23 optimal weight: 0.0980 chunk 32 optimal weight: 0.0020 chunk 49 optimal weight: 2.9990 chunk 52 optimal weight: 1.9990 chunk 46 optimal weight: 0.6980 chunk 14 optimal weight: 0.8980 chunk 43 optimal weight: 0.3980 overall best weight: 0.2588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: L 48 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8339 moved from start: 0.2024 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.079 4337 Z= 0.166 Angle : 0.473 4.490 5887 Z= 0.247 Chirality : 0.041 0.136 670 Planarity : 0.004 0.040 748 Dihedral : 4.538 55.462 601 Min Nonbonded Distance : 2.567 Molprobity Statistics. All-atom Clashscore : 3.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.74 % Favored : 94.26 % Rotamer: Outliers : 1.71 % Allowed : 14.50 % Favored : 83.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.76 % 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: -2.28 (0.34), residues: 541 helix: -0.72 (0.48), residues: 111 sheet: -0.76 (0.43), residues: 149 loop : -2.31 (0.33), residues: 281 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP H 47 HIS 0.001 0.000 HIS A 414 PHE 0.007 0.001 PHE A 475 TYR 0.015 0.001 TYR A 532 ARG 0.005 0.000 ARG H 87 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1082 Ramachandran restraints generated. 541 Oldfield, 0 Emsley, 541 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1082 Ramachandran restraints generated. 541 Oldfield, 0 Emsley, 541 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 59 residues out of total 467 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 51 time to evaluate : 0.478 Fit side-chains REVERT: A 389 TYR cc_start: 0.7794 (t80) cc_final: 0.7541 (t80) REVERT: A 575 SER cc_start: 0.9010 (t) cc_final: 0.8718 (m) REVERT: A 650 ASP cc_start: 0.8383 (t0) cc_final: 0.8102 (t0) REVERT: H 3 LYS cc_start: 0.8700 (tttm) cc_final: 0.7872 (tmtt) REVERT: L 56 TRP cc_start: 0.8693 (m-10) cc_final: 0.8430 (m-10) outliers start: 8 outliers final: 7 residues processed: 57 average time/residue: 0.1848 time to fit residues: 13.3830 Evaluate side-chains 54 residues out of total 467 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 47 time to evaluate : 0.436 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 381 VAL Chi-restraints excluded: chain A residue 436 VAL Chi-restraints excluded: chain A residue 474 LEU Chi-restraints excluded: chain A residue 620 LEU Chi-restraints excluded: chain L residue 3 VAL Chi-restraints excluded: chain L residue 84 VAL Chi-restraints excluded: chain L residue 107 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 54 random chunks: chunk 29 optimal weight: 1.9990 chunk 0 optimal weight: 1.9990 chunk 38 optimal weight: 0.7980 chunk 21 optimal weight: 0.9980 chunk 44 optimal weight: 0.7980 chunk 36 optimal weight: 0.9980 chunk 26 optimal weight: 0.5980 chunk 46 optimal weight: 0.9990 chunk 13 optimal weight: 1.9990 chunk 17 optimal weight: 0.5980 chunk 47 optimal weight: 0.9980 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: L 48 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8410 moved from start: 0.1940 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.081 4337 Z= 0.319 Angle : 0.558 5.480 5887 Z= 0.287 Chirality : 0.043 0.145 670 Planarity : 0.004 0.041 748 Dihedral : 4.831 58.853 601 Min Nonbonded Distance : 2.540 Molprobity Statistics. All-atom Clashscore : 4.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.85 % Favored : 93.15 % Rotamer: Outliers : 2.56 % Allowed : 15.99 % Favored : 81.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.76 % 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: -2.28 (0.34), residues: 541 helix: -0.71 (0.48), residues: 111 sheet: -0.98 (0.42), residues: 157 loop : -2.19 (0.35), residues: 273 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP H 33 HIS 0.002 0.001 HIS A 655 PHE 0.009 0.001 PHE A 578 TYR 0.012 0.001 TYR A 532 ARG 0.004 0.000 ARG H 87 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1082 Ramachandran restraints generated. 541 Oldfield, 0 Emsley, 541 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1082 Ramachandran restraints generated. 541 Oldfield, 0 Emsley, 541 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 65 residues out of total 467 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 53 time to evaluate : 0.477 Fit side-chains REVERT: A 474 LEU cc_start: 0.8828 (OUTLIER) cc_final: 0.8621 (tt) REVERT: A 650 ASP cc_start: 0.8426 (t0) cc_final: 0.8125 (t0) REVERT: H 3 LYS cc_start: 0.8791 (tttm) cc_final: 0.8029 (tmtt) REVERT: H 87 ARG cc_start: 0.8528 (ttm-80) cc_final: 0.8058 (tpm170) outliers start: 12 outliers final: 10 residues processed: 64 average time/residue: 0.1856 time to fit residues: 14.8370 Evaluate side-chains 62 residues out of total 467 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 51 time to evaluate : 0.468 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 381 VAL Chi-restraints excluded: chain A residue 436 VAL Chi-restraints excluded: chain A residue 474 LEU Chi-restraints excluded: chain A residue 620 LEU Chi-restraints excluded: chain A residue 636 SER Chi-restraints excluded: chain H residue 12 VAL Chi-restraints excluded: chain H residue 83 VAL Chi-restraints excluded: chain L residue 3 VAL Chi-restraints excluded: chain L residue 39 LEU Chi-restraints excluded: chain L residue 84 VAL Chi-restraints excluded: chain L residue 107 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 54 random chunks: chunk 10 optimal weight: 1.9990 chunk 30 optimal weight: 0.8980 chunk 12 optimal weight: 1.9990 chunk 52 optimal weight: 0.9990 chunk 43 optimal weight: 0.2980 chunk 24 optimal weight: 0.0980 chunk 4 optimal weight: 0.0060 chunk 17 optimal weight: 0.9990 chunk 27 optimal weight: 0.0470 chunk 50 optimal weight: 1.9990 chunk 5 optimal weight: 0.6980 overall best weight: 0.2294 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: L 48 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8347 moved from start: 0.2204 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.099 4337 Z= 0.173 Angle : 0.470 5.006 5887 Z= 0.245 Chirality : 0.041 0.139 670 Planarity : 0.004 0.039 748 Dihedral : 4.390 50.925 601 Min Nonbonded Distance : 2.561 Molprobity Statistics. All-atom Clashscore : 4.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.19 % Favored : 94.81 % Rotamer: Outliers : 1.92 % Allowed : 16.42 % Favored : 81.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.76 % 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: -1.92 (0.35), residues: 541 helix: -0.11 (0.51), residues: 111 sheet: -0.76 (0.42), residues: 154 loop : -2.10 (0.35), residues: 276 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP H 47 HIS 0.001 0.000 HIS A 414 PHE 0.007 0.001 PHE A 475 TYR 0.016 0.001 TYR H 60 ARG 0.004 0.000 ARG H 87 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1082 Ramachandran restraints generated. 541 Oldfield, 0 Emsley, 541 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1082 Ramachandran restraints generated. 541 Oldfield, 0 Emsley, 541 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 59 residues out of total 467 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 50 time to evaluate : 0.464 Fit side-chains REVERT: A 650 ASP cc_start: 0.8388 (t0) cc_final: 0.8060 (t0) REVERT: H 3 LYS cc_start: 0.8726 (tttm) cc_final: 0.7916 (tmtt) REVERT: H 85 LYS cc_start: 0.8759 (mtmt) cc_final: 0.8553 (mtmt) REVERT: H 87 ARG cc_start: 0.8519 (ttm-80) cc_final: 0.8111 (tpm170) outliers start: 9 outliers final: 8 residues processed: 57 average time/residue: 0.1967 time to fit residues: 13.9294 Evaluate side-chains 57 residues out of total 467 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 49 time to evaluate : 0.464 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 381 VAL Chi-restraints excluded: chain A residue 436 VAL Chi-restraints excluded: chain A residue 474 LEU Chi-restraints excluded: chain A residue 620 LEU Chi-restraints excluded: chain H residue 83 VAL Chi-restraints excluded: chain L residue 3 VAL Chi-restraints excluded: chain L residue 84 VAL Chi-restraints excluded: chain L residue 107 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 54 random chunks: chunk 29 optimal weight: 1.9990 chunk 38 optimal weight: 1.9990 chunk 43 optimal weight: 0.0000 chunk 52 optimal weight: 0.9990 chunk 32 optimal weight: 0.4980 chunk 31 optimal weight: 1.9990 chunk 24 optimal weight: 0.7980 chunk 20 optimal weight: 1.9990 chunk 15 optimal weight: 0.5980 chunk 10 optimal weight: 0.9990 chunk 33 optimal weight: 0.7980 overall best weight: 0.5384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 43 GLN L 48 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8384 moved from start: 0.2166 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.093 4337 Z= 0.251 Angle : 0.510 5.534 5887 Z= 0.262 Chirality : 0.042 0.139 670 Planarity : 0.004 0.039 748 Dihedral : 4.447 50.451 601 Min Nonbonded Distance : 2.544 Molprobity Statistics. All-atom Clashscore : 4.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.67 % Favored : 93.33 % Rotamer: Outliers : 2.99 % Allowed : 15.57 % Favored : 81.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.76 % 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: -1.89 (0.35), residues: 541 helix: -0.13 (0.50), residues: 111 sheet: -0.78 (0.41), residues: 155 loop : -2.03 (0.35), residues: 275 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP L 56 HIS 0.001 0.000 HIS A 655 PHE 0.010 0.001 PHE A 475 TYR 0.014 0.001 TYR A 532 ARG 0.003 0.000 ARG H 87 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1082 Ramachandran restraints generated. 541 Oldfield, 0 Emsley, 541 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1082 Ramachandran restraints generated. 541 Oldfield, 0 Emsley, 541 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 67 residues out of total 467 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 53 time to evaluate : 0.473 Fit side-chains REVERT: H 3 LYS cc_start: 0.8782 (tttm) cc_final: 0.7955 (tmtt) REVERT: H 87 ARG cc_start: 0.8520 (ttm-80) cc_final: 0.8100 (tpm170) outliers start: 14 outliers final: 10 residues processed: 63 average time/residue: 0.1818 time to fit residues: 14.3628 Evaluate side-chains 63 residues out of total 467 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 53 time to evaluate : 0.436 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 381 VAL Chi-restraints excluded: chain A residue 388 VAL Chi-restraints excluded: chain A residue 436 VAL Chi-restraints excluded: chain A residue 620 LEU Chi-restraints excluded: chain H residue 17 SER Chi-restraints excluded: chain H residue 83 VAL Chi-restraints excluded: chain L residue 3 VAL Chi-restraints excluded: chain L residue 39 LEU Chi-restraints excluded: chain L residue 84 VAL Chi-restraints excluded: chain L residue 107 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 54 random chunks: chunk 35 optimal weight: 0.9980 chunk 25 optimal weight: 1.9990 chunk 4 optimal weight: 0.1980 chunk 40 optimal weight: 0.5980 chunk 47 optimal weight: 0.0970 chunk 49 optimal weight: 0.4980 chunk 45 optimal weight: 0.0000 chunk 48 optimal weight: 0.7980 chunk 29 optimal weight: 0.7980 chunk 21 optimal weight: 0.4980 chunk 38 optimal weight: 0.9990 overall best weight: 0.2582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 43 GLN L 48 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8338 moved from start: 0.2326 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.102 4337 Z= 0.180 Angle : 0.469 5.809 5887 Z= 0.244 Chirality : 0.041 0.134 670 Planarity : 0.004 0.039 748 Dihedral : 4.146 42.829 601 Min Nonbonded Distance : 2.535 Molprobity Statistics. All-atom Clashscore : 4.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.56 % Favored : 94.44 % Rotamer: Outliers : 2.35 % Allowed : 16.63 % Favored : 81.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.76 % 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: -1.62 (0.36), residues: 541 helix: 0.35 (0.51), residues: 111 sheet: -0.62 (0.42), residues: 154 loop : -1.98 (0.36), residues: 276 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP L 56 HIS 0.001 0.000 HIS A 414 PHE 0.008 0.001 PHE A 475 TYR 0.012 0.001 TYR H 60 ARG 0.004 0.000 ARG H 87 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1082 Ramachandran restraints generated. 541 Oldfield, 0 Emsley, 541 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1082 Ramachandran restraints generated. 541 Oldfield, 0 Emsley, 541 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 66 residues out of total 467 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 55 time to evaluate : 0.577 Fit side-chains REVERT: H 3 LYS cc_start: 0.8729 (tttm) cc_final: 0.7921 (tmtt) REVERT: H 85 LYS cc_start: 0.8763 (mtmt) cc_final: 0.8538 (mtmt) REVERT: H 87 ARG cc_start: 0.8481 (ttm-80) cc_final: 0.8134 (tpm170) outliers start: 11 outliers final: 8 residues processed: 63 average time/residue: 0.1934 time to fit residues: 15.2434 Evaluate side-chains 63 residues out of total 467 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 55 time to evaluate : 0.461 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 436 VAL Chi-restraints excluded: chain A residue 620 LEU Chi-restraints excluded: chain A residue 636 SER Chi-restraints excluded: chain H residue 17 SER Chi-restraints excluded: chain H residue 83 VAL Chi-restraints excluded: chain L residue 3 VAL Chi-restraints excluded: chain L residue 84 VAL Chi-restraints excluded: chain L residue 107 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 54 random chunks: chunk 14 optimal weight: 0.9980 chunk 43 optimal weight: 0.9980 chunk 45 optimal weight: 0.9990 chunk 48 optimal weight: 0.9980 chunk 31 optimal weight: 0.8980 chunk 51 optimal weight: 0.2980 chunk 24 optimal weight: 0.4980 chunk 35 optimal weight: 0.5980 chunk 53 optimal weight: 0.6980 chunk 49 optimal weight: 0.6980 chunk 42 optimal weight: 0.7980 overall best weight: 0.5580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: L 48 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8383 moved from start: 0.2255 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.111 4337 Z= 0.265 Angle : 0.517 6.326 5887 Z= 0.265 Chirality : 0.042 0.138 670 Planarity : 0.004 0.039 748 Dihedral : 4.252 41.787 601 Min Nonbonded Distance : 2.494 Molprobity Statistics. All-atom Clashscore : 4.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.67 % Favored : 93.33 % Rotamer: Outliers : 2.13 % Allowed : 17.06 % Favored : 80.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.76 % 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: -1.64 (0.36), residues: 541 helix: 0.29 (0.51), residues: 111 sheet: -0.65 (0.42), residues: 154 loop : -1.95 (0.36), residues: 276 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP L 56 HIS 0.001 0.001 HIS A 655 PHE 0.009 0.001 PHE A 475 TYR 0.012 0.001 TYR H 60 ARG 0.003 0.000 ARG H 87 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1082 Ramachandran restraints generated. 541 Oldfield, 0 Emsley, 541 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1082 Ramachandran restraints generated. 541 Oldfield, 0 Emsley, 541 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 65 residues out of total 467 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 55 time to evaluate : 0.460 Fit side-chains REVERT: H 3 LYS cc_start: 0.8783 (tttm) cc_final: 0.7978 (tmtt) REVERT: H 87 ARG cc_start: 0.8485 (ttm-80) cc_final: 0.8095 (tpm170) outliers start: 10 outliers final: 9 residues processed: 62 average time/residue: 0.1954 time to fit residues: 15.1941 Evaluate side-chains 62 residues out of total 467 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 53 time to evaluate : 0.465 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 381 VAL Chi-restraints excluded: chain A residue 436 VAL Chi-restraints excluded: chain A residue 620 LEU Chi-restraints excluded: chain A residue 636 SER Chi-restraints excluded: chain H residue 17 SER Chi-restraints excluded: chain H residue 83 VAL Chi-restraints excluded: chain L residue 3 VAL Chi-restraints excluded: chain L residue 84 VAL Chi-restraints excluded: chain L residue 107 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 54 random chunks: chunk 4 optimal weight: 0.0980 chunk 33 optimal weight: 0.5980 chunk 26 optimal weight: 0.9990 chunk 34 optimal weight: 0.9980 chunk 45 optimal weight: 0.7980 chunk 13 optimal weight: 0.8980 chunk 39 optimal weight: 0.9990 chunk 6 optimal weight: 0.9980 chunk 11 optimal weight: 0.0670 chunk 42 optimal weight: 0.4980 chunk 17 optimal weight: 0.0070 overall best weight: 0.2536 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: L 48 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8336 moved from start: 0.2402 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.137 4337 Z= 0.208 Angle : 0.488 8.558 5887 Z= 0.253 Chirality : 0.041 0.203 670 Planarity : 0.004 0.038 748 Dihedral : 4.020 34.437 601 Min Nonbonded Distance : 2.563 Molprobity Statistics. All-atom Clashscore : 4.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.56 % Favored : 94.44 % Rotamer: Outliers : 1.92 % Allowed : 17.91 % Favored : 80.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.76 % 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: -1.37 (0.36), residues: 541 helix: 0.73 (0.52), residues: 111 sheet: -0.50 (0.42), residues: 154 loop : -1.89 (0.36), residues: 276 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP L 56 HIS 0.001 0.000 HIS A 414 PHE 0.009 0.001 PHE A 475 TYR 0.011 0.001 TYR H 60 ARG 0.003 0.000 ARG H 87 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1082 Ramachandran restraints generated. 541 Oldfield, 0 Emsley, 541 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1082 Ramachandran restraints generated. 541 Oldfield, 0 Emsley, 541 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 63 residues out of total 467 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 54 time to evaluate : 0.476 Fit side-chains REVERT: H 3 LYS cc_start: 0.8604 (tttm) cc_final: 0.7771 (tmtt) REVERT: H 85 LYS cc_start: 0.8745 (mtmt) cc_final: 0.8532 (mtmt) REVERT: H 87 ARG cc_start: 0.8452 (ttm-80) cc_final: 0.8160 (tpm170) outliers start: 9 outliers final: 8 residues processed: 60 average time/residue: 0.1952 time to fit residues: 14.7019 Evaluate side-chains 62 residues out of total 467 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 54 time to evaluate : 0.465 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 436 VAL Chi-restraints excluded: chain A residue 620 LEU Chi-restraints excluded: chain A residue 636 SER Chi-restraints excluded: chain H residue 17 SER Chi-restraints excluded: chain H residue 83 VAL Chi-restraints excluded: chain L residue 3 VAL Chi-restraints excluded: chain L residue 84 VAL Chi-restraints excluded: chain L residue 107 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 54 random chunks: chunk 44 optimal weight: 1.9990 chunk 5 optimal weight: 3.9990 chunk 7 optimal weight: 0.2980 chunk 37 optimal weight: 0.0030 chunk 2 optimal weight: 0.2980 chunk 30 optimal weight: 0.0980 chunk 49 optimal weight: 0.7980 chunk 28 optimal weight: 0.9990 chunk 36 optimal weight: 0.9980 chunk 1 optimal weight: 0.6980 chunk 34 optimal weight: 0.8980 overall best weight: 0.2790 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: L 48 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3226 r_free = 0.3226 target = 0.119208 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.2999 r_free = 0.2999 target = 0.100838 restraints weight = 10406.471| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 25)----------------| | r_work = 0.3051 r_free = 0.3051 target = 0.104985 restraints weight = 5648.410| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3064 r_free = 0.3064 target = 0.106139 restraints weight = 3744.213| |-----------------------------------------------------------------------------| r_work (final): 0.3059 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3062 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3062 r_free = 0.3062 target_work(ls_wunit_k1) = 0.106 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3062 r_free = 0.3062 target_work(ls_wunit_k1) = 0.106 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 7 | |-----------------------------------------------------------------------------| r_final: 0.3062 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8191 moved from start: 0.2469 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.137 4337 Z= 0.213 Angle : 0.485 8.294 5887 Z= 0.250 Chirality : 0.041 0.198 670 Planarity : 0.004 0.038 748 Dihedral : 3.884 28.495 601 Min Nonbonded Distance : 2.571 Molprobity Statistics. All-atom Clashscore : 4.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.74 % Favored : 94.26 % Rotamer: Outliers : 1.49 % Allowed : 18.34 % Favored : 80.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.76 % 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: -1.25 (0.36), residues: 541 helix: 0.93 (0.53), residues: 111 sheet: -0.46 (0.42), residues: 154 loop : -1.83 (0.36), residues: 276 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP L 56 HIS 0.001 0.000 HIS A 414 PHE 0.008 0.001 PHE A 475 TYR 0.011 0.001 TYR H 60 ARG 0.004 0.000 ARG H 87 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1596.23 seconds wall clock time: 28 minutes 46.16 seconds (1726.16 seconds total)