Starting phenix.real_space_refine on Thu Nov 14 03:15:57 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8uah_42064/11_2024/8uah_42064.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8uah_42064/11_2024/8uah_42064.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.3 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8uah_42064/11_2024/8uah_42064.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8uah_42064/11_2024/8uah_42064.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8uah_42064/11_2024/8uah_42064.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8uah_42064/11_2024/8uah_42064.cif" } resolution = 3.3 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= -0.001 sd= 0.023 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 30 5.16 5 C 2260 2.51 5 N 580 2.21 5 O 664 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 9 residue(s): 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5513/modules/chem_data/mon_lib" Total number of atoms: 3534 Number of models: 1 Model: "" Number of chains: 2 Chain: "B" Number of atoms: 2606 Number of conformers: 1 Conformer: "" Number of residues, atoms: 334, 2606 Classifications: {'peptide': 334} Link IDs: {'PTRANS': 4, 'TRANS': 329} Unresolved non-hydrogen bonds: 42 Unresolved non-hydrogen angles: 68 Unresolved non-hydrogen dihedrals: 30 Planarities with less than four sites: {'ARG:plan': 14} Unresolved non-hydrogen planarities: 40 Chain: "C" Number of atoms: 928 Number of conformers: 1 Conformer: "" Number of residues, atoms: 117, 928 Classifications: {'peptide': 117} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 2, 'TRANS': 114} Unresolved non-hydrogen bonds: 12 Unresolved non-hydrogen angles: 19 Unresolved non-hydrogen dihedrals: 7 Planarities with less than four sites: {'ARG:plan': 5} Unresolved non-hydrogen planarities: 12 Time building chain proxies: 2.97, per 1000 atoms: 0.84 Number of scatterers: 3534 At special positions: 0 Unit cell: (76.529, 83.216, 73.557, 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 30 16.00 O 664 8.00 N 580 7.00 C 2260 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=1, symmetry=0 Simple disulfide: pdb=" SG CYS B 396 " - pdb=" SG CYS B 422 " 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: 0.84 Conformation dependent library (CDL) restraints added in 438.2 milliseconds 894 Ramachandran restraints generated. 447 Oldfield, 0 Emsley, 447 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 860 Finding SS restraints... Secondary structure from input PDB file: 20 helices and 3 sheets defined 37.0% alpha, 6.9% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.38 Creating SS restraints... Processing helix chain 'B' and resid 379 through 384 removed outlier: 3.739A pdb=" N ARG B 384 " --> pdb=" O LYS B 380 " (cutoff:3.500A) Processing helix chain 'B' and resid 400 through 404 Processing helix chain 'B' and resid 426 through 434 removed outlier: 4.204A pdb=" N ILE B 430 " --> pdb=" O SER B 426 " (cutoff:3.500A) Processing helix chain 'B' and resid 452 through 457 removed outlier: 3.853A pdb=" N LEU B 456 " --> pdb=" O THR B 452 " (cutoff:3.500A) removed outlier: 3.806A pdb=" N LYS B 457 " --> pdb=" O ASP B 453 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 452 through 457' Processing helix chain 'B' and resid 478 through 488 removed outlier: 3.719A pdb=" N MET B 482 " --> pdb=" O SER B 478 " (cutoff:3.500A) removed outlier: 3.521A pdb=" N VAL B 484 " --> pdb=" O GLU B 480 " (cutoff:3.500A) Processing helix chain 'B' and resid 504 through 509 removed outlier: 3.654A pdb=" N VAL B 508 " --> pdb=" O THR B 504 " (cutoff:3.500A) Processing helix chain 'B' and resid 529 through 534 Processing helix chain 'B' and resid 555 through 563 removed outlier: 3.767A pdb=" N MET B 559 " --> pdb=" O ASN B 555 " (cutoff:3.500A) removed outlier: 3.618A pdb=" N VAL B 562 " --> pdb=" O VAL B 558 " (cutoff:3.500A) Processing helix chain 'B' and resid 580 through 591 removed outlier: 4.012A pdb=" N VAL B 584 " --> pdb=" O ASN B 580 " (cutoff:3.500A) Processing helix chain 'B' and resid 607 through 615 Processing helix chain 'B' and resid 633 through 642 removed outlier: 3.548A pdb=" N ALA B 639 " --> pdb=" O ALA B 635 " (cutoff:3.500A) removed outlier: 3.852A pdb=" N GLN B 640 " --> pdb=" O THR B 636 " (cutoff:3.500A) Processing helix chain 'B' and resid 659 through 664 Processing helix chain 'B' and resid 681 through 688 removed outlier: 5.135A pdb=" N ARG B 686 " --> pdb=" O THR B 683 " (cutoff:3.500A) removed outlier: 3.717A pdb=" N ALA B 687 " --> pdb=" O LEU B 684 " (cutoff:3.500A) removed outlier: 3.566A pdb=" N TYR B 688 " --> pdb=" O GLU B 685 " (cutoff:3.500A) Processing helix chain 'C' and resid 20 through 30 removed outlier: 3.602A pdb=" N LEU C 24 " --> pdb=" O VAL C 20 " (cutoff:3.500A) Processing helix chain 'C' and resid 49 through 56 Processing helix chain 'C' and resid 56 through 65 removed outlier: 4.121A pdb=" N ARG C 62 " --> pdb=" O TYR C 58 " (cutoff:3.500A) removed outlier: 4.178A pdb=" N GLY C 65 " --> pdb=" O SER C 61 " (cutoff:3.500A) Processing helix chain 'C' and resid 80 through 85 Processing helix chain 'C' and resid 87 through 94 Processing helix chain 'C' and resid 103 through 114 Processing helix chain 'C' and resid 124 through 132 removed outlier: 3.561A pdb=" N PHE C 128 " --> pdb=" O GLN C 124 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'B' and resid 416 through 419 Processing sheet with id=AA2, first strand: chain 'B' and resid 520 through 522 removed outlier: 3.579A pdb=" N LEU B 545 " --> pdb=" O SER B 570 " (cutoff:3.500A) removed outlier: 4.195A pdb=" N SER B 674 " --> pdb=" O LEU B 648 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'C' and resid 43 through 47 92 hydrogen bonds defined for protein. 258 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 0.88 Time building geometry restraints manager: 0.99 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 1046 1.33 - 1.46: 552 1.46 - 1.58: 1947 1.58 - 1.70: 1 1.70 - 1.82: 38 Bond restraints: 3584 Sorted by residual: bond pdb=" CA VAL C 20 " pdb=" C VAL C 20 " ideal model delta sigma weight residual 1.524 1.465 0.059 1.06e-02 8.90e+03 3.14e+01 bond pdb=" CA SER C 17 " pdb=" C SER C 17 " ideal model delta sigma weight residual 1.523 1.457 0.065 1.35e-02 5.49e+03 2.35e+01 bond pdb=" N LEU C 21 " pdb=" CA LEU C 21 " ideal model delta sigma weight residual 1.459 1.403 0.056 1.28e-02 6.10e+03 1.88e+01 bond pdb=" N ASN C 19 " pdb=" CA ASN C 19 " ideal model delta sigma weight residual 1.459 1.416 0.043 1.15e-02 7.56e+03 1.42e+01 bond pdb=" CA ASP C 68 " pdb=" C ASP C 68 " ideal model delta sigma weight residual 1.523 1.475 0.049 1.34e-02 5.57e+03 1.31e+01 ... (remaining 3579 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.75: 4701 2.75 - 5.49: 95 5.49 - 8.24: 13 8.24 - 10.99: 4 10.99 - 13.73: 4 Bond angle restraints: 4817 Sorted by residual: angle pdb=" N VAL C 20 " pdb=" CA VAL C 20 " pdb=" C VAL C 20 " ideal model delta sigma weight residual 111.62 100.53 11.09 7.90e-01 1.60e+00 1.97e+02 angle pdb=" N SER C 17 " pdb=" CA SER C 17 " pdb=" C SER C 17 " ideal model delta sigma weight residual 111.82 98.42 13.40 1.16e+00 7.43e-01 1.33e+02 angle pdb=" C GLY C 69 " pdb=" N GLU C 70 " pdb=" CA GLU C 70 " ideal model delta sigma weight residual 123.07 111.14 11.93 1.46e+00 4.69e-01 6.68e+01 angle pdb=" N ALA C 67 " pdb=" CA ALA C 67 " pdb=" C ALA C 67 " ideal model delta sigma weight residual 107.20 120.93 -13.73 1.70e+00 3.46e-01 6.53e+01 angle pdb=" CA PRO B 438 " pdb=" N PRO B 438 " pdb=" CD PRO B 438 " ideal model delta sigma weight residual 112.00 103.04 8.96 1.40e+00 5.10e-01 4.09e+01 ... (remaining 4812 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.38: 1774 17.38 - 34.76: 280 34.76 - 52.14: 107 52.14 - 69.51: 27 69.51 - 86.89: 11 Dihedral angle restraints: 2199 sinusoidal: 889 harmonic: 1310 Sorted by residual: dihedral pdb=" CB CYS B 396 " pdb=" SG CYS B 396 " pdb=" SG CYS B 422 " pdb=" CB CYS B 422 " ideal model delta sinusoidal sigma weight residual 93.00 170.73 -77.73 1 1.00e+01 1.00e-02 7.56e+01 dihedral pdb=" CA VAL B 661 " pdb=" C VAL B 661 " pdb=" N GLU B 662 " pdb=" CA GLU B 662 " ideal model delta harmonic sigma weight residual 180.00 146.65 33.35 0 5.00e+00 4.00e-02 4.45e+01 dihedral pdb=" CG ARG B 614 " pdb=" CD ARG B 614 " pdb=" NE ARG B 614 " pdb=" CZ ARG B 614 " ideal model delta sinusoidal sigma weight residual 90.00 10.35 79.65 2 1.50e+01 4.44e-03 2.06e+01 ... (remaining 2196 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.037: 363 0.037 - 0.075: 148 0.075 - 0.112: 50 0.112 - 0.150: 8 0.150 - 0.187: 4 Chirality restraints: 573 Sorted by residual: chirality pdb=" CA ALA C 67 " pdb=" N ALA C 67 " pdb=" C ALA C 67 " pdb=" CB ALA C 67 " both_signs ideal model delta sigma weight residual False 2.48 2.30 0.19 2.00e-01 2.50e+01 8.74e-01 chirality pdb=" CA ASP C 68 " pdb=" N ASP C 68 " pdb=" C ASP C 68 " pdb=" CB ASP C 68 " both_signs ideal model delta sigma weight residual False 2.51 2.35 0.16 2.00e-01 2.50e+01 6.49e-01 chirality pdb=" CA VAL C 20 " pdb=" N VAL C 20 " pdb=" C VAL C 20 " pdb=" CB VAL C 20 " both_signs ideal model delta sigma weight residual False 2.44 2.59 -0.15 2.00e-01 2.50e+01 5.87e-01 ... (remaining 570 not shown) Planarity restraints: 601 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA LEU C 87 " -0.017 2.00e-02 2.50e+03 3.35e-02 1.12e+01 pdb=" C LEU C 87 " 0.058 2.00e-02 2.50e+03 pdb=" O LEU C 87 " -0.022 2.00e-02 2.50e+03 pdb=" N ILE C 88 " -0.020 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C CYS B 437 " -0.056 5.00e-02 4.00e+02 7.96e-02 1.01e+01 pdb=" N PRO B 438 " 0.137 5.00e-02 4.00e+02 pdb=" CA PRO B 438 " -0.038 5.00e-02 4.00e+02 pdb=" CD PRO B 438 " -0.044 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA GLN B 633 " 0.014 2.00e-02 2.50e+03 2.76e-02 7.64e+00 pdb=" C GLN B 633 " -0.048 2.00e-02 2.50e+03 pdb=" O GLN B 633 " 0.018 2.00e-02 2.50e+03 pdb=" N GLY B 634 " 0.016 2.00e-02 2.50e+03 ... (remaining 598 not shown) Histogram of nonbonded interaction distances: 2.18 - 2.73: 238 2.73 - 3.27: 3480 3.27 - 3.81: 5251 3.81 - 4.36: 6732 4.36 - 4.90: 11171 Nonbonded interactions: 26872 Sorted by model distance: nonbonded pdb=" OD2 ASP B 453 " pdb=" OG SER B 478 " model vdw 2.182 3.040 nonbonded pdb=" OE1 GLU B 513 " pdb=" NZ LYS B 538 " model vdw 2.255 3.120 nonbonded pdb=" O SER B 527 " pdb=" OG SER B 527 " model vdw 2.261 3.040 nonbonded pdb=" NZ LYS B 628 " pdb=" OE1 GLU B 629 " model vdw 2.267 3.120 nonbonded pdb=" O ILE B 381 " pdb=" OG SER B 385 " model vdw 2.330 3.040 ... (remaining 26867 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=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.340 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.150 Check model and map are aligned: 0.030 Set scattering table: 0.030 Process input model: 13.150 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:2.900 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 17.650 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8020 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 : 0.005 0.107 3584 Z= 0.348 Angle : 1.028 13.733 4817 Z= 0.696 Chirality : 0.046 0.187 573 Planarity : 0.005 0.080 601 Dihedral : 20.840 86.893 1336 Min Nonbonded Distance : 2.182 Molprobity Statistics. All-atom Clashscore : 11.87 Ramachandran Plot: Outliers : 0.67 % Allowed : 12.98 % Favored : 86.35 % Rotamer: Outliers : 3.90 % Allowed : 30.24 % Favored : 65.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.23 % 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: -4.43 (0.36), residues: 447 helix: -3.05 (0.31), residues: 177 sheet: -2.98 (0.72), residues: 59 loop : -2.73 (0.41), residues: 211 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP B 692 HIS 0.004 0.001 HIS B 470 PHE 0.011 0.001 PHE C 112 TYR 0.006 0.001 TYR B 417 ARG 0.001 0.000 ARG B 686 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 894 Ramachandran restraints generated. 447 Oldfield, 0 Emsley, 447 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 894 Ramachandran restraints generated. 447 Oldfield, 0 Emsley, 447 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 65 residues out of total 410 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 49 time to evaluate : 0.387 Fit side-chains revert: symmetry clash outliers start: 16 outliers final: 12 residues processed: 62 average time/residue: 0.1460 time to fit residues: 11.5682 Evaluate side-chains 53 residues out of total 410 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 41 time to evaluate : 0.414 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 370 ARG Chi-restraints excluded: chain B residue 397 ARG Chi-restraints excluded: chain B residue 416 ARG Chi-restraints excluded: chain B residue 494 ARG Chi-restraints excluded: chain B residue 540 ARG Chi-restraints excluded: chain B residue 614 ARG Chi-restraints excluded: chain B residue 619 ILE Chi-restraints excluded: chain B residue 652 ARG Chi-restraints excluded: chain C residue 22 LEU Chi-restraints excluded: chain C residue 44 ARG Chi-restraints excluded: chain C residue 49 ARG Chi-restraints excluded: chain C residue 62 ARG Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 44 random chunks: chunk 37 optimal weight: 0.7980 chunk 33 optimal weight: 4.9990 chunk 18 optimal weight: 0.0040 chunk 11 optimal weight: 2.9990 chunk 22 optimal weight: 3.9990 chunk 17 optimal weight: 0.7980 chunk 34 optimal weight: 0.9990 chunk 13 optimal weight: 0.9990 chunk 20 optimal weight: 1.9990 chunk 25 optimal weight: 0.9980 chunk 39 optimal weight: 0.9990 overall best weight: 0.7194 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 89 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8025 moved from start: 0.1228 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.052 3584 Z= 0.212 Angle : 0.684 7.887 4817 Z= 0.384 Chirality : 0.043 0.161 573 Planarity : 0.004 0.038 601 Dihedral : 9.210 57.514 497 Min Nonbonded Distance : 2.497 Molprobity Statistics. All-atom Clashscore : 7.35 Ramachandran Plot: Outliers : 0.67 % Allowed : 13.20 % Favored : 86.13 % Rotamer: Outliers : 3.41 % Allowed : 26.34 % Favored : 70.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.23 % 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: -4.12 (0.37), residues: 447 helix: -2.81 (0.31), residues: 179 sheet: -2.77 (0.74), residues: 58 loop : -2.56 (0.42), residues: 210 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP B 692 HIS 0.005 0.001 HIS B 470 PHE 0.026 0.001 PHE B 409 TYR 0.006 0.001 TYR B 598 ARG 0.001 0.000 ARG B 686 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 894 Ramachandran restraints generated. 447 Oldfield, 0 Emsley, 447 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 894 Ramachandran restraints generated. 447 Oldfield, 0 Emsley, 447 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 61 residues out of total 410 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 47 time to evaluate : 0.392 Fit side-chains revert: symmetry clash REVERT: B 690 MET cc_start: 0.4274 (tpt) cc_final: 0.3603 (mtp) outliers start: 14 outliers final: 9 residues processed: 61 average time/residue: 0.1297 time to fit residues: 10.4175 Evaluate side-chains 50 residues out of total 410 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 41 time to evaluate : 0.427 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 397 ARG Chi-restraints excluded: chain B residue 429 SER Chi-restraints excluded: chain B residue 507 SER Chi-restraints excluded: chain B residue 548 ARG Chi-restraints excluded: chain B residue 561 ILE Chi-restraints excluded: chain B residue 664 LEU Chi-restraints excluded: chain B residue 675 THR Chi-restraints excluded: chain C residue 16 HIS Chi-restraints excluded: chain C residue 44 ARG Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 44 random chunks: chunk 22 optimal weight: 3.9990 chunk 12 optimal weight: 2.9990 chunk 33 optimal weight: 2.9990 chunk 27 optimal weight: 4.9990 chunk 11 optimal weight: 2.9990 chunk 40 optimal weight: 2.9990 chunk 43 optimal weight: 0.1980 chunk 35 optimal weight: 1.9990 chunk 39 optimal weight: 1.9990 chunk 13 optimal weight: 0.7980 chunk 32 optimal weight: 2.9990 overall best weight: 1.5986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 555 ASN C 89 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8151 moved from start: 0.1950 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.039 3584 Z= 0.318 Angle : 0.725 7.816 4817 Z= 0.407 Chirality : 0.046 0.146 573 Planarity : 0.004 0.037 601 Dihedral : 7.572 56.977 461 Min Nonbonded Distance : 2.476 Molprobity Statistics. All-atom Clashscore : 8.34 Ramachandran Plot: Outliers : 0.45 % Allowed : 13.65 % Favored : 85.91 % Rotamer: Outliers : 6.10 % Allowed : 26.34 % Favored : 67.56 % 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: -4.33 (0.36), residues: 447 helix: -2.89 (0.31), residues: 179 sheet: -2.97 (0.68), residues: 60 loop : -2.72 (0.41), residues: 208 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP B 692 HIS 0.005 0.001 HIS B 470 PHE 0.021 0.002 PHE B 409 TYR 0.009 0.002 TYR B 417 ARG 0.001 0.000 ARG B 686 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 894 Ramachandran restraints generated. 447 Oldfield, 0 Emsley, 447 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 894 Ramachandran restraints generated. 447 Oldfield, 0 Emsley, 447 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 71 residues out of total 410 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 46 time to evaluate : 0.395 Fit side-chains revert: symmetry clash REVERT: B 572 ASN cc_start: 0.8633 (OUTLIER) cc_final: 0.8142 (t0) REVERT: B 690 MET cc_start: 0.4918 (tpt) cc_final: 0.3779 (mtp) REVERT: C 82 LYS cc_start: 0.8496 (mtmt) cc_final: 0.8284 (ttmm) REVERT: C 95 LYS cc_start: 0.7803 (ttpt) cc_final: 0.7534 (ttmt) outliers start: 25 outliers final: 16 residues processed: 67 average time/residue: 0.1449 time to fit residues: 12.7287 Evaluate side-chains 58 residues out of total 410 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 41 time to evaluate : 0.441 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 377 LEU Chi-restraints excluded: chain B residue 397 ARG Chi-restraints excluded: chain B residue 429 SER Chi-restraints excluded: chain B residue 499 GLU Chi-restraints excluded: chain B residue 507 SER Chi-restraints excluded: chain B residue 548 ARG Chi-restraints excluded: chain B residue 554 ASP Chi-restraints excluded: chain B residue 555 ASN Chi-restraints excluded: chain B residue 572 ASN Chi-restraints excluded: chain B residue 664 LEU Chi-restraints excluded: chain B residue 675 THR Chi-restraints excluded: chain C residue 16 HIS Chi-restraints excluded: chain C residue 22 LEU Chi-restraints excluded: chain C residue 28 ARG Chi-restraints excluded: chain C residue 61 SER Chi-restraints excluded: chain C residue 79 VAL Chi-restraints excluded: chain C residue 93 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 44 random chunks: chunk 39 optimal weight: 0.9980 chunk 30 optimal weight: 1.9990 chunk 20 optimal weight: 3.9990 chunk 4 optimal weight: 1.9990 chunk 19 optimal weight: 0.8980 chunk 26 optimal weight: 0.9980 chunk 40 optimal weight: 0.9980 chunk 42 optimal weight: 3.9990 chunk 38 optimal weight: 0.8980 chunk 11 optimal weight: 2.9990 chunk 35 optimal weight: 0.9980 overall best weight: 0.9580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 89 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8117 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 : 0.003 0.037 3584 Z= 0.222 Angle : 0.654 8.380 4817 Z= 0.368 Chirality : 0.044 0.133 573 Planarity : 0.003 0.037 601 Dihedral : 7.156 54.466 457 Min Nonbonded Distance : 2.507 Molprobity Statistics. All-atom Clashscore : 7.35 Ramachandran Plot: Outliers : 0.22 % Allowed : 12.75 % Favored : 87.02 % Rotamer: Outliers : 6.83 % Allowed : 25.37 % Favored : 67.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.23 % 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: -4.20 (0.36), residues: 447 helix: -2.75 (0.31), residues: 179 sheet: -2.98 (0.67), residues: 60 loop : -2.65 (0.42), residues: 208 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP B 692 HIS 0.003 0.001 HIS B 470 PHE 0.006 0.001 PHE B 409 TYR 0.006 0.001 TYR B 475 ARG 0.001 0.000 ARG B 686 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 894 Ramachandran restraints generated. 447 Oldfield, 0 Emsley, 447 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 894 Ramachandran restraints generated. 447 Oldfield, 0 Emsley, 447 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 71 residues out of total 410 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 43 time to evaluate : 0.425 Fit side-chains revert: symmetry clash REVERT: B 572 ASN cc_start: 0.8618 (OUTLIER) cc_final: 0.8147 (t0) REVERT: B 690 MET cc_start: 0.4767 (tpt) cc_final: 0.3715 (mtp) REVERT: C 82 LYS cc_start: 0.8487 (mtmt) cc_final: 0.8258 (ttmm) outliers start: 28 outliers final: 18 residues processed: 67 average time/residue: 0.1154 time to fit residues: 10.3173 Evaluate side-chains 61 residues out of total 410 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 42 time to evaluate : 0.374 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 373 VAL Chi-restraints excluded: chain B residue 377 LEU Chi-restraints excluded: chain B residue 397 ARG Chi-restraints excluded: chain B residue 429 SER Chi-restraints excluded: chain B residue 507 SER Chi-restraints excluded: chain B residue 513 GLU Chi-restraints excluded: chain B residue 548 ARG Chi-restraints excluded: chain B residue 561 ILE Chi-restraints excluded: chain B residue 572 ASN Chi-restraints excluded: chain B residue 574 CYS Chi-restraints excluded: chain B residue 619 ILE Chi-restraints excluded: chain B residue 664 LEU Chi-restraints excluded: chain B residue 675 THR Chi-restraints excluded: chain C residue 16 HIS Chi-restraints excluded: chain C residue 22 LEU Chi-restraints excluded: chain C residue 28 ARG Chi-restraints excluded: chain C residue 61 SER Chi-restraints excluded: chain C residue 64 VAL Chi-restraints excluded: chain C residue 79 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 44 random chunks: chunk 24 optimal weight: 2.9990 chunk 0 optimal weight: 4.9990 chunk 31 optimal weight: 0.9980 chunk 17 optimal weight: 0.7980 chunk 36 optimal weight: 5.9990 chunk 29 optimal weight: 1.9990 chunk 21 optimal weight: 1.9990 chunk 38 optimal weight: 6.9990 chunk 10 optimal weight: 0.6980 chunk 14 optimal weight: 2.9990 chunk 8 optimal weight: 0.9980 overall best weight: 1.0982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 555 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8136 moved from start: 0.2427 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 3584 Z= 0.241 Angle : 0.650 9.361 4817 Z= 0.364 Chirality : 0.044 0.135 573 Planarity : 0.003 0.037 601 Dihedral : 7.120 57.631 457 Min Nonbonded Distance : 2.510 Molprobity Statistics. All-atom Clashscore : 6.92 Ramachandran Plot: Outliers : 0.22 % Allowed : 12.98 % Favored : 86.80 % Rotamer: Outliers : 6.59 % Allowed : 26.10 % Favored : 67.32 % 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: -4.12 (0.36), residues: 447 helix: -2.55 (0.33), residues: 176 sheet: -3.09 (0.65), residues: 60 loop : -2.71 (0.42), residues: 211 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.002 TRP B 692 HIS 0.004 0.001 HIS B 470 PHE 0.020 0.001 PHE B 409 TYR 0.006 0.001 TYR B 475 ARG 0.001 0.000 ARG B 686 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 894 Ramachandran restraints generated. 447 Oldfield, 0 Emsley, 447 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 894 Ramachandran restraints generated. 447 Oldfield, 0 Emsley, 447 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 68 residues out of total 410 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 41 time to evaluate : 0.408 Fit side-chains revert: symmetry clash REVERT: B 364 GLN cc_start: 0.8006 (OUTLIER) cc_final: 0.7725 (tp40) REVERT: B 572 ASN cc_start: 0.8629 (OUTLIER) cc_final: 0.8131 (t0) REVERT: B 690 MET cc_start: 0.4895 (tpt) cc_final: 0.3587 (mtt) REVERT: C 105 GLU cc_start: 0.7127 (OUTLIER) cc_final: 0.6737 (pt0) outliers start: 27 outliers final: 20 residues processed: 64 average time/residue: 0.1314 time to fit residues: 11.0081 Evaluate side-chains 61 residues out of total 410 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 38 time to evaluate : 0.411 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 364 GLN Chi-restraints excluded: chain B residue 373 VAL Chi-restraints excluded: chain B residue 377 LEU Chi-restraints excluded: chain B residue 397 ARG Chi-restraints excluded: chain B residue 429 SER Chi-restraints excluded: chain B residue 499 GLU Chi-restraints excluded: chain B residue 507 SER Chi-restraints excluded: chain B residue 513 GLU Chi-restraints excluded: chain B residue 548 ARG Chi-restraints excluded: chain B residue 554 ASP Chi-restraints excluded: chain B residue 555 ASN Chi-restraints excluded: chain B residue 561 ILE Chi-restraints excluded: chain B residue 572 ASN Chi-restraints excluded: chain B residue 574 CYS Chi-restraints excluded: chain B residue 619 ILE Chi-restraints excluded: chain B residue 664 LEU Chi-restraints excluded: chain B residue 675 THR Chi-restraints excluded: chain C residue 16 HIS Chi-restraints excluded: chain C residue 22 LEU Chi-restraints excluded: chain C residue 28 ARG Chi-restraints excluded: chain C residue 61 SER Chi-restraints excluded: chain C residue 64 VAL Chi-restraints excluded: chain C residue 105 GLU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 44 random chunks: chunk 24 optimal weight: 2.9990 chunk 10 optimal weight: 3.9990 chunk 42 optimal weight: 0.9990 chunk 35 optimal weight: 0.0570 chunk 19 optimal weight: 2.9990 chunk 3 optimal weight: 3.9990 chunk 14 optimal weight: 2.9990 chunk 22 optimal weight: 0.7980 chunk 41 optimal weight: 0.7980 chunk 4 optimal weight: 0.9980 chunk 31 optimal weight: 0.4980 overall best weight: 0.6298 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 555 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8086 moved from start: 0.2543 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 3584 Z= 0.179 Angle : 0.604 9.110 4817 Z= 0.340 Chirality : 0.043 0.141 573 Planarity : 0.003 0.036 601 Dihedral : 6.855 58.230 457 Min Nonbonded Distance : 2.511 Molprobity Statistics. All-atom Clashscore : 6.92 Ramachandran Plot: Outliers : 0.22 % Allowed : 12.75 % Favored : 87.02 % Rotamer: Outliers : 7.07 % Allowed : 25.37 % Favored : 67.56 % 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: -3.90 (0.37), residues: 447 helix: -2.35 (0.33), residues: 176 sheet: -3.08 (0.64), residues: 60 loop : -2.56 (0.43), residues: 211 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP B 692 HIS 0.002 0.001 HIS B 470 PHE 0.020 0.001 PHE B 409 TYR 0.006 0.001 TYR B 598 ARG 0.000 0.000 ARG B 686 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 894 Ramachandran restraints generated. 447 Oldfield, 0 Emsley, 447 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 894 Ramachandran restraints generated. 447 Oldfield, 0 Emsley, 447 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 67 residues out of total 410 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 38 time to evaluate : 0.376 Fit side-chains revert: symmetry clash REVERT: B 364 GLN cc_start: 0.7891 (OUTLIER) cc_final: 0.7597 (tp40) REVERT: B 524 MET cc_start: 0.9159 (tmm) cc_final: 0.8924 (tmm) REVERT: B 555 ASN cc_start: 0.8777 (OUTLIER) cc_final: 0.8451 (m110) REVERT: B 572 ASN cc_start: 0.8590 (OUTLIER) cc_final: 0.8140 (t0) REVERT: B 690 MET cc_start: 0.4836 (tpt) cc_final: 0.3706 (mtm) REVERT: C 78 GLU cc_start: 0.7614 (OUTLIER) cc_final: 0.7054 (pt0) REVERT: C 105 GLU cc_start: 0.7095 (OUTLIER) cc_final: 0.6685 (pt0) outliers start: 29 outliers final: 18 residues processed: 63 average time/residue: 0.1097 time to fit residues: 9.3577 Evaluate side-chains 61 residues out of total 410 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 38 time to evaluate : 0.425 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 364 GLN Chi-restraints excluded: chain B residue 373 VAL Chi-restraints excluded: chain B residue 377 LEU Chi-restraints excluded: chain B residue 397 ARG Chi-restraints excluded: chain B residue 429 SER Chi-restraints excluded: chain B residue 490 LEU Chi-restraints excluded: chain B residue 507 SER Chi-restraints excluded: chain B residue 513 GLU Chi-restraints excluded: chain B residue 528 VAL Chi-restraints excluded: chain B residue 548 ARG Chi-restraints excluded: chain B residue 554 ASP Chi-restraints excluded: chain B residue 555 ASN Chi-restraints excluded: chain B residue 561 ILE Chi-restraints excluded: chain B residue 572 ASN Chi-restraints excluded: chain B residue 619 ILE Chi-restraints excluded: chain B residue 664 LEU Chi-restraints excluded: chain B residue 675 THR Chi-restraints excluded: chain C residue 16 HIS Chi-restraints excluded: chain C residue 61 SER Chi-restraints excluded: chain C residue 64 VAL Chi-restraints excluded: chain C residue 78 GLU Chi-restraints excluded: chain C residue 79 VAL Chi-restraints excluded: chain C residue 105 GLU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 44 random chunks: chunk 24 optimal weight: 3.9990 chunk 35 optimal weight: 0.7980 chunk 23 optimal weight: 2.9990 chunk 42 optimal weight: 0.8980 chunk 26 optimal weight: 1.9990 chunk 25 optimal weight: 0.9980 chunk 19 optimal weight: 1.9990 chunk 16 optimal weight: 0.9990 chunk 12 optimal weight: 1.9990 chunk 8 optimal weight: 0.9980 chunk 28 optimal weight: 0.9990 overall best weight: 0.9382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8110 moved from start: 0.2602 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 3584 Z= 0.217 Angle : 0.641 9.021 4817 Z= 0.360 Chirality : 0.044 0.138 573 Planarity : 0.003 0.036 601 Dihedral : 6.855 59.036 457 Min Nonbonded Distance : 2.515 Molprobity Statistics. All-atom Clashscore : 6.92 Ramachandran Plot: Outliers : 0.22 % Allowed : 13.65 % Favored : 86.13 % Rotamer: Outliers : 6.34 % Allowed : 26.59 % Favored : 67.07 % 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: -3.90 (0.37), residues: 447 helix: -2.31 (0.34), residues: 176 sheet: -3.15 (0.64), residues: 60 loop : -2.58 (0.43), residues: 211 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP B 692 HIS 0.003 0.001 HIS B 470 PHE 0.014 0.001 PHE B 409 TYR 0.005 0.001 TYR B 475 ARG 0.000 0.000 ARG B 686 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 894 Ramachandran restraints generated. 447 Oldfield, 0 Emsley, 447 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 894 Ramachandran restraints generated. 447 Oldfield, 0 Emsley, 447 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 67 residues out of total 410 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 41 time to evaluate : 0.412 Fit side-chains revert: symmetry clash REVERT: B 364 GLN cc_start: 0.7977 (OUTLIER) cc_final: 0.7682 (tp40) REVERT: B 572 ASN cc_start: 0.8599 (OUTLIER) cc_final: 0.8147 (t0) REVERT: B 690 MET cc_start: 0.4816 (tpt) cc_final: 0.3534 (mtt) REVERT: C 78 GLU cc_start: 0.7616 (OUTLIER) cc_final: 0.6267 (mp0) REVERT: C 105 GLU cc_start: 0.7093 (OUTLIER) cc_final: 0.6708 (pt0) outliers start: 26 outliers final: 18 residues processed: 64 average time/residue: 0.1189 time to fit residues: 10.4758 Evaluate side-chains 60 residues out of total 410 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 38 time to evaluate : 0.400 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 364 GLN Chi-restraints excluded: chain B residue 373 VAL Chi-restraints excluded: chain B residue 397 ARG Chi-restraints excluded: chain B residue 429 SER Chi-restraints excluded: chain B residue 490 LEU Chi-restraints excluded: chain B residue 507 SER Chi-restraints excluded: chain B residue 513 GLU Chi-restraints excluded: chain B residue 548 ARG Chi-restraints excluded: chain B residue 561 ILE Chi-restraints excluded: chain B residue 572 ASN Chi-restraints excluded: chain B residue 574 CYS Chi-restraints excluded: chain B residue 619 ILE Chi-restraints excluded: chain B residue 638 ILE Chi-restraints excluded: chain B residue 664 LEU Chi-restraints excluded: chain B residue 675 THR Chi-restraints excluded: chain C residue 16 HIS Chi-restraints excluded: chain C residue 22 LEU Chi-restraints excluded: chain C residue 61 SER Chi-restraints excluded: chain C residue 64 VAL Chi-restraints excluded: chain C residue 78 GLU Chi-restraints excluded: chain C residue 79 VAL Chi-restraints excluded: chain C residue 105 GLU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 44 random chunks: chunk 20 optimal weight: 2.9990 chunk 3 optimal weight: 3.9990 chunk 33 optimal weight: 2.9990 chunk 38 optimal weight: 2.9990 chunk 40 optimal weight: 0.9980 chunk 37 optimal weight: 0.7980 chunk 39 optimal weight: 0.0040 chunk 23 optimal weight: 3.9990 chunk 17 optimal weight: 3.9990 chunk 31 optimal weight: 0.7980 chunk 12 optimal weight: 1.9990 overall best weight: 0.9194 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 555 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8113 moved from start: 0.2765 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 3584 Z= 0.211 Angle : 0.641 9.302 4817 Z= 0.358 Chirality : 0.044 0.144 573 Planarity : 0.003 0.036 601 Dihedral : 6.866 60.788 457 Min Nonbonded Distance : 2.501 Molprobity Statistics. All-atom Clashscore : 7.49 Ramachandran Plot: Outliers : 0.22 % Allowed : 13.42 % Favored : 86.35 % Rotamer: Outliers : 7.32 % Allowed : 25.61 % Favored : 67.07 % 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: -3.80 (0.37), residues: 447 helix: -2.20 (0.34), residues: 175 sheet: -3.25 (0.62), residues: 60 loop : -2.49 (0.43), residues: 212 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP B 692 HIS 0.003 0.001 HIS B 470 PHE 0.012 0.001 PHE B 409 TYR 0.005 0.001 TYR B 475 ARG 0.001 0.000 ARG B 686 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 894 Ramachandran restraints generated. 447 Oldfield, 0 Emsley, 447 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 894 Ramachandran restraints generated. 447 Oldfield, 0 Emsley, 447 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 69 residues out of total 410 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 39 time to evaluate : 0.429 Fit side-chains revert: symmetry clash REVERT: B 364 GLN cc_start: 0.7989 (OUTLIER) cc_final: 0.7692 (tp40) REVERT: B 572 ASN cc_start: 0.8605 (OUTLIER) cc_final: 0.8122 (t0) REVERT: B 690 MET cc_start: 0.4927 (tpt) cc_final: 0.3501 (mtt) REVERT: C 78 GLU cc_start: 0.7638 (OUTLIER) cc_final: 0.7060 (pt0) REVERT: C 105 GLU cc_start: 0.7116 (OUTLIER) cc_final: 0.6709 (pt0) outliers start: 30 outliers final: 22 residues processed: 65 average time/residue: 0.1131 time to fit residues: 9.9749 Evaluate side-chains 63 residues out of total 410 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 37 time to evaluate : 0.412 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 364 GLN Chi-restraints excluded: chain B residue 373 VAL Chi-restraints excluded: chain B residue 377 LEU Chi-restraints excluded: chain B residue 429 SER Chi-restraints excluded: chain B residue 490 LEU Chi-restraints excluded: chain B residue 499 GLU Chi-restraints excluded: chain B residue 507 SER Chi-restraints excluded: chain B residue 513 GLU Chi-restraints excluded: chain B residue 548 ARG Chi-restraints excluded: chain B residue 554 ASP Chi-restraints excluded: chain B residue 555 ASN Chi-restraints excluded: chain B residue 561 ILE Chi-restraints excluded: chain B residue 572 ASN Chi-restraints excluded: chain B residue 574 CYS Chi-restraints excluded: chain B residue 619 ILE Chi-restraints excluded: chain B residue 638 ILE Chi-restraints excluded: chain B residue 664 LEU Chi-restraints excluded: chain B residue 675 THR Chi-restraints excluded: chain C residue 16 HIS Chi-restraints excluded: chain C residue 22 LEU Chi-restraints excluded: chain C residue 28 ARG Chi-restraints excluded: chain C residue 61 SER Chi-restraints excluded: chain C residue 64 VAL Chi-restraints excluded: chain C residue 78 GLU Chi-restraints excluded: chain C residue 79 VAL Chi-restraints excluded: chain C residue 105 GLU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 44 random chunks: chunk 35 optimal weight: 1.9990 chunk 37 optimal weight: 0.7980 chunk 39 optimal weight: 0.5980 chunk 25 optimal weight: 3.9990 chunk 41 optimal weight: 0.7980 chunk 19 optimal weight: 0.7980 chunk 29 optimal weight: 1.9990 chunk 43 optimal weight: 1.9990 chunk 40 optimal weight: 1.9990 chunk 34 optimal weight: 0.7980 chunk 3 optimal weight: 2.9990 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8098 moved from start: 0.2811 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 3584 Z= 0.193 Angle : 0.635 9.406 4817 Z= 0.356 Chirality : 0.043 0.147 573 Planarity : 0.003 0.036 601 Dihedral : 6.232 61.433 453 Min Nonbonded Distance : 2.515 Molprobity Statistics. All-atom Clashscore : 7.21 Ramachandran Plot: Outliers : 0.22 % Allowed : 13.20 % Favored : 86.58 % Rotamer: Outliers : 5.85 % Allowed : 26.59 % Favored : 67.56 % 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: -3.68 (0.38), residues: 447 helix: -2.06 (0.35), residues: 175 sheet: -3.25 (0.63), residues: 60 loop : -2.44 (0.44), residues: 212 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP B 692 HIS 0.002 0.001 HIS B 470 PHE 0.012 0.001 PHE C 125 TYR 0.005 0.001 TYR B 598 ARG 0.000 0.000 ARG B 686 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 894 Ramachandran restraints generated. 447 Oldfield, 0 Emsley, 447 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 894 Ramachandran restraints generated. 447 Oldfield, 0 Emsley, 447 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 62 residues out of total 410 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 38 time to evaluate : 0.426 Fit side-chains revert: symmetry clash REVERT: B 364 GLN cc_start: 0.7966 (OUTLIER) cc_final: 0.7672 (tp40) REVERT: B 572 ASN cc_start: 0.8593 (OUTLIER) cc_final: 0.8123 (t0) REVERT: B 690 MET cc_start: 0.4820 (tpt) cc_final: 0.3523 (mtt) REVERT: C 78 GLU cc_start: 0.7630 (OUTLIER) cc_final: 0.6259 (mp0) REVERT: C 105 GLU cc_start: 0.7108 (OUTLIER) cc_final: 0.6724 (pt0) outliers start: 24 outliers final: 16 residues processed: 58 average time/residue: 0.1149 time to fit residues: 9.1529 Evaluate side-chains 58 residues out of total 410 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 38 time to evaluate : 0.441 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 364 GLN Chi-restraints excluded: chain B residue 373 VAL Chi-restraints excluded: chain B residue 429 SER Chi-restraints excluded: chain B residue 490 LEU Chi-restraints excluded: chain B residue 507 SER Chi-restraints excluded: chain B residue 513 GLU Chi-restraints excluded: chain B residue 548 ARG Chi-restraints excluded: chain B residue 554 ASP Chi-restraints excluded: chain B residue 572 ASN Chi-restraints excluded: chain B residue 574 CYS Chi-restraints excluded: chain B residue 619 ILE Chi-restraints excluded: chain B residue 638 ILE Chi-restraints excluded: chain B residue 664 LEU Chi-restraints excluded: chain B residue 675 THR Chi-restraints excluded: chain C residue 16 HIS Chi-restraints excluded: chain C residue 61 SER Chi-restraints excluded: chain C residue 64 VAL Chi-restraints excluded: chain C residue 78 GLU Chi-restraints excluded: chain C residue 79 VAL Chi-restraints excluded: chain C residue 105 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 44 random chunks: chunk 26 optimal weight: 3.9990 chunk 21 optimal weight: 3.9990 chunk 27 optimal weight: 1.9990 chunk 37 optimal weight: 1.9990 chunk 10 optimal weight: 2.9990 chunk 32 optimal weight: 1.9990 chunk 5 optimal weight: 2.9990 chunk 9 optimal weight: 2.9990 chunk 34 optimal weight: 2.9990 chunk 14 optimal weight: 3.9990 chunk 35 optimal weight: 0.9990 overall best weight: 1.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 448 GLN B 555 ASN ** C 124 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8195 moved from start: 0.2979 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.043 3584 Z= 0.376 Angle : 0.732 9.512 4817 Z= 0.405 Chirality : 0.048 0.144 573 Planarity : 0.004 0.035 601 Dihedral : 6.825 65.153 453 Min Nonbonded Distance : 2.513 Molprobity Statistics. All-atom Clashscore : 8.48 Ramachandran Plot: Outliers : 0.22 % Allowed : 14.54 % Favored : 85.23 % Rotamer: Outliers : 6.59 % Allowed : 26.34 % Favored : 67.07 % 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: -3.91 (0.38), residues: 447 helix: -2.25 (0.35), residues: 174 sheet: -3.45 (0.62), residues: 60 loop : -2.55 (0.44), residues: 213 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.002 TRP B 692 HIS 0.005 0.001 HIS B 470 PHE 0.015 0.002 PHE C 125 TYR 0.010 0.002 TYR B 475 ARG 0.001 0.000 ARG B 686 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 894 Ramachandran restraints generated. 447 Oldfield, 0 Emsley, 447 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 894 Ramachandran restraints generated. 447 Oldfield, 0 Emsley, 447 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 64 residues out of total 410 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 37 time to evaluate : 0.384 Fit side-chains revert: symmetry clash REVERT: B 447 ASN cc_start: 0.9009 (m110) cc_final: 0.8781 (m110) REVERT: B 572 ASN cc_start: 0.8642 (OUTLIER) cc_final: 0.8132 (t0) REVERT: B 690 MET cc_start: 0.5252 (tpt) cc_final: 0.3517 (mtt) REVERT: C 78 GLU cc_start: 0.7680 (OUTLIER) cc_final: 0.7106 (pt0) REVERT: C 95 LYS cc_start: 0.7826 (ttpt) cc_final: 0.7604 (ttmt) REVERT: C 105 GLU cc_start: 0.7269 (OUTLIER) cc_final: 0.6890 (pt0) outliers start: 27 outliers final: 20 residues processed: 62 average time/residue: 0.1320 time to fit residues: 10.7399 Evaluate side-chains 56 residues out of total 410 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 33 time to evaluate : 0.404 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 372 GLN Chi-restraints excluded: chain B residue 429 SER Chi-restraints excluded: chain B residue 490 LEU Chi-restraints excluded: chain B residue 499 GLU Chi-restraints excluded: chain B residue 507 SER Chi-restraints excluded: chain B residue 513 GLU Chi-restraints excluded: chain B residue 548 ARG Chi-restraints excluded: chain B residue 553 LEU Chi-restraints excluded: chain B residue 554 ASP Chi-restraints excluded: chain B residue 555 ASN Chi-restraints excluded: chain B residue 572 ASN Chi-restraints excluded: chain B residue 574 CYS Chi-restraints excluded: chain B residue 619 ILE Chi-restraints excluded: chain B residue 664 LEU Chi-restraints excluded: chain B residue 675 THR Chi-restraints excluded: chain C residue 16 HIS Chi-restraints excluded: chain C residue 22 LEU Chi-restraints excluded: chain C residue 28 ARG Chi-restraints excluded: chain C residue 61 SER Chi-restraints excluded: chain C residue 64 VAL Chi-restraints excluded: chain C residue 78 GLU Chi-restraints excluded: chain C residue 79 VAL Chi-restraints excluded: chain C residue 105 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 44 random chunks: chunk 4 optimal weight: 0.9990 chunk 6 optimal weight: 0.1980 chunk 30 optimal weight: 0.3980 chunk 1 optimal weight: 2.9990 chunk 25 optimal weight: 2.9990 chunk 40 optimal weight: 0.8980 chunk 23 optimal weight: 0.7980 chunk 29 optimal weight: 0.8980 chunk 27 optimal weight: 0.8980 chunk 26 optimal weight: 1.9990 chunk 17 optimal weight: 2.9990 overall best weight: 0.6380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 555 ASN ** C 124 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3866 r_free = 0.3866 target = 0.156975 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3605 r_free = 0.3605 target = 0.134865 restraints weight = 4595.082| |-----------------------------------------------------------------------------| r_work (start): 0.3590 rms_B_bonded: 1.86 r_work: 0.3467 rms_B_bonded: 2.32 restraints_weight: 0.5000 r_work: 0.3340 rms_B_bonded: 4.00 restraints_weight: 0.2500 r_work (final): 0.3340 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8225 moved from start: 0.3010 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.066 3584 Z= 0.318 Angle : 1.368 59.195 4817 Z= 0.852 Chirality : 0.047 0.195 573 Planarity : 0.004 0.049 601 Dihedral : 6.842 65.161 453 Min Nonbonded Distance : 2.229 Molprobity Statistics. All-atom Clashscore : 9.47 Ramachandran Plot: Outliers : 0.45 % Allowed : 14.54 % Favored : 85.01 % Rotamer: Outliers : 6.10 % Allowed : 27.56 % Favored : 66.34 % Cbeta Deviations : 0.23 % 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: -3.92 (0.38), residues: 447 helix: -2.24 (0.34), residues: 174 sheet: -3.48 (0.61), residues: 60 loop : -2.56 (0.44), residues: 213 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP B 692 HIS 0.005 0.001 HIS B 470 PHE 0.011 0.001 PHE C 125 TYR 0.010 0.001 TYR B 475 ARG 0.001 0.000 ARG B 686 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1201.39 seconds wall clock time: 22 minutes 30.30 seconds (1350.30 seconds total)