Starting phenix.real_space_refine on Thu Nov 14 04:37:14 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8s4u_19716/11_2024/8s4u_19716.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8s4u_19716/11_2024/8s4u_19716.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.09 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8s4u_19716/11_2024/8s4u_19716.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8s4u_19716/11_2024/8s4u_19716.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8s4u_19716/11_2024/8s4u_19716.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8s4u_19716/11_2024/8s4u_19716.cif" } resolution = 3.09 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= 0.041 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 2640 2.51 5 N 616 2.21 5 O 705 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 2 residue(s): 0.01s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5513/modules/chem_data/mon_lib" Total number of atoms: 3980 Number of models: 1 Model: "" Number of chains: 3 Chain: "B" Number of atoms: 982 Number of conformers: 1 Conformer: "" Number of residues, atoms: 128, 982 Classifications: {'peptide': 128} Link IDs: {'PTRANS': 3, 'TRANS': 124} Chain: "A" Number of atoms: 2984 Number of conformers: 1 Conformer: "" Number of residues, atoms: 374, 2984 Classifications: {'peptide': 374} Link IDs: {'PTRANS': 13, 'TRANS': 360} Chain breaks: 1 Chain: "A" Number of atoms: 14 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 14 Unusual residues: {'NAG': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Time building chain proxies: 3.59, per 1000 atoms: 0.90 Number of scatterers: 3980 At special positions: 0 Unit cell: (88.81, 67.23, 89.64, 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 705 8.00 N 616 7.00 C 2640 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=1, symmetry=0 Simple disulfide: pdb=" SG CYS B 22 " - pdb=" SG CYS B 96 " 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 Links applied NAG-ASN " NAG A 601 " - " ASN A 45 " Time building additional restraints: 1.02 Conformation dependent library (CDL) restraints added in 473.6 milliseconds 992 Ramachandran restraints generated. 496 Oldfield, 0 Emsley, 496 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 940 Finding SS restraints... Secondary structure from input PDB file: 21 helices and 3 sheets defined 67.1% alpha, 11.6% 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 28 through 32 removed outlier: 3.556A pdb=" N TYR B 32 " --> pdb=" O PHE B 29 " (cutoff:3.500A) Processing helix chain 'B' and resid 87 through 91 removed outlier: 3.577A pdb=" N THR B 91 " --> pdb=" O PRO B 88 " (cutoff:3.500A) Processing helix chain 'B' and resid 110 through 113 Processing helix chain 'A' and resid 12 through 28 Processing helix chain 'A' and resid 31 through 33 No H-bonds generated for 'chain 'A' and resid 31 through 33' Processing helix chain 'A' and resid 34 through 40 Processing helix chain 'A' and resid 47 through 54 Processing helix chain 'A' and resid 55 through 74 removed outlier: 3.876A pdb=" N TRP A 59 " --> pdb=" O ILE A 55 " (cutoff:3.500A) removed outlier: 3.791A pdb=" N THR A 60 " --> pdb=" O PHE A 56 " (cutoff:3.500A) removed outlier: 4.027A pdb=" N LEU A 68 " --> pdb=" O LEU A 64 " (cutoff:3.500A) Proline residue: A 69 - end of helix Processing helix chain 'A' and resid 79 through 100 Processing helix chain 'A' and resid 103 through 119 Processing helix chain 'A' and resid 120 through 131 removed outlier: 3.654A pdb=" N TYR A 124 " --> pdb=" O GLU A 120 " (cutoff:3.500A) removed outlier: 4.335A pdb=" N ILE A 127 " --> pdb=" O TYR A 123 " (cutoff:3.500A) removed outlier: 5.073A pdb=" N TYR A 128 " --> pdb=" O TYR A 124 " (cutoff:3.500A) removed outlier: 4.380A pdb=" N SER A 129 " --> pdb=" O ALA A 125 " (cutoff:3.500A) removed outlier: 3.895A pdb=" N VAL A 130 " --> pdb=" O TYR A 126 " (cutoff:3.500A) Processing helix chain 'A' and resid 132 through 134 No H-bonds generated for 'chain 'A' and resid 132 through 134' Processing helix chain 'A' and resid 135 through 164 removed outlier: 3.732A pdb=" N THR A 147 " --> pdb=" O CYS A 143 " (cutoff:3.500A) Processing helix chain 'A' and resid 168 through 188 removed outlier: 3.841A pdb=" N LEU A 188 " --> pdb=" O PHE A 184 " (cutoff:3.500A) Processing helix chain 'A' and resid 275 through 296 removed outlier: 3.577A pdb=" N ALA A 290 " --> pdb=" O ALA A 286 " (cutoff:3.500A) Processing helix chain 'A' and resid 298 through 307 Processing helix chain 'A' and resid 311 through 337 removed outlier: 3.816A pdb=" N TYR A 315 " --> pdb=" O ASP A 311 " (cutoff:3.500A) removed outlier: 3.900A pdb=" N GLY A 335 " --> pdb=" O ALA A 331 " (cutoff:3.500A) removed outlier: 3.591A pdb=" N TYR A 336 " --> pdb=" O PHE A 332 " (cutoff:3.500A) Processing helix chain 'A' and resid 340 through 366 removed outlier: 5.568A pdb=" N GLU A 346 " --> pdb=" O ASP A 342 " (cutoff:3.500A) removed outlier: 4.331A pdb=" N LEU A 347 " --> pdb=" O LEU A 343 " (cutoff:3.500A) removed outlier: 3.696A pdb=" N LEU A 360 " --> pdb=" O ASN A 356 " (cutoff:3.500A) Processing helix chain 'A' and resid 368 through 397 removed outlier: 3.505A pdb=" N ILE A 389 " --> pdb=" O LEU A 385 " (cutoff:3.500A) removed outlier: 3.880A pdb=" N ASN A 397 " --> pdb=" O GLN A 393 " (cutoff:3.500A) Processing helix chain 'A' and resid 402 through 426 Processing helix chain 'A' and resid 434 through 455 removed outlier: 4.134A pdb=" N PHE A 439 " --> pdb=" O VAL A 435 " (cutoff:3.500A) removed outlier: 5.167A pdb=" N LEU A 440 " --> pdb=" O SER A 436 " (cutoff:3.500A) removed outlier: 3.502A pdb=" N ILE A 449 " --> pdb=" O TYR A 445 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'B' and resid 6 through 7 removed outlier: 3.530A pdb=" N TYR B 80 " --> pdb=" O SER B 71 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'B' and resid 11 through 13 removed outlier: 3.678A pdb=" N VAL B 93 " --> pdb=" O GLN B 39 " (cutoff:3.500A) removed outlier: 6.898A pdb=" N MET B 34 " --> pdb=" O ALA B 50 " (cutoff:3.500A) removed outlier: 4.711A pdb=" N ALA B 50 " --> pdb=" O MET B 34 " (cutoff:3.500A) removed outlier: 6.544A pdb=" N TRP B 36 " --> pdb=" O VAL B 48 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 11 through 13 268 hydrogen bonds defined for protein. 777 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: 1.14 Time building geometry restraints manager: 1.20 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: 773 1.33 - 1.45: 1090 1.45 - 1.57: 2194 1.57 - 1.69: 0 1.69 - 1.81: 32 Bond restraints: 4089 Sorted by residual: bond pdb=" CA TYR A 79 " pdb=" C TYR A 79 " ideal model delta sigma weight residual 1.523 1.484 0.040 1.34e-02 5.57e+03 8.71e+00 bond pdb=" CA SER A 40 " pdb=" C SER A 40 " ideal model delta sigma weight residual 1.523 1.485 0.038 1.41e-02 5.03e+03 7.22e+00 bond pdb=" CA LYS A 80 " pdb=" C LYS A 80 " ideal model delta sigma weight residual 1.522 1.488 0.034 1.26e-02 6.30e+03 7.15e+00 bond pdb=" CA SER B 85 " pdb=" C SER B 85 " ideal model delta sigma weight residual 1.532 1.507 0.025 9.60e-03 1.09e+04 7.00e+00 bond pdb=" C LYS A 80 " pdb=" O LYS A 80 " ideal model delta sigma weight residual 1.244 1.219 0.025 9.80e-03 1.04e+04 6.47e+00 ... (remaining 4084 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.30: 5507 2.30 - 4.61: 66 4.61 - 6.91: 4 6.91 - 9.22: 0 9.22 - 11.52: 1 Bond angle restraints: 5578 Sorted by residual: angle pdb=" N TYR A 79 " pdb=" CA TYR A 79 " pdb=" C TYR A 79 " ideal model delta sigma weight residual 110.80 122.32 -11.52 2.13e+00 2.20e-01 2.93e+01 angle pdb=" C ARG A 78 " pdb=" CA ARG A 78 " pdb=" CB ARG A 78 " ideal model delta sigma weight residual 111.39 116.63 -5.24 1.55e+00 4.16e-01 1.14e+01 angle pdb=" N ASN A 53 " pdb=" CA ASN A 53 " pdb=" C ASN A 53 " ideal model delta sigma weight residual 113.41 117.49 -4.08 1.22e+00 6.72e-01 1.12e+01 angle pdb=" N ASP A 427 " pdb=" CA ASP A 427 " pdb=" C ASP A 427 " ideal model delta sigma weight residual 110.23 114.94 -4.71 1.45e+00 4.76e-01 1.06e+01 angle pdb=" N ASN A 53 " pdb=" CA ASN A 53 " pdb=" CB ASN A 53 " ideal model delta sigma weight residual 110.47 105.99 4.48 1.46e+00 4.69e-01 9.43e+00 ... (remaining 5573 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 14.30: 2001 14.30 - 28.60: 249 28.60 - 42.90: 69 42.90 - 57.20: 26 57.20 - 71.50: 6 Dihedral angle restraints: 2351 sinusoidal: 876 harmonic: 1475 Sorted by residual: dihedral pdb=" C ARG A 78 " pdb=" N ARG A 78 " pdb=" CA ARG A 78 " pdb=" CB ARG A 78 " ideal model delta harmonic sigma weight residual -122.60 -133.68 11.08 0 2.50e+00 1.60e-01 1.96e+01 dihedral pdb=" CA TYR A 126 " pdb=" C TYR A 126 " pdb=" N ILE A 127 " pdb=" CA ILE A 127 " ideal model delta harmonic sigma weight residual -180.00 -160.20 -19.80 0 5.00e+00 4.00e-02 1.57e+01 dihedral pdb=" CB CYS B 22 " pdb=" SG CYS B 22 " pdb=" SG CYS B 96 " pdb=" CB CYS B 96 " ideal model delta sinusoidal sigma weight residual 93.00 63.36 29.64 1 1.00e+01 1.00e-02 1.26e+01 ... (remaining 2348 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.079: 595 0.079 - 0.157: 44 0.157 - 0.236: 1 0.236 - 0.314: 1 0.314 - 0.393: 1 Chirality restraints: 642 Sorted by residual: chirality pdb=" CA ARG A 78 " pdb=" N ARG A 78 " pdb=" C ARG A 78 " pdb=" CB ARG A 78 " both_signs ideal model delta sigma weight residual False 2.51 2.12 0.39 2.00e-01 2.50e+01 3.86e+00 chirality pdb=" CA TYR A 79 " pdb=" N TYR A 79 " pdb=" C TYR A 79 " pdb=" CB TYR A 79 " both_signs ideal model delta sigma weight residual False 2.51 2.21 0.30 2.00e-01 2.50e+01 2.30e+00 chirality pdb=" CA ASN A 45 " pdb=" N ASN A 45 " pdb=" C ASN A 45 " pdb=" CB ASN A 45 " both_signs ideal model delta sigma weight residual False 2.51 2.31 0.20 2.00e-01 2.50e+01 9.60e-01 ... (remaining 639 not shown) Planarity restraints: 680 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C2 NAG A 601 " 0.323 2.00e-02 2.50e+03 2.77e-01 9.58e+02 pdb=" C7 NAG A 601 " -0.081 2.00e-02 2.50e+03 pdb=" C8 NAG A 601 " 0.168 2.00e-02 2.50e+03 pdb=" N2 NAG A 601 " -0.488 2.00e-02 2.50e+03 pdb=" O7 NAG A 601 " 0.078 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ASP A 75 " 0.011 2.00e-02 2.50e+03 2.20e-02 4.83e+00 pdb=" C ASP A 75 " -0.038 2.00e-02 2.50e+03 pdb=" O ASP A 75 " 0.014 2.00e-02 2.50e+03 pdb=" N TYR A 76 " 0.013 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB PHE A 71 " -0.013 2.00e-02 2.50e+03 1.32e-02 3.04e+00 pdb=" CG PHE A 71 " 0.031 2.00e-02 2.50e+03 pdb=" CD1 PHE A 71 " -0.008 2.00e-02 2.50e+03 pdb=" CD2 PHE A 71 " -0.004 2.00e-02 2.50e+03 pdb=" CE1 PHE A 71 " -0.001 2.00e-02 2.50e+03 pdb=" CE2 PHE A 71 " -0.004 2.00e-02 2.50e+03 pdb=" CZ PHE A 71 " -0.001 2.00e-02 2.50e+03 ... (remaining 677 not shown) Histogram of nonbonded interaction distances: 2.27 - 2.80: 1143 2.80 - 3.32: 3886 3.32 - 3.85: 6611 3.85 - 4.37: 8178 4.37 - 4.90: 13988 Nonbonded interactions: 33806 Sorted by model distance: nonbonded pdb=" O GLN A 428 " pdb=" OE1 GLN A 428 " model vdw 2.272 3.040 nonbonded pdb=" O LEU A 349 " pdb=" OG SER A 353 " model vdw 2.312 3.040 nonbonded pdb=" O ARG A 144 " pdb=" OG1 THR A 147 " model vdw 2.354 3.040 nonbonded pdb=" O TRP A 285 " pdb=" OG1 THR A 289 " model vdw 2.359 3.040 nonbonded pdb=" OG SER A 309 " pdb=" OD1 ASP A 311 " model vdw 2.361 3.040 ... (remaining 33801 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: 4.460 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: 0.160 Check model and map are aligned: 0.030 Set scattering table: 0.050 Process input model: 14.630 Find NCS groups from input model: 0.030 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.840 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 22.230 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7848 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 : 0.006 0.040 4089 Z= 0.376 Angle : 0.649 11.523 5578 Z= 0.384 Chirality : 0.047 0.393 642 Planarity : 0.011 0.277 679 Dihedral : 14.848 71.500 1408 Min Nonbonded Distance : 2.272 Molprobity Statistics. All-atom Clashscore : 7.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.23 % Favored : 95.77 % Rotamer: Outliers : 0.24 % Allowed : 19.15 % Favored : 80.61 % Cbeta Deviations : 0.21 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.73 (0.37), residues: 496 helix: 0.27 (0.30), residues: 284 sheet: -2.99 (0.76), residues: 33 loop : -1.05 (0.47), residues: 179 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP A 94 HIS 0.002 0.001 HIS A 135 PHE 0.031 0.002 PHE A 71 TYR 0.015 0.002 TYR B 94 ARG 0.003 0.001 ARG A 277 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 992 Ramachandran restraints generated. 496 Oldfield, 0 Emsley, 496 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 992 Ramachandran restraints generated. 496 Oldfield, 0 Emsley, 496 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 73 residues out of total 423 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 72 time to evaluate : 0.437 Fit side-chains REVERT: B 80 TYR cc_start: 0.7940 (m-80) cc_final: 0.7425 (m-80) outliers start: 1 outliers final: 1 residues processed: 73 average time/residue: 0.1958 time to fit residues: 17.4988 Evaluate side-chains 67 residues out of total 423 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 66 time to evaluate : 0.444 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 97 LEU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 49 random chunks: chunk 41 optimal weight: 1.9990 chunk 37 optimal weight: 0.7980 chunk 20 optimal weight: 0.9990 chunk 12 optimal weight: 0.4980 chunk 25 optimal weight: 0.5980 chunk 19 optimal weight: 0.2980 chunk 38 optimal weight: 0.5980 chunk 14 optimal weight: 0.9980 chunk 23 optimal weight: 0.9980 chunk 28 optimal weight: 0.5980 chunk 44 optimal weight: 0.7980 overall best weight: 0.5180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 294 GLN A 397 ASN A 428 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7781 moved from start: 0.1470 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 4089 Z= 0.248 Angle : 0.594 8.263 5578 Z= 0.312 Chirality : 0.043 0.203 642 Planarity : 0.004 0.029 679 Dihedral : 4.978 42.208 573 Min Nonbonded Distance : 2.516 Molprobity Statistics. All-atom Clashscore : 4.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.42 % Favored : 97.58 % Rotamer: Outliers : 2.36 % Allowed : 16.31 % Favored : 81.32 % 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: 0.43 (0.38), residues: 496 helix: 1.26 (0.30), residues: 298 sheet: -2.16 (0.66), residues: 45 loop : -0.74 (0.52), residues: 153 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.002 TRP A 94 HIS 0.001 0.001 HIS A 364 PHE 0.021 0.002 PHE A 71 TYR 0.014 0.002 TYR A 14 ARG 0.002 0.000 ARG B 38 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 992 Ramachandran restraints generated. 496 Oldfield, 0 Emsley, 496 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 992 Ramachandran restraints generated. 496 Oldfield, 0 Emsley, 496 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 86 residues out of total 423 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 76 time to evaluate : 0.444 Fit side-chains revert: symmetry clash REVERT: B 80 TYR cc_start: 0.7724 (m-80) cc_final: 0.7161 (m-80) REVERT: A 66 LEU cc_start: 0.8755 (OUTLIER) cc_final: 0.8487 (mm) REVERT: A 320 GLU cc_start: 0.7189 (mm-30) cc_final: 0.6678 (mm-30) outliers start: 10 outliers final: 4 residues processed: 82 average time/residue: 0.1516 time to fit residues: 15.8730 Evaluate side-chains 72 residues out of total 423 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 67 time to evaluate : 0.442 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 71 SER Chi-restraints excluded: chain A residue 66 LEU Chi-restraints excluded: chain A residue 134 GLU Chi-restraints excluded: chain A residue 400 VAL Chi-restraints excluded: chain A residue 401 GLU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 49 random chunks: chunk 24 optimal weight: 0.8980 chunk 13 optimal weight: 0.9990 chunk 37 optimal weight: 2.9990 chunk 30 optimal weight: 0.9980 chunk 12 optimal weight: 0.5980 chunk 44 optimal weight: 0.5980 chunk 48 optimal weight: 0.9990 chunk 39 optimal weight: 0.6980 chunk 15 optimal weight: 0.9980 chunk 35 optimal weight: 2.9990 chunk 33 optimal weight: 0.9990 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 294 GLN A 300 GLN A 316 ASN A 428 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7807 moved from start: 0.1600 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.050 4089 Z= 0.318 Angle : 0.612 8.927 5578 Z= 0.318 Chirality : 0.044 0.202 642 Planarity : 0.004 0.032 679 Dihedral : 4.568 19.038 571 Min Nonbonded Distance : 2.437 Molprobity Statistics. All-atom Clashscore : 5.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.02 % Favored : 96.98 % Rotamer: Outliers : 2.84 % Allowed : 17.26 % Favored : 79.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.64 (0.38), residues: 496 helix: 1.37 (0.30), residues: 299 sheet: -1.67 (0.69), residues: 45 loop : -0.69 (0.52), residues: 152 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.002 TRP A 94 HIS 0.001 0.001 HIS A 135 PHE 0.024 0.002 PHE A 71 TYR 0.014 0.002 TYR B 94 ARG 0.002 0.000 ARG B 38 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 992 Ramachandran restraints generated. 496 Oldfield, 0 Emsley, 496 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 992 Ramachandran restraints generated. 496 Oldfield, 0 Emsley, 496 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 80 residues out of total 423 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 68 time to evaluate : 0.444 Fit side-chains REVERT: B 80 TYR cc_start: 0.7651 (m-80) cc_final: 0.7147 (m-80) REVERT: A 66 LEU cc_start: 0.8752 (OUTLIER) cc_final: 0.8476 (mm) outliers start: 12 outliers final: 8 residues processed: 77 average time/residue: 0.1475 time to fit residues: 14.6504 Evaluate side-chains 73 residues out of total 423 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 64 time to evaluate : 0.475 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 71 SER Chi-restraints excluded: chain B residue 111 LEU Chi-restraints excluded: chain A residue 66 LEU Chi-restraints excluded: chain A residue 116 VAL Chi-restraints excluded: chain A residue 134 GLU Chi-restraints excluded: chain A residue 185 LEU Chi-restraints excluded: chain A residue 312 SER Chi-restraints excluded: chain A residue 400 VAL Chi-restraints excluded: chain A residue 401 GLU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 49 random chunks: chunk 23 optimal weight: 0.4980 chunk 4 optimal weight: 0.9990 chunk 21 optimal weight: 1.9990 chunk 29 optimal weight: 0.7980 chunk 44 optimal weight: 0.9990 chunk 47 optimal weight: 0.9980 chunk 42 optimal weight: 0.5980 chunk 12 optimal weight: 0.6980 chunk 39 optimal weight: 0.5980 chunk 26 optimal weight: 3.9990 chunk 0 optimal weight: 1.9990 overall best weight: 0.6380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 428 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7791 moved from start: 0.1771 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.047 4089 Z= 0.275 Angle : 0.578 8.936 5578 Z= 0.300 Chirality : 0.042 0.182 642 Planarity : 0.004 0.033 679 Dihedral : 4.488 19.503 571 Min Nonbonded Distance : 2.458 Molprobity Statistics. All-atom Clashscore : 4.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.82 % Favored : 97.18 % Rotamer: Outliers : 2.84 % Allowed : 16.08 % Favored : 81.09 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.94 (0.38), residues: 496 helix: 1.50 (0.30), residues: 299 sheet: -0.86 (0.69), residues: 52 loop : -0.54 (0.55), residues: 145 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.002 TRP A 94 HIS 0.001 0.001 HIS A 135 PHE 0.023 0.002 PHE A 71 TYR 0.013 0.002 TYR A 14 ARG 0.001 0.000 ARG B 67 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 992 Ramachandran restraints generated. 496 Oldfield, 0 Emsley, 496 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 992 Ramachandran restraints generated. 496 Oldfield, 0 Emsley, 496 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 78 residues out of total 423 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 66 time to evaluate : 0.417 Fit side-chains REVERT: B 80 TYR cc_start: 0.7548 (m-80) cc_final: 0.7018 (m-80) REVERT: A 66 LEU cc_start: 0.8734 (OUTLIER) cc_final: 0.8445 (mm) REVERT: A 320 GLU cc_start: 0.7084 (mm-30) cc_final: 0.6643 (mm-30) outliers start: 12 outliers final: 9 residues processed: 76 average time/residue: 0.1540 time to fit residues: 14.9673 Evaluate side-chains 75 residues out of total 423 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 65 time to evaluate : 0.429 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 71 SER Chi-restraints excluded: chain B residue 111 LEU Chi-restraints excluded: chain A residue 21 LEU Chi-restraints excluded: chain A residue 66 LEU Chi-restraints excluded: chain A residue 116 VAL Chi-restraints excluded: chain A residue 134 GLU Chi-restraints excluded: chain A residue 185 LEU Chi-restraints excluded: chain A residue 312 SER Chi-restraints excluded: chain A residue 344 LEU Chi-restraints excluded: chain A residue 400 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 49 random chunks: chunk 35 optimal weight: 2.9990 chunk 19 optimal weight: 0.9990 chunk 40 optimal weight: 0.9980 chunk 32 optimal weight: 2.9990 chunk 0 optimal weight: 1.9990 chunk 24 optimal weight: 0.7980 chunk 42 optimal weight: 0.6980 chunk 11 optimal weight: 0.6980 chunk 15 optimal weight: 1.9990 chunk 9 optimal weight: 0.6980 chunk 27 optimal weight: 1.9990 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 316 ASN A 428 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7805 moved from start: 0.1786 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.052 4089 Z= 0.318 Angle : 0.601 9.134 5578 Z= 0.311 Chirality : 0.044 0.186 642 Planarity : 0.004 0.034 679 Dihedral : 4.551 19.925 571 Min Nonbonded Distance : 2.397 Molprobity Statistics. All-atom Clashscore : 4.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.82 % Favored : 97.18 % Rotamer: Outliers : 4.02 % Allowed : 15.37 % Favored : 80.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.91 (0.38), residues: 496 helix: 1.43 (0.29), residues: 299 sheet: -0.74 (0.70), residues: 52 loop : -0.48 (0.55), residues: 145 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.002 TRP A 94 HIS 0.001 0.001 HIS A 135 PHE 0.025 0.002 PHE A 71 TYR 0.014 0.002 TYR B 94 ARG 0.001 0.000 ARG B 112 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 992 Ramachandran restraints generated. 496 Oldfield, 0 Emsley, 496 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 992 Ramachandran restraints generated. 496 Oldfield, 0 Emsley, 496 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 83 residues out of total 423 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 66 time to evaluate : 0.443 Fit side-chains REVERT: B 80 TYR cc_start: 0.7593 (m-80) cc_final: 0.7070 (m-80) REVERT: B 100 GLN cc_start: 0.8187 (mt0) cc_final: 0.7979 (mt0) REVERT: A 66 LEU cc_start: 0.8743 (OUTLIER) cc_final: 0.8457 (mm) REVERT: A 113 TYR cc_start: 0.7811 (t80) cc_final: 0.7606 (t80) REVERT: A 320 GLU cc_start: 0.7080 (mm-30) cc_final: 0.6634 (mm-30) outliers start: 17 outliers final: 15 residues processed: 79 average time/residue: 0.1497 time to fit residues: 15.1954 Evaluate side-chains 79 residues out of total 423 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 63 time to evaluate : 0.368 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 33 ASP Chi-restraints excluded: chain B residue 71 SER Chi-restraints excluded: chain B residue 111 LEU Chi-restraints excluded: chain A residue 21 LEU Chi-restraints excluded: chain A residue 66 LEU Chi-restraints excluded: chain A residue 105 THR Chi-restraints excluded: chain A residue 116 VAL Chi-restraints excluded: chain A residue 134 GLU Chi-restraints excluded: chain A residue 157 LEU Chi-restraints excluded: chain A residue 168 SER Chi-restraints excluded: chain A residue 185 LEU Chi-restraints excluded: chain A residue 312 SER Chi-restraints excluded: chain A residue 339 VAL Chi-restraints excluded: chain A residue 344 LEU Chi-restraints excluded: chain A residue 400 VAL Chi-restraints excluded: chain A residue 401 GLU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 49 random chunks: chunk 11 optimal weight: 0.5980 chunk 47 optimal weight: 0.9990 chunk 39 optimal weight: 0.3980 chunk 21 optimal weight: 0.9980 chunk 3 optimal weight: 1.9990 chunk 15 optimal weight: 2.9990 chunk 24 optimal weight: 0.5980 chunk 45 optimal weight: 0.5980 chunk 5 optimal weight: 1.9990 chunk 27 optimal weight: 1.9990 chunk 34 optimal weight: 0.5980 overall best weight: 0.5580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 428 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7782 moved from start: 0.1920 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.046 4089 Z= 0.249 Angle : 0.567 9.051 5578 Z= 0.293 Chirality : 0.042 0.147 642 Planarity : 0.004 0.033 679 Dihedral : 4.451 20.079 571 Min Nonbonded Distance : 2.395 Molprobity Statistics. All-atom Clashscore : 4.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.02 % Favored : 96.98 % Rotamer: Outliers : 3.78 % Allowed : 16.78 % Favored : 79.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.11 (0.38), residues: 496 helix: 1.56 (0.30), residues: 299 sheet: -0.62 (0.70), residues: 52 loop : -0.36 (0.55), residues: 145 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.002 TRP A 94 HIS 0.002 0.001 HIS A 364 PHE 0.022 0.002 PHE A 71 TYR 0.014 0.002 TYR A 79 ARG 0.001 0.000 ARG A 456 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 992 Ramachandran restraints generated. 496 Oldfield, 0 Emsley, 496 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 992 Ramachandran restraints generated. 496 Oldfield, 0 Emsley, 496 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 82 residues out of total 423 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 66 time to evaluate : 0.452 Fit side-chains REVERT: B 80 TYR cc_start: 0.7514 (m-80) cc_final: 0.7029 (m-80) REVERT: B 100 GLN cc_start: 0.8181 (mt0) cc_final: 0.7976 (mt0) REVERT: A 66 LEU cc_start: 0.8718 (OUTLIER) cc_final: 0.8438 (mm) REVERT: A 320 GLU cc_start: 0.7037 (mm-30) cc_final: 0.6602 (mm-30) outliers start: 16 outliers final: 12 residues processed: 79 average time/residue: 0.1524 time to fit residues: 15.4510 Evaluate side-chains 78 residues out of total 423 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 65 time to evaluate : 0.452 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 71 SER Chi-restraints excluded: chain B residue 111 LEU Chi-restraints excluded: chain A residue 66 LEU Chi-restraints excluded: chain A residue 105 THR Chi-restraints excluded: chain A residue 116 VAL Chi-restraints excluded: chain A residue 134 GLU Chi-restraints excluded: chain A residue 168 SER Chi-restraints excluded: chain A residue 185 LEU Chi-restraints excluded: chain A residue 312 SER Chi-restraints excluded: chain A residue 339 VAL Chi-restraints excluded: chain A residue 344 LEU Chi-restraints excluded: chain A residue 400 VAL Chi-restraints excluded: chain A residue 401 GLU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 49 random chunks: chunk 26 optimal weight: 1.9990 chunk 39 optimal weight: 0.9990 chunk 47 optimal weight: 0.7980 chunk 29 optimal weight: 0.7980 chunk 28 optimal weight: 0.5980 chunk 21 optimal weight: 0.0470 chunk 18 optimal weight: 0.1980 chunk 14 optimal weight: 0.4980 chunk 9 optimal weight: 0.7980 chunk 30 optimal weight: 0.6980 chunk 32 optimal weight: 1.9990 overall best weight: 0.4078 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 316 ASN A 428 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7757 moved from start: 0.2094 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 4089 Z= 0.206 Angle : 0.542 9.062 5578 Z= 0.279 Chirality : 0.040 0.132 642 Planarity : 0.004 0.032 679 Dihedral : 4.277 19.819 571 Min Nonbonded Distance : 2.382 Molprobity Statistics. All-atom Clashscore : 4.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.42 % Favored : 97.58 % Rotamer: Outliers : 3.55 % Allowed : 17.26 % Favored : 79.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.42 (0.39), residues: 496 helix: 1.78 (0.30), residues: 299 sheet: -0.41 (0.71), residues: 52 loop : -0.19 (0.56), residues: 145 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.002 TRP A 94 HIS 0.002 0.001 HIS A 364 PHE 0.020 0.002 PHE A 71 TYR 0.014 0.001 TYR A 79 ARG 0.001 0.000 ARG A 456 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 992 Ramachandran restraints generated. 496 Oldfield, 0 Emsley, 496 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 992 Ramachandran restraints generated. 496 Oldfield, 0 Emsley, 496 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 82 residues out of total 423 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 67 time to evaluate : 0.448 Fit side-chains revert: symmetry clash REVERT: B 80 TYR cc_start: 0.7365 (m-80) cc_final: 0.6931 (m-80) REVERT: B 100 GLN cc_start: 0.8265 (mt0) cc_final: 0.8062 (mt0) REVERT: A 66 LEU cc_start: 0.8706 (OUTLIER) cc_final: 0.8406 (mm) REVERT: A 320 GLU cc_start: 0.7014 (mm-30) cc_final: 0.6593 (mm-30) outliers start: 15 outliers final: 12 residues processed: 80 average time/residue: 0.1652 time to fit residues: 16.8180 Evaluate side-chains 82 residues out of total 423 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 69 time to evaluate : 0.443 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 33 ASP Chi-restraints excluded: chain B residue 71 SER Chi-restraints excluded: chain B residue 111 LEU Chi-restraints excluded: chain A residue 21 LEU Chi-restraints excluded: chain A residue 66 LEU Chi-restraints excluded: chain A residue 105 THR Chi-restraints excluded: chain A residue 116 VAL Chi-restraints excluded: chain A residue 134 GLU Chi-restraints excluded: chain A residue 185 LEU Chi-restraints excluded: chain A residue 312 SER Chi-restraints excluded: chain A residue 344 LEU Chi-restraints excluded: chain A residue 400 VAL Chi-restraints excluded: chain A residue 401 GLU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 49 random chunks: chunk 23 optimal weight: 0.5980 chunk 4 optimal weight: 0.4980 chunk 37 optimal weight: 0.9990 chunk 42 optimal weight: 0.9990 chunk 45 optimal weight: 1.9990 chunk 41 optimal weight: 1.9990 chunk 44 optimal weight: 0.5980 chunk 26 optimal weight: 1.9990 chunk 19 optimal weight: 0.0870 chunk 34 optimal weight: 0.2980 chunk 13 optimal weight: 0.0570 overall best weight: 0.3076 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 316 ASN A 428 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7739 moved from start: 0.2248 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 4089 Z= 0.176 Angle : 0.538 8.454 5578 Z= 0.273 Chirality : 0.040 0.130 642 Planarity : 0.004 0.033 679 Dihedral : 4.160 19.409 571 Min Nonbonded Distance : 2.350 Molprobity Statistics. All-atom Clashscore : 5.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.42 % Favored : 97.58 % Rotamer: Outliers : 2.84 % Allowed : 18.20 % Favored : 78.96 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.65 (0.39), residues: 496 helix: 1.93 (0.30), residues: 299 sheet: -0.27 (0.71), residues: 52 loop : -0.04 (0.56), residues: 145 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.002 TRP A 94 HIS 0.003 0.001 HIS A 364 PHE 0.019 0.001 PHE A 71 TYR 0.014 0.001 TYR A 79 ARG 0.002 0.000 ARG A 456 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 992 Ramachandran restraints generated. 496 Oldfield, 0 Emsley, 496 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 992 Ramachandran restraints generated. 496 Oldfield, 0 Emsley, 496 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 79 residues out of total 423 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 67 time to evaluate : 0.439 Fit side-chains revert: symmetry clash REVERT: B 38 ARG cc_start: 0.7560 (ptt180) cc_final: 0.7358 (ptt180) REVERT: B 80 TYR cc_start: 0.7311 (m-80) cc_final: 0.6915 (m-80) REVERT: A 66 LEU cc_start: 0.8694 (OUTLIER) cc_final: 0.8418 (mm) REVERT: A 271 GLU cc_start: 0.4676 (pm20) cc_final: 0.3980 (pt0) REVERT: A 320 GLU cc_start: 0.6991 (mm-30) cc_final: 0.6579 (mm-30) outliers start: 12 outliers final: 11 residues processed: 76 average time/residue: 0.1596 time to fit residues: 15.3031 Evaluate side-chains 79 residues out of total 423 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 67 time to evaluate : 0.396 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 33 ASP Chi-restraints excluded: chain B residue 71 SER Chi-restraints excluded: chain A residue 21 LEU Chi-restraints excluded: chain A residue 66 LEU Chi-restraints excluded: chain A residue 116 VAL Chi-restraints excluded: chain A residue 134 GLU Chi-restraints excluded: chain A residue 185 LEU Chi-restraints excluded: chain A residue 312 SER Chi-restraints excluded: chain A residue 339 VAL Chi-restraints excluded: chain A residue 344 LEU Chi-restraints excluded: chain A residue 400 VAL Chi-restraints excluded: chain A residue 401 GLU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 49 random chunks: chunk 39 optimal weight: 0.9980 chunk 41 optimal weight: 2.9990 chunk 43 optimal weight: 1.9990 chunk 28 optimal weight: 0.9980 chunk 46 optimal weight: 0.7980 chunk 22 optimal weight: 0.9980 chunk 32 optimal weight: 1.9990 chunk 48 optimal weight: 1.9990 chunk 44 optimal weight: 0.6980 chunk 38 optimal weight: 0.5980 chunk 4 optimal weight: 0.9990 overall best weight: 0.8180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 100 GLN A 316 ASN A 428 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7806 moved from start: 0.2015 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.053 4089 Z= 0.329 Angle : 0.618 9.715 5578 Z= 0.316 Chirality : 0.044 0.167 642 Planarity : 0.004 0.032 679 Dihedral : 4.468 19.160 571 Min Nonbonded Distance : 2.308 Molprobity Statistics. All-atom Clashscore : 5.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.82 % Favored : 97.18 % Rotamer: Outliers : 3.55 % Allowed : 17.97 % Favored : 78.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.21 (0.38), residues: 496 helix: 1.59 (0.30), residues: 298 sheet: -0.44 (0.70), residues: 52 loop : -0.23 (0.54), residues: 146 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP A 284 HIS 0.002 0.001 HIS A 135 PHE 0.025 0.002 PHE A 71 TYR 0.014 0.002 TYR B 94 ARG 0.002 0.000 ARG A 456 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 992 Ramachandran restraints generated. 496 Oldfield, 0 Emsley, 496 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 992 Ramachandran restraints generated. 496 Oldfield, 0 Emsley, 496 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 82 residues out of total 423 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 67 time to evaluate : 0.410 Fit side-chains REVERT: B 80 TYR cc_start: 0.7548 (m-80) cc_final: 0.7068 (m-80) REVERT: A 66 LEU cc_start: 0.8723 (OUTLIER) cc_final: 0.8432 (mm) REVERT: A 271 GLU cc_start: 0.4696 (pm20) cc_final: 0.3981 (pt0) REVERT: A 320 GLU cc_start: 0.7027 (mm-30) cc_final: 0.6578 (mm-30) outliers start: 15 outliers final: 14 residues processed: 79 average time/residue: 0.1660 time to fit residues: 16.4809 Evaluate side-chains 81 residues out of total 423 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 66 time to evaluate : 0.468 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 33 ASP Chi-restraints excluded: chain B residue 71 SER Chi-restraints excluded: chain B residue 111 LEU Chi-restraints excluded: chain A residue 21 LEU Chi-restraints excluded: chain A residue 66 LEU Chi-restraints excluded: chain A residue 105 THR Chi-restraints excluded: chain A residue 116 VAL Chi-restraints excluded: chain A residue 134 GLU Chi-restraints excluded: chain A residue 168 SER Chi-restraints excluded: chain A residue 185 LEU Chi-restraints excluded: chain A residue 312 SER Chi-restraints excluded: chain A residue 339 VAL Chi-restraints excluded: chain A residue 344 LEU Chi-restraints excluded: chain A residue 400 VAL Chi-restraints excluded: chain A residue 401 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 49 random chunks: chunk 30 optimal weight: 0.9980 chunk 23 optimal weight: 0.7980 chunk 41 optimal weight: 2.9990 chunk 11 optimal weight: 0.9990 chunk 35 optimal weight: 0.9990 chunk 5 optimal weight: 0.9980 chunk 10 optimal weight: 0.9980 chunk 38 optimal weight: 0.6980 chunk 16 optimal weight: 0.8980 chunk 39 optimal weight: 0.9990 chunk 4 optimal weight: 0.0980 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 100 GLN A 316 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7795 moved from start: 0.2035 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.051 4089 Z= 0.294 Angle : 0.605 9.614 5578 Z= 0.309 Chirality : 0.043 0.141 642 Planarity : 0.004 0.031 679 Dihedral : 4.457 19.954 571 Min Nonbonded Distance : 2.558 Molprobity Statistics. All-atom Clashscore : 5.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.02 % Favored : 96.98 % Rotamer: Outliers : 3.55 % Allowed : 18.20 % Favored : 78.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.22 (0.38), residues: 496 helix: 1.64 (0.30), residues: 297 sheet: -0.48 (0.72), residues: 52 loop : -0.30 (0.54), residues: 147 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP A 94 HIS 0.001 0.001 HIS A 135 PHE 0.025 0.002 PHE A 71 TYR 0.015 0.002 TYR A 445 ARG 0.002 0.000 ARG A 456 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 992 Ramachandran restraints generated. 496 Oldfield, 0 Emsley, 496 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 992 Ramachandran restraints generated. 496 Oldfield, 0 Emsley, 496 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 78 residues out of total 423 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 63 time to evaluate : 0.433 Fit side-chains revert: symmetry clash REVERT: B 80 TYR cc_start: 0.7555 (m-80) cc_final: 0.7074 (m-80) REVERT: A 66 LEU cc_start: 0.8720 (OUTLIER) cc_final: 0.8422 (mm) REVERT: A 271 GLU cc_start: 0.4713 (pm20) cc_final: 0.3989 (pt0) REVERT: A 320 GLU cc_start: 0.7057 (mm-30) cc_final: 0.6633 (mm-30) outliers start: 15 outliers final: 14 residues processed: 75 average time/residue: 0.1615 time to fit residues: 15.4043 Evaluate side-chains 80 residues out of total 423 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 65 time to evaluate : 0.511 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 33 ASP Chi-restraints excluded: chain B residue 71 SER Chi-restraints excluded: chain B residue 111 LEU Chi-restraints excluded: chain A residue 21 LEU Chi-restraints excluded: chain A residue 66 LEU Chi-restraints excluded: chain A residue 105 THR Chi-restraints excluded: chain A residue 116 VAL Chi-restraints excluded: chain A residue 134 GLU Chi-restraints excluded: chain A residue 168 SER Chi-restraints excluded: chain A residue 185 LEU Chi-restraints excluded: chain A residue 312 SER Chi-restraints excluded: chain A residue 339 VAL Chi-restraints excluded: chain A residue 344 LEU Chi-restraints excluded: chain A residue 400 VAL Chi-restraints excluded: chain A residue 401 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 49 random chunks: chunk 7 optimal weight: 1.9990 chunk 34 optimal weight: 2.9990 chunk 2 optimal weight: 0.7980 chunk 28 optimal weight: 0.5980 chunk 44 optimal weight: 0.9980 chunk 26 optimal weight: 1.9990 chunk 33 optimal weight: 0.5980 chunk 1 optimal weight: 0.5980 chunk 31 optimal weight: 1.9990 chunk 29 optimal weight: 0.0970 chunk 19 optimal weight: 0.9990 overall best weight: 0.5378 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 100 GLN A 316 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3615 r_free = 0.3615 target = 0.143991 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3469 r_free = 0.3469 target = 0.131850 restraints weight = 5031.976| |-----------------------------------------------------------------------------| r_work (start): 0.3464 rms_B_bonded: 1.01 r_work: 0.3372 rms_B_bonded: 1.80 restraints_weight: 0.5000 r_work: 0.3269 rms_B_bonded: 3.21 restraints_weight: 0.2500 r_work (final): 0.3269 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8216 moved from start: 0.2126 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 4089 Z= 0.245 Angle : 0.573 9.329 5578 Z= 0.292 Chirality : 0.041 0.134 642 Planarity : 0.004 0.032 679 Dihedral : 4.368 19.870 571 Min Nonbonded Distance : 2.595 Molprobity Statistics. All-atom Clashscore : 5.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.82 % Favored : 97.18 % Rotamer: Outliers : 3.31 % Allowed : 18.44 % Favored : 78.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.36 (0.39), residues: 496 helix: 1.75 (0.30), residues: 297 sheet: -0.47 (0.72), residues: 52 loop : -0.21 (0.55), residues: 147 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP A 94 HIS 0.001 0.001 HIS A 364 PHE 0.022 0.002 PHE A 71 TYR 0.015 0.002 TYR A 445 ARG 0.002 0.000 ARG A 456 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1346.07 seconds wall clock time: 29 minutes 33.35 seconds (1773.35 seconds total)