Starting phenix.real_space_refine on Thu Nov 14 03:56:48 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8sdu_40352/11_2024/8sdu_40352.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8sdu_40352/11_2024/8sdu_40352.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.05 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8sdu_40352/11_2024/8sdu_40352.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8sdu_40352/11_2024/8sdu_40352.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8sdu_40352/11_2024/8sdu_40352.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8sdu_40352/11_2024/8sdu_40352.cif" } resolution = 2.05 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= 0.008 sd= 0.092 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 2520 2.51 5 N 653 2.21 5 O 739 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 6 residue(s): 0.01s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5513/modules/chem_data/mon_lib" Total number of atoms: 3942 Number of models: 1 Model: "" Number of chains: 2 Chain: "A" Number of atoms: 3872 Number of conformers: 1 Conformer: "" Number of residues, atoms: 500, 3872 Classifications: {'peptide': 500} Link IDs: {'PTRANS': 26, 'TRANS': 473} Chain breaks: 3 Chain: "A" Number of atoms: 70 Number of conformers: 1 Conformer: "" Number of residues, atoms: 70, 70 Classifications: {'water': 70} Link IDs: {None: 69} Time building chain proxies: 3.22, per 1000 atoms: 0.82 Number of scatterers: 3942 At special positions: 0 Unit cell: (76.9133, 68.6133, 97.9399, 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 739 8.00 N 653 7.00 C 2520 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=2, symmetry=0 Simple disulfide: pdb=" SG CYS A 49 " - pdb=" SG CYS A 105 " distance=2.03 Simple disulfide: pdb=" SG CYS A 78 " - pdb=" SG CYS A 128 " 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: 1.06 Conformation dependent library (CDL) restraints added in 559.2 milliseconds 984 Ramachandran restraints generated. 492 Oldfield, 0 Emsley, 492 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 928 Finding SS restraints... Secondary structure from input PDB file: 28 helices and 2 sheets defined 81.0% alpha, 1.2% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.32 Creating SS restraints... Processing helix chain 'A' and resid 2 through 10 removed outlier: 3.559A pdb=" N LEU A 6 " --> pdb=" O ALA A 2 " (cutoff:3.500A) Processing helix chain 'A' and resid 14 through 26 Processing helix chain 'A' and resid 27 through 36 removed outlier: 4.059A pdb=" N ALA A 32 " --> pdb=" O LEU A 28 " (cutoff:3.500A) removed outlier: 4.567A pdb=" N SER A 33 " --> pdb=" O LEU A 29 " (cutoff:3.500A) Processing helix chain 'A' and resid 37 through 42 Processing helix chain 'A' and resid 119 through 125 Processing helix chain 'A' and resid 127 through 130 Processing helix chain 'A' and resid 131 through 160 removed outlier: 4.185A pdb=" N GLN A 135 " --> pdb=" O ARG A 131 " (cutoff:3.500A) removed outlier: 3.636A pdb=" N ASP A 157 " --> pdb=" O GLY A 153 " (cutoff:3.500A) Processing helix chain 'A' and resid 160 through 181 Processing helix chain 'A' and resid 184 through 213 removed outlier: 3.640A pdb=" N MET A 207 " --> pdb=" O ALA A 203 " (cutoff:3.500A) Processing helix chain 'A' and resid 214 through 217 removed outlier: 6.055A pdb=" N HIS A 217 " --> pdb=" O MET A 214 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 214 through 217' Processing helix chain 'A' and resid 218 through 244 removed outlier: 3.613A pdb=" N VAL A 222 " --> pdb=" O THR A 218 " (cutoff:3.500A) removed outlier: 3.542A pdb=" N GLY A 223 " --> pdb=" O ARG A 219 " (cutoff:3.500A) removed outlier: 3.801A pdb=" N PHE A 235 " --> pdb=" O SER A 231 " (cutoff:3.500A) Processing helix chain 'A' and resid 246 through 256 Processing helix chain 'A' and resid 256 through 266 removed outlier: 3.936A pdb=" N ILE A 260 " --> pdb=" O VAL A 256 " (cutoff:3.500A) removed outlier: 4.009A pdb=" N TRP A 266 " --> pdb=" O PHE A 262 " (cutoff:3.500A) Processing helix chain 'A' and resid 271 through 278 Processing helix chain 'A' and resid 280 through 296 Processing helix chain 'A' and resid 297 through 303 Processing helix chain 'A' and resid 305 through 313 Processing helix chain 'A' and resid 327 through 332 Processing helix chain 'A' and resid 332 through 358 removed outlier: 3.914A pdb=" N LEU A 338 " --> pdb=" O THR A 334 " (cutoff:3.500A) Processing helix chain 'A' and resid 359 through 364 removed outlier: 3.600A pdb=" N PHE A 363 " --> pdb=" O LEU A 360 " (cutoff:3.500A) removed outlier: 3.973A pdb=" N GLY A 364 " --> pdb=" O GLN A 361 " (cutoff:3.500A) Processing helix chain 'A' and resid 366 through 392 removed outlier: 3.866A pdb=" N ASP A 378 " --> pdb=" O PHE A 374 " (cutoff:3.500A) removed outlier: 4.533A pdb=" N LEU A 379 " --> pdb=" O GLY A 375 " (cutoff:3.500A) Proline residue: A 380 - end of helix Processing helix chain 'A' and resid 393 through 415 removed outlier: 3.520A pdb=" N ILE A 414 " --> pdb=" O LEU A 410 " (cutoff:3.500A) Processing helix chain 'A' and resid 419 through 449 removed outlier: 3.650A pdb=" N LEU A 443 " --> pdb=" O ASN A 439 " (cutoff:3.500A) Processing helix chain 'A' and resid 453 through 477 Proline residue: A 473 - end of helix Processing helix chain 'A' and resid 478 through 481 Processing helix chain 'A' and resid 484 through 501 Proline residue: A 494 - end of helix Processing helix chain 'A' and resid 502 through 504 No H-bonds generated for 'chain 'A' and resid 502 through 504' Processing helix chain 'A' and resid 515 through 524 Processing sheet with id=AA1, first strand: chain 'A' and resid 47 through 49 Processing sheet with id=AA2, first strand: chain 'A' and resid 80 through 81 274 hydrogen bonds defined for protein. 810 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: 1.20 Time building geometry restraints manager: 1.23 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.34: 1215 1.34 - 1.46: 935 1.46 - 1.58: 1767 1.58 - 1.70: 0 1.70 - 1.81: 47 Bond restraints: 3964 Sorted by residual: bond pdb=" CB ARG A 158 " pdb=" CG ARG A 158 " ideal model delta sigma weight residual 1.520 1.551 -0.031 3.00e-02 1.11e+03 1.05e+00 bond pdb=" CA ALA A 26 " pdb=" C ALA A 26 " ideal model delta sigma weight residual 1.522 1.534 -0.013 1.29e-02 6.01e+03 9.97e-01 bond pdb=" C PRO A 27 " pdb=" O PRO A 27 " ideal model delta sigma weight residual 1.237 1.249 -0.012 1.32e-02 5.74e+03 8.45e-01 bond pdb=" N PRO A 27 " pdb=" CA PRO A 27 " ideal model delta sigma weight residual 1.471 1.482 -0.012 1.32e-02 5.74e+03 7.83e-01 bond pdb=" CA PRO A 27 " pdb=" C PRO A 27 " ideal model delta sigma weight residual 1.516 1.530 -0.014 1.75e-02 3.27e+03 6.37e-01 ... (remaining 3959 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.41: 5296 1.41 - 2.82: 73 2.82 - 4.23: 12 4.23 - 5.64: 10 5.64 - 7.06: 2 Bond angle restraints: 5393 Sorted by residual: angle pdb=" CA TYR A 264 " pdb=" CB TYR A 264 " pdb=" CG TYR A 264 " ideal model delta sigma weight residual 113.90 119.07 -5.17 1.80e+00 3.09e-01 8.26e+00 angle pdb=" CA ARG A 158 " pdb=" CB ARG A 158 " pdb=" CG ARG A 158 " ideal model delta sigma weight residual 114.10 119.51 -5.41 2.00e+00 2.50e-01 7.31e+00 angle pdb=" CB ARG A 158 " pdb=" CG ARG A 158 " pdb=" CD ARG A 158 " ideal model delta sigma weight residual 111.30 117.20 -5.90 2.30e+00 1.89e-01 6.58e+00 angle pdb=" N VAL A 256 " pdb=" CA VAL A 256 " pdb=" C VAL A 256 " ideal model delta sigma weight residual 108.88 114.27 -5.39 2.16e+00 2.14e-01 6.23e+00 angle pdb=" CA VAL A 256 " pdb=" C VAL A 256 " pdb=" N PRO A 257 " ideal model delta sigma weight residual 118.88 121.99 -3.11 1.54e+00 4.22e-01 4.08e+00 ... (remaining 5388 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.89: 2091 17.89 - 35.78: 204 35.78 - 53.67: 40 53.67 - 71.56: 9 71.56 - 89.44: 3 Dihedral angle restraints: 2347 sinusoidal: 904 harmonic: 1443 Sorted by residual: dihedral pdb=" CB GLU A 270 " pdb=" CG GLU A 270 " pdb=" CD GLU A 270 " pdb=" OE1 GLU A 270 " ideal model delta sinusoidal sigma weight residual 0.00 -88.70 88.70 1 3.00e+01 1.11e-03 1.04e+01 dihedral pdb=" CA CYS A 49 " pdb=" CB CYS A 49 " pdb=" SG CYS A 49 " pdb=" SG CYS A 105 " ideal model delta sinusoidal sigma weight residual -73.00 -19.30 -53.70 1 2.00e+01 2.50e-03 9.79e+00 dihedral pdb=" CG LYS A 382 " pdb=" CD LYS A 382 " pdb=" CE LYS A 382 " pdb=" NZ LYS A 382 " ideal model delta sinusoidal sigma weight residual -60.00 -117.09 57.09 3 1.50e+01 4.44e-03 9.43e+00 ... (remaining 2344 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.027: 398 0.027 - 0.055: 148 0.055 - 0.082: 55 0.082 - 0.110: 25 0.110 - 0.137: 5 Chirality restraints: 631 Sorted by residual: chirality pdb=" CA ILE A 415 " pdb=" N ILE A 415 " pdb=" C ILE A 415 " pdb=" CB ILE A 415 " both_signs ideal model delta sigma weight residual False 2.43 2.57 -0.14 2.00e-01 2.50e+01 4.70e-01 chirality pdb=" CA TYR A 264 " pdb=" N TYR A 264 " pdb=" C TYR A 264 " pdb=" CB TYR A 264 " both_signs ideal model delta sigma weight residual False 2.51 2.38 0.13 2.00e-01 2.50e+01 3.98e-01 chirality pdb=" CA VAL A 110 " pdb=" N VAL A 110 " pdb=" C VAL A 110 " pdb=" CB VAL A 110 " both_signs ideal model delta sigma weight residual False 2.44 2.56 -0.12 2.00e-01 2.50e+01 3.64e-01 ... (remaining 628 not shown) Planarity restraints: 671 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C GLU A 103 " -0.030 5.00e-02 4.00e+02 4.58e-02 3.36e+00 pdb=" N PRO A 104 " 0.079 5.00e-02 4.00e+02 pdb=" CA PRO A 104 " -0.024 5.00e-02 4.00e+02 pdb=" CD PRO A 104 " -0.026 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ALA A 26 " -0.022 5.00e-02 4.00e+02 3.37e-02 1.81e+00 pdb=" N PRO A 27 " 0.058 5.00e-02 4.00e+02 pdb=" CA PRO A 27 " -0.017 5.00e-02 4.00e+02 pdb=" CD PRO A 27 " -0.019 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C VAL A 244 " -0.022 5.00e-02 4.00e+02 3.35e-02 1.79e+00 pdb=" N PRO A 245 " 0.058 5.00e-02 4.00e+02 pdb=" CA PRO A 245 " -0.017 5.00e-02 4.00e+02 pdb=" CD PRO A 245 " -0.019 5.00e-02 4.00e+02 ... (remaining 668 not shown) Histogram of nonbonded interaction distances: 2.23 - 2.76: 733 2.76 - 3.30: 4114 3.30 - 3.83: 7456 3.83 - 4.37: 8554 4.37 - 4.90: 14073 Nonbonded interactions: 34930 Sorted by model distance: nonbonded pdb=" OH TYR A 444 " pdb=" O PRO A 505 " model vdw 2.231 3.040 nonbonded pdb=" OH TYR A 230 " pdb=" O HOH A 601 " model vdw 2.239 3.040 nonbonded pdb=" O LEU A 28 " pdb=" O HOH A 602 " model vdw 2.245 3.040 nonbonded pdb=" O HOH A 603 " pdb=" O HOH A 656 " model vdw 2.253 3.040 nonbonded pdb=" OG SER A 118 " pdb=" O HOH A 603 " model vdw 2.254 3.040 ... (remaining 34925 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as 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: 0.770 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: 0.230 Check model and map are aligned: 0.030 Set scattering table: 0.040 Process input model: 14.610 Find NCS groups from input model: 0.040 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:12.570 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 28.320 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8463 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 : 0.002 0.031 3964 Z= 0.150 Angle : 0.490 7.056 5393 Z= 0.248 Chirality : 0.037 0.137 631 Planarity : 0.004 0.046 671 Dihedral : 14.855 89.444 1413 Min Nonbonded Distance : 2.231 Molprobity Statistics. All-atom Clashscore : 4.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.02 % Favored : 98.98 % Rotamer: Outliers : 0.71 % Allowed : 13.57 % Favored : 85.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.05 (0.38), residues: 492 helix: 1.37 (0.26), residues: 368 sheet: -0.05 (1.59), residues: 10 loop : 1.90 (0.68), residues: 114 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP A 274 HIS 0.004 0.001 HIS A 34 PHE 0.012 0.001 PHE A 16 TYR 0.017 0.001 TYR A 264 ARG 0.003 0.000 ARG A 219 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 984 Ramachandran restraints generated. 492 Oldfield, 0 Emsley, 492 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 984 Ramachandran restraints generated. 492 Oldfield, 0 Emsley, 492 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 69 residues out of total 420 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 66 time to evaluate : 0.416 Fit side-chains REVERT: A 300 GLU cc_start: 0.7221 (mp0) cc_final: 0.7004 (mp0) outliers start: 3 outliers final: 2 residues processed: 68 average time/residue: 1.4374 time to fit residues: 100.6329 Evaluate side-chains 63 residues out of total 420 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 61 time to evaluate : 0.447 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 224 THR Chi-restraints excluded: chain A residue 278 SER Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 50 random chunks: chunk 42 optimal weight: 5.9990 chunk 37 optimal weight: 0.7980 chunk 21 optimal weight: 8.9990 chunk 12 optimal weight: 0.7980 chunk 25 optimal weight: 0.7980 chunk 20 optimal weight: 3.9990 chunk 39 optimal weight: 6.9990 chunk 15 optimal weight: 10.0000 chunk 23 optimal weight: 0.5980 chunk 29 optimal weight: 10.0000 chunk 45 optimal weight: 8.9990 overall best weight: 1.3982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 4 ASN A 9 GLN A 205 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8411 moved from start: 0.0982 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 3964 Z= 0.188 Angle : 0.554 6.943 5393 Z= 0.297 Chirality : 0.039 0.142 631 Planarity : 0.005 0.035 671 Dihedral : 3.843 15.383 544 Min Nonbonded Distance : 2.540 Molprobity Statistics. All-atom Clashscore : 3.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.81 % Favored : 99.19 % Rotamer: Outliers : 0.95 % Allowed : 12.62 % Favored : 86.43 % 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: 2.65 (0.38), residues: 492 helix: 1.85 (0.26), residues: 371 sheet: -0.28 (1.66), residues: 10 loop : 1.98 (0.66), residues: 111 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP A 274 HIS 0.005 0.001 HIS A 34 PHE 0.014 0.002 PHE A 351 TYR 0.020 0.002 TYR A 264 ARG 0.004 0.000 ARG A 134 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 984 Ramachandran restraints generated. 492 Oldfield, 0 Emsley, 492 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 984 Ramachandran restraints generated. 492 Oldfield, 0 Emsley, 492 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 69 residues out of total 420 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 65 time to evaluate : 0.469 Fit side-chains outliers start: 4 outliers final: 3 residues processed: 66 average time/residue: 1.3679 time to fit residues: 93.3852 Evaluate side-chains 65 residues out of total 420 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 62 time to evaluate : 0.473 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 25 VAL Chi-restraints excluded: chain A residue 327 MET Chi-restraints excluded: chain A residue 337 HIS Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 50 random chunks: chunk 25 optimal weight: 5.9990 chunk 14 optimal weight: 0.8980 chunk 37 optimal weight: 5.9990 chunk 30 optimal weight: 7.9990 chunk 12 optimal weight: 0.9990 chunk 45 optimal weight: 8.9990 chunk 49 optimal weight: 5.9990 chunk 40 optimal weight: 10.0000 chunk 15 optimal weight: 5.9990 chunk 36 optimal weight: 0.9990 chunk 44 optimal weight: 2.9990 overall best weight: 2.3788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 9 GLN A 205 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8442 moved from start: 0.1001 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 3964 Z= 0.241 Angle : 0.574 6.938 5393 Z= 0.314 Chirality : 0.041 0.147 631 Planarity : 0.005 0.036 671 Dihedral : 3.956 15.839 542 Min Nonbonded Distance : 2.568 Molprobity Statistics. All-atom Clashscore : 3.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.81 % Favored : 99.19 % Rotamer: Outliers : 2.38 % Allowed : 10.71 % Favored : 86.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.47 (0.37), residues: 492 helix: 1.71 (0.26), residues: 371 sheet: -0.42 (1.60), residues: 10 loop : 1.96 (0.66), residues: 111 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP A 274 HIS 0.007 0.001 HIS A 34 PHE 0.017 0.002 PHE A 40 TYR 0.023 0.002 TYR A 264 ARG 0.005 0.000 ARG A 134 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 984 Ramachandran restraints generated. 492 Oldfield, 0 Emsley, 492 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 984 Ramachandran restraints generated. 492 Oldfield, 0 Emsley, 492 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 73 residues out of total 420 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 63 time to evaluate : 0.474 Fit side-chains outliers start: 10 outliers final: 5 residues processed: 67 average time/residue: 1.3128 time to fit residues: 90.9060 Evaluate side-chains 66 residues out of total 420 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 61 time to evaluate : 0.448 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 25 VAL Chi-restraints excluded: chain A residue 211 VAL Chi-restraints excluded: chain A residue 297 LYS Chi-restraints excluded: chain A residue 327 MET Chi-restraints excluded: chain A residue 337 HIS Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 50 random chunks: chunk 34 optimal weight: 1.9990 chunk 23 optimal weight: 8.9990 chunk 5 optimal weight: 0.0060 chunk 21 optimal weight: 10.0000 chunk 30 optimal weight: 2.9990 chunk 45 optimal weight: 0.8980 chunk 48 optimal weight: 6.9990 chunk 43 optimal weight: 0.6980 chunk 13 optimal weight: 1.9990 chunk 40 optimal weight: 10.0000 chunk 27 optimal weight: 6.9990 overall best weight: 1.1200 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 9 GLN A 205 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8391 moved from start: 0.1213 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 3964 Z= 0.167 Angle : 0.512 6.821 5393 Z= 0.276 Chirality : 0.038 0.133 631 Planarity : 0.004 0.030 671 Dihedral : 3.794 14.426 542 Min Nonbonded Distance : 2.577 Molprobity Statistics. All-atom Clashscore : 2.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.81 % Favored : 99.19 % Rotamer: Outliers : 1.67 % Allowed : 11.90 % Favored : 86.43 % 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: 2.68 (0.38), residues: 492 helix: 1.92 (0.26), residues: 374 sheet: -0.13 (1.62), residues: 10 loop : 1.74 (0.66), residues: 108 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP A 274 HIS 0.004 0.001 HIS A 34 PHE 0.014 0.002 PHE A 351 TYR 0.019 0.001 TYR A 264 ARG 0.003 0.000 ARG A 134 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 984 Ramachandran restraints generated. 492 Oldfield, 0 Emsley, 492 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 984 Ramachandran restraints generated. 492 Oldfield, 0 Emsley, 492 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 71 residues out of total 420 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 64 time to evaluate : 0.466 Fit side-chains outliers start: 7 outliers final: 6 residues processed: 66 average time/residue: 1.3128 time to fit residues: 89.4641 Evaluate side-chains 67 residues out of total 420 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 61 time to evaluate : 0.462 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 25 VAL Chi-restraints excluded: chain A residue 206 CYS Chi-restraints excluded: chain A residue 207 MET Chi-restraints excluded: chain A residue 232 LEU Chi-restraints excluded: chain A residue 297 LYS Chi-restraints excluded: chain A residue 337 HIS Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 50 random chunks: chunk 0 optimal weight: 10.0000 chunk 35 optimal weight: 1.9990 chunk 19 optimal weight: 7.9990 chunk 41 optimal weight: 5.9990 chunk 33 optimal weight: 5.9990 chunk 24 optimal weight: 5.9990 chunk 43 optimal weight: 10.0000 chunk 12 optimal weight: 0.7980 chunk 16 optimal weight: 4.9990 chunk 9 optimal weight: 5.9990 chunk 28 optimal weight: 0.6980 overall best weight: 2.8986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 4 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 9 GLN A 205 ASN A 419 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8450 moved from start: 0.1074 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.048 3964 Z= 0.270 Angle : 0.593 6.936 5393 Z= 0.324 Chirality : 0.042 0.153 631 Planarity : 0.005 0.037 671 Dihedral : 3.991 15.107 542 Min Nonbonded Distance : 2.582 Molprobity Statistics. All-atom Clashscore : 3.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.02 % Favored : 98.98 % Rotamer: Outliers : 3.10 % Allowed : 11.19 % Favored : 85.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.45 (0.37), residues: 492 helix: 1.68 (0.26), residues: 371 sheet: -0.36 (1.58), residues: 10 loop : 2.02 (0.66), residues: 111 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP A 274 HIS 0.008 0.001 HIS A 34 PHE 0.019 0.003 PHE A 40 TYR 0.025 0.002 TYR A 264 ARG 0.005 0.000 ARG A 134 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 984 Ramachandran restraints generated. 492 Oldfield, 0 Emsley, 492 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 984 Ramachandran restraints generated. 492 Oldfield, 0 Emsley, 492 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 75 residues out of total 420 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 62 time to evaluate : 0.419 Fit side-chains outliers start: 13 outliers final: 8 residues processed: 70 average time/residue: 1.3254 time to fit residues: 95.7867 Evaluate side-chains 69 residues out of total 420 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 61 time to evaluate : 0.471 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 25 VAL Chi-restraints excluded: chain A residue 206 CYS Chi-restraints excluded: chain A residue 207 MET Chi-restraints excluded: chain A residue 211 VAL Chi-restraints excluded: chain A residue 232 LEU Chi-restraints excluded: chain A residue 297 LYS Chi-restraints excluded: chain A residue 327 MET Chi-restraints excluded: chain A residue 391 SER Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 50 random chunks: chunk 11 optimal weight: 6.9990 chunk 48 optimal weight: 1.9990 chunk 40 optimal weight: 4.9990 chunk 22 optimal weight: 6.9990 chunk 4 optimal weight: 0.5980 chunk 16 optimal weight: 3.9990 chunk 25 optimal weight: 4.9990 chunk 46 optimal weight: 7.9990 chunk 5 optimal weight: 0.6980 chunk 27 optimal weight: 10.0000 chunk 35 optimal weight: 0.9990 overall best weight: 1.6586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 4 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 9 GLN A 205 ASN A 419 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8418 moved from start: 0.1175 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 3964 Z= 0.196 Angle : 0.540 6.861 5393 Z= 0.293 Chirality : 0.039 0.141 631 Planarity : 0.004 0.034 671 Dihedral : 3.891 14.535 542 Min Nonbonded Distance : 2.585 Molprobity Statistics. All-atom Clashscore : 2.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.81 % Favored : 99.19 % Rotamer: Outliers : 1.90 % Allowed : 12.38 % Favored : 85.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.66 (0.38), residues: 492 helix: 1.86 (0.26), residues: 371 sheet: -0.22 (1.59), residues: 10 loop : 1.97 (0.66), residues: 111 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP A 274 HIS 0.005 0.001 HIS A 34 PHE 0.015 0.002 PHE A 40 TYR 0.021 0.002 TYR A 264 ARG 0.004 0.000 ARG A 134 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 984 Ramachandran restraints generated. 492 Oldfield, 0 Emsley, 492 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 984 Ramachandran restraints generated. 492 Oldfield, 0 Emsley, 492 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 69 residues out of total 420 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 61 time to evaluate : 0.472 Fit side-chains outliers start: 8 outliers final: 6 residues processed: 65 average time/residue: 1.3762 time to fit residues: 92.3001 Evaluate side-chains 69 residues out of total 420 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 63 time to evaluate : 0.413 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 25 VAL Chi-restraints excluded: chain A residue 206 CYS Chi-restraints excluded: chain A residue 232 LEU Chi-restraints excluded: chain A residue 297 LYS Chi-restraints excluded: chain A residue 337 HIS Chi-restraints excluded: chain A residue 391 SER Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 50 random chunks: chunk 27 optimal weight: 7.9990 chunk 40 optimal weight: 9.9990 chunk 48 optimal weight: 1.9990 chunk 30 optimal weight: 0.0370 chunk 29 optimal weight: 6.9990 chunk 22 optimal weight: 3.9990 chunk 19 optimal weight: 10.0000 chunk 28 optimal weight: 5.9990 chunk 14 optimal weight: 0.9990 chunk 9 optimal weight: 4.9990 chunk 32 optimal weight: 5.9990 overall best weight: 2.4066 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 4 ASN A 9 GLN A 205 ASN A 419 HIS A 439 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8441 moved from start: 0.1183 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 3964 Z= 0.240 Angle : 0.575 6.904 5393 Z= 0.313 Chirality : 0.041 0.148 631 Planarity : 0.005 0.035 671 Dihedral : 3.970 14.776 542 Min Nonbonded Distance : 2.587 Molprobity Statistics. All-atom Clashscore : 3.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.81 % Favored : 99.19 % Rotamer: Outliers : 1.90 % Allowed : 13.10 % Favored : 85.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.52 (0.38), residues: 492 helix: 1.74 (0.26), residues: 371 sheet: -0.44 (1.58), residues: 10 loop : 2.01 (0.66), residues: 111 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP A 274 HIS 0.007 0.001 HIS A 34 PHE 0.018 0.002 PHE A 40 TYR 0.024 0.002 TYR A 264 ARG 0.004 0.000 ARG A 134 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 984 Ramachandran restraints generated. 492 Oldfield, 0 Emsley, 492 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 984 Ramachandran restraints generated. 492 Oldfield, 0 Emsley, 492 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 68 residues out of total 420 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 60 time to evaluate : 0.401 Fit side-chains outliers start: 8 outliers final: 6 residues processed: 65 average time/residue: 1.3267 time to fit residues: 88.9925 Evaluate side-chains 68 residues out of total 420 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 62 time to evaluate : 0.427 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 25 VAL Chi-restraints excluded: chain A residue 206 CYS Chi-restraints excluded: chain A residue 207 MET Chi-restraints excluded: chain A residue 232 LEU Chi-restraints excluded: chain A residue 297 LYS Chi-restraints excluded: chain A residue 391 SER Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 50 random chunks: chunk 23 optimal weight: 7.9990 chunk 4 optimal weight: 0.0980 chunk 37 optimal weight: 0.8980 chunk 43 optimal weight: 5.9990 chunk 46 optimal weight: 0.7980 chunk 42 optimal weight: 1.9990 chunk 44 optimal weight: 2.9990 chunk 27 optimal weight: 5.9990 chunk 19 optimal weight: 7.9990 chunk 35 optimal weight: 3.9990 chunk 13 optimal weight: 4.9990 overall best weight: 1.3584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 4 ASN A 9 GLN A 205 ASN A 419 HIS A 439 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8405 moved from start: 0.1256 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 3964 Z= 0.179 Angle : 0.529 6.836 5393 Z= 0.285 Chirality : 0.039 0.136 631 Planarity : 0.004 0.033 671 Dihedral : 3.846 14.377 542 Min Nonbonded Distance : 2.585 Molprobity Statistics. All-atom Clashscore : 2.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.81 % Favored : 99.19 % Rotamer: Outliers : 1.67 % Allowed : 13.10 % Favored : 85.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.64 (0.38), residues: 492 helix: 1.89 (0.26), residues: 374 sheet: -0.09 (1.58), residues: 10 loop : 1.73 (0.66), residues: 108 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP A 274 HIS 0.005 0.001 HIS A 34 PHE 0.015 0.002 PHE A 386 TYR 0.020 0.002 TYR A 264 ARG 0.004 0.000 ARG A 134 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 984 Ramachandran restraints generated. 492 Oldfield, 0 Emsley, 492 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 984 Ramachandran restraints generated. 492 Oldfield, 0 Emsley, 492 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 68 residues out of total 420 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 61 time to evaluate : 0.469 Fit side-chains REVERT: A 103 GLU cc_start: 0.7731 (pt0) cc_final: 0.7423 (pt0) outliers start: 7 outliers final: 7 residues processed: 64 average time/residue: 1.3817 time to fit residues: 91.2392 Evaluate side-chains 69 residues out of total 420 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 62 time to evaluate : 0.459 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 25 VAL Chi-restraints excluded: chain A residue 206 CYS Chi-restraints excluded: chain A residue 207 MET Chi-restraints excluded: chain A residue 232 LEU Chi-restraints excluded: chain A residue 297 LYS Chi-restraints excluded: chain A residue 337 HIS Chi-restraints excluded: chain A residue 391 SER Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 50 random chunks: chunk 40 optimal weight: 1.9990 chunk 42 optimal weight: 4.9990 chunk 44 optimal weight: 6.9990 chunk 29 optimal weight: 5.9990 chunk 47 optimal weight: 3.9990 chunk 28 optimal weight: 6.9990 chunk 22 optimal weight: 2.9990 chunk 33 optimal weight: 5.9990 chunk 49 optimal weight: 7.9990 chunk 45 optimal weight: 5.9990 chunk 39 optimal weight: 8.9990 overall best weight: 3.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 4 ASN A 9 GLN A 205 ASN A 419 HIS A 439 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8468 moved from start: 0.1126 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.057 3964 Z= 0.342 Angle : 0.654 6.914 5393 Z= 0.357 Chirality : 0.045 0.161 631 Planarity : 0.005 0.036 671 Dihedral : 4.129 15.124 542 Min Nonbonded Distance : 2.572 Molprobity Statistics. All-atom Clashscore : 3.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.02 % Favored : 98.98 % Rotamer: Outliers : 1.90 % Allowed : 13.33 % Favored : 84.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.22 (0.37), residues: 492 helix: 1.50 (0.25), residues: 371 sheet: -0.67 (1.53), residues: 10 loop : 1.99 (0.66), residues: 111 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.003 TRP A 274 HIS 0.009 0.002 HIS A 34 PHE 0.023 0.003 PHE A 40 TYR 0.026 0.003 TYR A 264 ARG 0.005 0.001 ARG A 134 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 984 Ramachandran restraints generated. 492 Oldfield, 0 Emsley, 492 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 984 Ramachandran restraints generated. 492 Oldfield, 0 Emsley, 492 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 69 residues out of total 420 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 61 time to evaluate : 0.543 Fit side-chains REVERT: A 103 GLU cc_start: 0.7794 (pt0) cc_final: 0.7506 (pt0) outliers start: 8 outliers final: 6 residues processed: 66 average time/residue: 1.3398 time to fit residues: 91.3461 Evaluate side-chains 69 residues out of total 420 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 63 time to evaluate : 0.464 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 25 VAL Chi-restraints excluded: chain A residue 206 CYS Chi-restraints excluded: chain A residue 207 MET Chi-restraints excluded: chain A residue 211 VAL Chi-restraints excluded: chain A residue 232 LEU Chi-restraints excluded: chain A residue 297 LYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 50 random chunks: chunk 4 optimal weight: 0.6980 chunk 30 optimal weight: 4.9990 chunk 24 optimal weight: 3.9990 chunk 31 optimal weight: 0.8980 chunk 42 optimal weight: 4.9990 chunk 12 optimal weight: 0.7980 chunk 36 optimal weight: 4.9990 chunk 5 optimal weight: 0.0570 chunk 11 optimal weight: 2.9990 chunk 39 optimal weight: 9.9990 chunk 16 optimal weight: 1.9990 overall best weight: 0.8900 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 4 ASN A 9 GLN A 205 ASN A 419 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8374 moved from start: 0.1361 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.028 3964 Z= 0.158 Angle : 0.520 6.875 5393 Z= 0.275 Chirality : 0.038 0.131 631 Planarity : 0.004 0.029 671 Dihedral : 3.812 14.512 542 Min Nonbonded Distance : 2.579 Molprobity Statistics. All-atom Clashscore : 2.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.81 % Favored : 99.19 % Rotamer: Outliers : 1.90 % Allowed : 13.57 % Favored : 84.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.72 (0.38), residues: 492 helix: 1.97 (0.27), residues: 374 sheet: -0.08 (1.56), residues: 10 loop : 1.67 (0.67), residues: 108 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP A 274 HIS 0.003 0.001 HIS A 34 PHE 0.015 0.002 PHE A 351 TYR 0.019 0.001 TYR A 264 ARG 0.004 0.000 ARG A 134 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 984 Ramachandran restraints generated. 492 Oldfield, 0 Emsley, 492 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 984 Ramachandran restraints generated. 492 Oldfield, 0 Emsley, 492 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 69 residues out of total 420 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 61 time to evaluate : 0.461 Fit side-chains REVERT: A 103 GLU cc_start: 0.7721 (pt0) cc_final: 0.7402 (pt0) outliers start: 8 outliers final: 3 residues processed: 66 average time/residue: 1.3509 time to fit residues: 91.9808 Evaluate side-chains 63 residues out of total 420 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 60 time to evaluate : 0.472 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 206 CYS Chi-restraints excluded: chain A residue 207 MET Chi-restraints excluded: chain A residue 297 LYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 50 random chunks: chunk 40 optimal weight: 1.9990 chunk 5 optimal weight: 0.0060 chunk 7 optimal weight: 4.9990 chunk 34 optimal weight: 1.9990 chunk 2 optimal weight: 2.9990 chunk 28 optimal weight: 8.9990 chunk 45 optimal weight: 0.0770 chunk 26 optimal weight: 20.0000 chunk 1 optimal weight: 2.9990 chunk 31 optimal weight: 6.9990 chunk 30 optimal weight: 4.9990 overall best weight: 1.4160 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 4 ASN A 9 GLN A 205 ASN A 419 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3977 r_free = 0.3977 target = 0.181036 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3614 r_free = 0.3614 target = 0.148108 restraints weight = 2807.387| |-----------------------------------------------------------------------------| r_work (start): 0.3584 rms_B_bonded: 0.89 r_work: 0.3313 rms_B_bonded: 1.93 restraints_weight: 0.5000 r_work: 0.3187 rms_B_bonded: 3.38 restraints_weight: 0.2500 r_work (final): 0.3187 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8503 moved from start: 0.1287 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 3964 Z= 0.184 Angle : 0.546 7.553 5393 Z= 0.289 Chirality : 0.039 0.134 631 Planarity : 0.004 0.030 671 Dihedral : 3.829 14.228 542 Min Nonbonded Distance : 2.585 Molprobity Statistics. All-atom Clashscore : 2.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.81 % Favored : 99.19 % Rotamer: Outliers : 0.71 % Allowed : 14.52 % Favored : 84.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.67 (0.38), residues: 492 helix: 1.93 (0.26), residues: 374 sheet: 0.07 (1.56), residues: 10 loop : 1.66 (0.67), residues: 108 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP A 274 HIS 0.005 0.001 HIS A 34 PHE 0.015 0.002 PHE A 386 TYR 0.020 0.002 TYR A 264 ARG 0.003 0.000 ARG A 134 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2276.44 seconds wall clock time: 45 minutes 35.36 seconds (2735.36 seconds total)