Starting phenix.real_space_refine on Sun Mar 10 18:28:06 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8sdu_40352/03_2024/8sdu_40352.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8sdu_40352/03_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_40352/03_2024/8sdu_40352.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8sdu_40352/03_2024/8sdu_40352.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8sdu_40352/03_2024/8sdu_40352.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8sdu_40352/03_2024/8sdu_40352.pdb" } 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 Residue "A GLU 76": "OE1" <-> "OE2" Residue "A GLU 123": "OE1" <-> "OE2" Residue "A GLU 212": "OE1" <-> "OE2" Residue "A TYR 242": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 378": "OD1" <-> "OD2" Residue "A GLU 447": "OE1" <-> "OE2" Time to flip residues: 0.01s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/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: 2.70, per 1000 atoms: 0.68 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 - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 1.80 Conformation dependent library (CDL) restraints added in 738.4 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: 0.46 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: 1.12 Time building geometry restraints manager: 1.92 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: 100.52 - 107.21: 150 107.21 - 113.91: 2241 113.91 - 120.61: 1676 120.61 - 127.30: 1282 127.30 - 134.00: 44 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 2.440 nonbonded pdb=" OH TYR A 230 " pdb=" O HOH A 601 " model vdw 2.239 2.440 nonbonded pdb=" O LEU A 28 " pdb=" O HOH A 602 " model vdw 2.245 2.440 nonbonded pdb=" O HOH A 603 " pdb=" O HOH A 656 " model vdw 2.253 2.440 nonbonded pdb=" OG SER A 118 " pdb=" O HOH A 603 " model vdw 2.254 2.440 ... (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: 0.650 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.000 Extract box with map and model: 2.970 Check model and map are aligned: 0.060 Set scattering table: 0.040 Process input model: 15.920 Find NCS groups from input model: 0.120 Set up NCS constraints: 0.010 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:12.320 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 32.090 ------------------------------------------------------------------------------- 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 fitting. rotamer outliers: 3 poor density : 66 time to evaluate : 0.460 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: 1.4041 time to fit residues: 98.3678 Evaluate side-chains 63 residues out of total 420 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 61 time to evaluate : 0.420 ------------------------------------------------------------------------------- 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: 7.9990 chunk 37 optimal weight: 0.7980 chunk 21 optimal weight: 9.9990 chunk 12 optimal weight: 0.8980 chunk 25 optimal weight: 3.9990 chunk 20 optimal weight: 5.9990 chunk 39 optimal weight: 6.9990 chunk 15 optimal weight: 9.9990 chunk 23 optimal weight: 0.8980 chunk 29 optimal weight: 5.9990 chunk 45 optimal weight: 6.9990 overall best weight: 2.5184 ------------------------------------------------------------------------------- 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: 0.8452 moved from start: 0.0825 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 3964 Z= 0.241 Angle : 0.598 7.115 5393 Z= 0.323 Chirality : 0.041 0.152 631 Planarity : 0.005 0.038 671 Dihedral : 4.032 15.009 544 Min Nonbonded Distance : 2.211 Molprobity Statistics. All-atom Clashscore : 4.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.02 % Favored : 98.98 % Rotamer: Outliers : 1.67 % Allowed : 11.67 % Favored : 86.67 % 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 (0.38), residues: 492 helix: 1.66 (0.26), residues: 370 sheet: -0.47 (1.65), residues: 10 loop : 2.12 (0.66), residues: 112 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP A 274 HIS 0.007 0.001 HIS A 34 PHE 0.018 0.002 PHE A 40 TYR 0.023 0.002 TYR A 264 ARG 0.004 0.001 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 71 residues out of total 420 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 64 time to evaluate : 0.466 Fit side-chains outliers start: 7 outliers final: 4 residues processed: 66 average time/residue: 1.3327 time to fit residues: 90.7827 Evaluate side-chains 63 residues out of total 420 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 59 time to evaluate : 0.465 ------------------------------------------------------------------------------- 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 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: 6.9990 chunk 30 optimal weight: 0.0870 chunk 12 optimal weight: 5.9990 chunk 45 optimal weight: 0.5980 chunk 49 optimal weight: 7.9990 chunk 40 optimal weight: 9.9990 chunk 15 optimal weight: 5.9990 chunk 36 optimal weight: 3.9990 chunk 44 optimal weight: 1.9990 overall best weight: 1.5162 ------------------------------------------------------------------------------- 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: 0.8420 moved from start: 0.1019 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 3964 Z= 0.181 Angle : 0.537 7.378 5393 Z= 0.287 Chirality : 0.039 0.139 631 Planarity : 0.004 0.033 671 Dihedral : 3.833 14.354 542 Min Nonbonded Distance : 2.234 Molprobity Statistics. All-atom Clashscore : 3.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.81 % Favored : 99.19 % Rotamer: Outliers : 2.38 % Allowed : 11.90 % 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: 1.87 (0.26), residues: 374 sheet: -0.27 (1.67), residues: 10 loop : 1.92 (0.67), residues: 108 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP A 274 HIS 0.004 0.001 HIS A 34 PHE 0.014 0.002 PHE A 351 TYR 0.020 0.002 TYR A 264 ARG 0.003 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 70 residues out of total 420 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 60 time to evaluate : 0.405 Fit side-chains outliers start: 10 outliers final: 3 residues processed: 65 average time/residue: 1.2105 time to fit residues: 81.3900 Evaluate side-chains 61 residues out of total 420 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 58 time to evaluate : 0.450 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 25 VAL Chi-restraints excluded: chain A residue 297 LYS Chi-restraints excluded: chain A residue 327 MET Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 50 random chunks: chunk 34 optimal weight: 0.0670 chunk 23 optimal weight: 0.9980 chunk 5 optimal weight: 20.0000 chunk 21 optimal weight: 10.0000 chunk 30 optimal weight: 5.9990 chunk 45 optimal weight: 0.8980 chunk 48 optimal weight: 3.9990 chunk 43 optimal weight: 1.9990 chunk 13 optimal weight: 1.9990 chunk 40 optimal weight: 1.9990 chunk 27 optimal weight: 1.9990 overall best weight: 1.1922 ------------------------------------------------------------------------------- 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: 0.8402 moved from start: 0.1093 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= 0.164 Angle : 0.517 7.455 5393 Z= 0.274 Chirality : 0.038 0.132 631 Planarity : 0.004 0.030 671 Dihedral : 3.764 14.328 542 Min Nonbonded Distance : 2.228 Molprobity Statistics. All-atom Clashscore : 3.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.02 % Favored : 98.98 % Rotamer: Outliers : 1.67 % Allowed : 12.86 % Favored : 85.48 % 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: 2.81 (0.38), residues: 492 helix: 1.99 (0.27), residues: 374 sheet: -0.09 (1.69), residues: 10 loop : 1.92 (0.67), 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 0.020 0.001 TYR A 264 ARG 0.002 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 63 residues out of total 420 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 56 time to evaluate : 0.445 Fit side-chains outliers start: 7 outliers final: 6 residues processed: 59 average time/residue: 1.2385 time to fit residues: 75.6053 Evaluate side-chains 62 residues out of total 420 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 56 time to evaluate : 0.448 ------------------------------------------------------------------------------- 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: 4.9990 chunk 19 optimal weight: 2.9990 chunk 41 optimal weight: 7.9990 chunk 33 optimal weight: 4.9990 chunk 24 optimal weight: 0.0970 chunk 43 optimal weight: 8.9990 chunk 12 optimal weight: 4.9990 chunk 16 optimal weight: 6.9990 chunk 9 optimal weight: 9.9990 chunk 28 optimal weight: 6.9990 overall best weight: 3.6186 ------------------------------------------------------------------------------- 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: 0.8467 moved from start: 0.0977 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.054 3964 Z= 0.303 Angle : 0.629 8.050 5393 Z= 0.341 Chirality : 0.044 0.156 631 Planarity : 0.005 0.039 671 Dihedral : 4.051 15.189 542 Min Nonbonded Distance : 2.195 Molprobity Statistics. All-atom Clashscore : 4.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.22 % Favored : 98.78 % Rotamer: Outliers : 2.62 % Allowed : 12.38 % 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: 2.42 (0.38), residues: 492 helix: 1.62 (0.26), residues: 371 sheet: -0.58 (1.63), residues: 10 loop : 2.20 (0.67), residues: 111 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.003 TRP A 274 HIS 0.008 0.001 HIS A 34 PHE 0.021 0.003 PHE A 40 TYR 0.026 0.003 TYR A 264 ARG 0.005 0.001 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 74 residues out of total 420 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 63 time to evaluate : 0.440 Fit side-chains outliers start: 11 outliers final: 7 residues processed: 70 average time/residue: 1.2011 time to fit residues: 87.0009 Evaluate side-chains 71 residues out of total 420 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 64 time to evaluate : 0.441 ------------------------------------------------------------------------------- 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 312 SER Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 50 random chunks: chunk 11 optimal weight: 5.9990 chunk 48 optimal weight: 0.9980 chunk 40 optimal weight: 10.0000 chunk 22 optimal weight: 3.9990 chunk 4 optimal weight: 0.8980 chunk 16 optimal weight: 5.9990 chunk 25 optimal weight: 2.9990 chunk 46 optimal weight: 0.6980 chunk 5 optimal weight: 0.0870 chunk 27 optimal weight: 5.9990 chunk 35 optimal weight: 2.9990 overall best weight: 1.1360 ------------------------------------------------------------------------------- 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: 0.8405 moved from start: 0.1108 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.032 3964 Z= 0.162 Angle : 0.522 7.142 5393 Z= 0.277 Chirality : 0.038 0.133 631 Planarity : 0.004 0.032 671 Dihedral : 3.813 14.569 542 Min Nonbonded Distance : 2.225 Molprobity Statistics. All-atom Clashscore : 3.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.02 % Favored : 98.98 % Rotamer: Outliers : 1.90 % Allowed : 13.81 % Favored : 84.29 % 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: 2.76 (0.38), residues: 492 helix: 1.94 (0.26), residues: 374 sheet: -0.34 (1.67), residues: 10 loop : 1.99 (0.68), residues: 108 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP A 274 HIS 0.004 0.001 HIS A 34 PHE 0.015 0.002 PHE A 386 TYR 0.020 0.001 TYR A 264 ARG 0.003 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 68 residues out of total 420 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 60 time to evaluate : 0.465 Fit side-chains outliers start: 8 outliers final: 6 residues processed: 65 average time/residue: 1.3256 time to fit residues: 88.8636 Evaluate side-chains 63 residues out of total 420 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 57 time to evaluate : 0.440 ------------------------------------------------------------------------------- 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=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 50 random chunks: chunk 27 optimal weight: 9.9990 chunk 40 optimal weight: 10.0000 chunk 48 optimal weight: 7.9990 chunk 30 optimal weight: 0.0010 chunk 29 optimal weight: 9.9990 chunk 22 optimal weight: 6.9990 chunk 19 optimal weight: 0.8980 chunk 28 optimal weight: 4.9990 chunk 14 optimal weight: 0.9980 chunk 9 optimal weight: 10.0000 chunk 32 optimal weight: 5.9990 overall best weight: 2.5790 ------------------------------------------------------------------------------- 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: 0.8448 moved from start: 0.1041 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 3964 Z= 0.241 Angle : 0.574 6.951 5393 Z= 0.312 Chirality : 0.041 0.148 631 Planarity : 0.005 0.036 671 Dihedral : 3.947 14.844 542 Min Nonbonded Distance : 2.213 Molprobity Statistics. All-atom Clashscore : 3.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.02 % Favored : 98.98 % Rotamer: Outliers : 1.67 % Allowed : 13.57 % 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: 2.62 (0.38), residues: 492 helix: 1.78 (0.26), residues: 371 sheet: -0.41 (1.66), residues: 10 loop : 2.19 (0.67), 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 67 residues out of total 420 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 60 time to evaluate : 0.393 Fit side-chains outliers start: 7 outliers final: 5 residues processed: 63 average time/residue: 1.3876 time to fit residues: 90.0618 Evaluate side-chains 62 residues out of total 420 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 57 time to evaluate : 0.410 ------------------------------------------------------------------------------- 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 Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 50 random chunks: chunk 23 optimal weight: 4.9990 chunk 4 optimal weight: 0.3980 chunk 37 optimal weight: 0.7980 chunk 43 optimal weight: 8.9990 chunk 46 optimal weight: 0.9990 chunk 42 optimal weight: 0.9990 chunk 44 optimal weight: 3.9990 chunk 27 optimal weight: 10.0000 chunk 19 optimal weight: 4.9990 chunk 35 optimal weight: 5.9990 chunk 13 optimal weight: 4.9990 overall best weight: 1.4386 ------------------------------------------------------------------------------- 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: 0.8416 moved from start: 0.1134 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 3964 Z= 0.177 Angle : 0.528 6.903 5393 Z= 0.283 Chirality : 0.039 0.136 631 Planarity : 0.004 0.033 671 Dihedral : 3.832 14.594 542 Min Nonbonded Distance : 2.235 Molprobity Statistics. All-atom Clashscore : 3.96 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: 2.72 (0.38), residues: 492 helix: 1.92 (0.26), residues: 374 sheet: -0.21 (1.68), residues: 10 loop : 1.94 (0.67), residues: 108 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP A 274 HIS 0.004 0.001 HIS A 34 PHE 0.015 0.002 PHE A 386 TYR 0.021 0.002 TYR A 264 ARG 0.003 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 63 residues out of total 420 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 55 time to evaluate : 0.441 Fit side-chains outliers start: 8 outliers final: 5 residues processed: 60 average time/residue: 1.2578 time to fit residues: 78.1113 Evaluate side-chains 60 residues out of total 420 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 55 time to evaluate : 0.421 ------------------------------------------------------------------------------- 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 Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 50 random chunks: chunk 40 optimal weight: 9.9990 chunk 42 optimal weight: 6.9990 chunk 44 optimal weight: 0.6980 chunk 29 optimal weight: 9.9990 chunk 47 optimal weight: 0.2980 chunk 28 optimal weight: 7.9990 chunk 22 optimal weight: 0.3980 chunk 33 optimal weight: 5.9990 chunk 49 optimal weight: 3.9990 chunk 45 optimal weight: 8.9990 chunk 39 optimal weight: 8.9990 overall best weight: 2.2784 ------------------------------------------------------------------------------- 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: 0.1086 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 3964 Z= 0.223 Angle : 0.565 6.930 5393 Z= 0.305 Chirality : 0.041 0.147 631 Planarity : 0.005 0.035 671 Dihedral : 3.923 14.687 542 Min Nonbonded Distance : 2.219 Molprobity Statistics. All-atom Clashscore : 4.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.02 % Favored : 98.98 % Rotamer: Outliers : 1.67 % Allowed : 13.57 % 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: 2.63 (0.38), residues: 492 helix: 1.80 (0.26), residues: 371 sheet: -0.40 (1.66), residues: 10 loop : 2.16 (0.67), residues: 111 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP A 274 HIS 0.006 0.001 HIS A 34 PHE 0.016 0.002 PHE A 40 TYR 0.024 0.002 TYR A 264 ARG 0.004 0.000 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 63 residues out of total 420 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 56 time to evaluate : 0.435 Fit side-chains outliers start: 7 outliers final: 5 residues processed: 60 average time/residue: 1.2758 time to fit residues: 79.1296 Evaluate side-chains 65 residues out of total 420 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 60 time to evaluate : 0.425 ------------------------------------------------------------------------------- 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 Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 50 random chunks: chunk 4 optimal weight: 0.1980 chunk 30 optimal weight: 0.9980 chunk 24 optimal weight: 3.9990 chunk 31 optimal weight: 5.9990 chunk 42 optimal weight: 4.9990 chunk 12 optimal weight: 1.9990 chunk 36 optimal weight: 4.9990 chunk 5 optimal weight: 0.0010 chunk 11 optimal weight: 3.9990 chunk 39 optimal weight: 9.9990 chunk 16 optimal weight: 2.9990 overall best weight: 1.2390 ------------------------------------------------------------------------------- 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: 0.1174 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= 0.167 Angle : 0.521 6.886 5393 Z= 0.278 Chirality : 0.038 0.134 631 Planarity : 0.004 0.032 671 Dihedral : 3.798 14.411 542 Min Nonbonded Distance : 2.231 Molprobity Statistics. All-atom Clashscore : 3.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.02 % Favored : 98.98 % Rotamer: Outliers : 1.19 % Allowed : 14.05 % 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: 2.79 (0.38), residues: 492 helix: 1.97 (0.26), residues: 374 sheet: -0.15 (1.68), residues: 10 loop : 1.94 (0.67), residues: 108 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP A 274 HIS 0.004 0.001 HIS A 34 PHE 0.015 0.002 PHE A 386 TYR 0.020 0.001 TYR A 264 ARG 0.002 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 64 residues out of total 420 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 59 time to evaluate : 0.402 Fit side-chains outliers start: 5 outliers final: 5 residues processed: 62 average time/residue: 1.4251 time to fit residues: 90.9880 Evaluate side-chains 62 residues out of total 420 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 57 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 Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 50 random chunks: chunk 40 optimal weight: 9.9990 chunk 5 optimal weight: 0.0170 chunk 7 optimal weight: 4.9990 chunk 34 optimal weight: 0.8980 chunk 2 optimal weight: 2.9990 chunk 28 optimal weight: 3.9990 chunk 45 optimal weight: 9.9990 chunk 26 optimal weight: 0.0870 chunk 1 optimal weight: 4.9990 chunk 31 optimal weight: 0.7980 chunk 30 optimal weight: 2.9990 overall best weight: 0.9598 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3992 r_free = 0.3992 target = 0.182406 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3614 r_free = 0.3614 target = 0.147984 restraints weight = 2791.088| |-----------------------------------------------------------------------------| r_work (start): 0.3615 rms_B_bonded: 0.83 r_work: 0.3372 rms_B_bonded: 1.76 restraints_weight: 0.5000 r_work: 0.3268 rms_B_bonded: 2.85 restraints_weight: 0.2500 r_work (final): 0.3268 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8461 moved from start: 0.1299 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.029 3964 Z= 0.154 Angle : 0.513 6.827 5393 Z= 0.269 Chirality : 0.038 0.129 631 Planarity : 0.004 0.030 671 Dihedral : 3.718 14.230 542 Min Nonbonded Distance : 2.223 Molprobity Statistics. All-atom Clashscore : 3.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.02 % Favored : 98.98 % Rotamer: Outliers : 1.19 % Allowed : 14.05 % 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: 2.93 (0.39), residues: 492 helix: 2.08 (0.27), residues: 374 sheet: -0.01 (1.71), residues: 10 loop : 1.94 (0.68), 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 0.016 0.002 PHE A 386 TYR 0.019 0.001 TYR A 264 ARG 0.002 0.000 ARG A 134 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2131.67 seconds wall clock time: 38 minutes 40.84 seconds (2320.84 seconds total)