Starting phenix.real_space_refine on Thu Dec 7 19:27:56 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8sdu_40352/12_2023/8sdu_40352.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8sdu_40352/12_2023/8sdu_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_40352/12_2023/8sdu_40352.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8sdu_40352/12_2023/8sdu_40352.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8sdu_40352/12_2023/8sdu_40352.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8sdu_40352/12_2023/8sdu_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-1.21rc1-5172/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: 2.62, per 1000 atoms: 0.66 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: 1.81 Conformation dependent library (CDL) restraints added in 694.3 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: 0.38 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: 1.07 Time building geometry restraints manager: 1.93 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: 0.570 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: 2.910 Check model and map are aligned: 0.050 Set scattering table: 0.030 Process input model: 15.200 Find NCS groups from input model: 0.080 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:12.810 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 31.660 ------------------------------------------------------------------------------- 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 : 0.461 Fit side-chains outliers start: 3 outliers final: 2 residues processed: 68 average time/residue: 1.3048 time to fit residues: 91.5178 Evaluate side-chains 63 residues out of total 420 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 61 time to evaluate : 0.440 Switching outliers to nearest non-outliers outliers start: 2 outliers final: 2 residues processed: 0 time to fit residues: 0.5977 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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: 3.9990 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: 2.1184 ------------------------------------------------------------------------------- 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: 0.8442 moved from start: 0.0845 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= 0.218 Angle : 0.581 7.022 5393 Z= 0.313 Chirality : 0.040 0.148 631 Planarity : 0.005 0.036 671 Dihedral : 3.886 14.684 542 Min Nonbonded Distance : 2.221 Molprobity Statistics. All-atom Clashscore : 4.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.02 % Favored : 98.98 % Rotamer: Outliers : 1.67 % Allowed : 12.38 % Favored : 85.95 % 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: 2.54 (0.38), residues: 492 helix: 1.73 (0.26), residues: 370 sheet: -0.38 (1.66), residues: 10 loop : 2.10 (0.66), residues: 112 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP A 274 HIS 0.006 0.001 HIS A 34 PHE 0.016 0.002 PHE A 40 TYR 0.022 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 : 0.436 Fit side-chains outliers start: 7 outliers final: 5 residues processed: 67 average time/residue: 1.2943 time to fit residues: 89.5461 Evaluate side-chains 64 residues out of total 420 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 59 time to evaluate : 0.451 Switching outliers to nearest non-outliers outliers start: 5 outliers final: 3 residues processed: 2 average time/residue: 0.6923 time to fit residues: 2.0615 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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: 0.9990 chunk 37 optimal weight: 6.9990 chunk 30 optimal weight: 0.0040 chunk 12 optimal weight: 4.9990 chunk 45 optimal weight: 9.9990 chunk 49 optimal weight: 6.9990 chunk 40 optimal weight: 10.0000 chunk 15 optimal weight: 5.9990 chunk 36 optimal weight: 1.9990 chunk 44 optimal weight: 2.9990 overall best weight: 2.2000 ------------------------------------------------------------------------------- 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: 0.8445 moved from start: 0.0966 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= 0.220 Angle : 0.568 7.232 5393 Z= 0.307 Chirality : 0.040 0.145 631 Planarity : 0.005 0.036 671 Dihedral : 3.928 14.820 542 Min Nonbonded Distance : 2.221 Molprobity Statistics. All-atom Clashscore : 4.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.02 % Favored : 98.98 % Rotamer: Outliers : 2.38 % Allowed : 12.14 % 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: 2.58 (0.38), residues: 492 helix: 1.76 (0.26), residues: 371 sheet: -0.43 (1.64), residues: 10 loop : 2.17 (0.67), residues: 111 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP A 274 HIS 0.006 0.001 HIS A 34 PHE 0.016 0.002 PHE A 40 TYR 0.022 0.002 TYR A 264 ARG 0.004 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 69 residues out of total 420 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 59 time to evaluate : 0.458 Fit side-chains outliers start: 10 outliers final: 6 residues processed: 64 average time/residue: 1.2366 time to fit residues: 82.0390 Evaluate side-chains 66 residues out of total 420 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 60 time to evaluate : 0.448 Switching outliers to nearest non-outliers outliers start: 6 outliers final: 4 residues processed: 3 average time/residue: 0.5419 time to fit residues: 2.3011 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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: 9.9990 chunk 5 optimal weight: 30.0000 chunk 21 optimal weight: 10.0000 chunk 30 optimal weight: 2.9990 chunk 45 optimal weight: 0.6980 chunk 48 optimal weight: 2.9990 chunk 43 optimal weight: 0.7980 chunk 13 optimal weight: 0.9990 chunk 40 optimal weight: 10.0000 chunk 27 optimal weight: 2.9990 overall best weight: 1.4986 ------------------------------------------------------------------------------- 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: 0.8419 moved from start: 0.1043 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= 0.179 Angle : 0.532 6.975 5393 Z= 0.285 Chirality : 0.039 0.138 631 Planarity : 0.004 0.033 671 Dihedral : 3.841 14.463 542 Min Nonbonded Distance : 2.233 Molprobity Statistics. All-atom Clashscore : 3.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.02 % Favored : 98.98 % Rotamer: Outliers : 1.90 % Allowed : 12.86 % 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: 2.67 (0.38), residues: 492 helix: 1.88 (0.26), residues: 374 sheet: -0.34 (1.66), residues: 10 loop : 1.95 (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 0.021 0.002 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 67 residues out of total 420 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 59 time to evaluate : 0.628 Fit side-chains outliers start: 8 outliers final: 7 residues processed: 63 average time/residue: 1.1762 time to fit residues: 77.0847 Evaluate side-chains 65 residues out of total 420 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 58 time to evaluate : 0.451 Switching outliers to nearest non-outliers outliers start: 7 outliers final: 4 residues processed: 3 average time/residue: 0.4206 time to fit residues: 1.9531 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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: 0.8980 chunk 41 optimal weight: 7.9990 chunk 33 optimal weight: 5.9990 chunk 24 optimal weight: 5.9990 chunk 43 optimal weight: 0.9990 chunk 12 optimal weight: 3.9990 chunk 16 optimal weight: 6.9990 chunk 9 optimal weight: 10.0000 chunk 28 optimal weight: 3.9990 overall best weight: 2.9788 ------------------------------------------------------------------------------- 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 A 439 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8458 moved from start: 0.0989 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.050 3964 Z= 0.266 Angle : 0.601 7.417 5393 Z= 0.325 Chirality : 0.042 0.152 631 Planarity : 0.005 0.037 671 Dihedral : 4.014 15.025 542 Min Nonbonded Distance : 2.205 Molprobity Statistics. All-atom Clashscore : 4.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.22 % Favored : 98.78 % Rotamer: Outliers : 2.86 % Allowed : 12.14 % 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: 2.49 (0.38), residues: 492 helix: 1.68 (0.26), residues: 371 sheet: -0.55 (1.62), residues: 10 loop : 2.18 (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 0.019 0.003 PHE A 40 TYR 0.024 0.002 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 71 residues out of total 420 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 59 time to evaluate : 0.465 Fit side-chains outliers start: 12 outliers final: 7 residues processed: 67 average time/residue: 1.1583 time to fit residues: 80.5451 Evaluate side-chains 70 residues out of total 420 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 63 time to evaluate : 0.419 Switching outliers to nearest non-outliers outliers start: 7 outliers final: 5 residues processed: 2 average time/residue: 0.5794 time to fit residues: 1.7625 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 50 random chunks: chunk 11 optimal weight: 1.9990 chunk 48 optimal weight: 1.9990 chunk 40 optimal weight: 6.9990 chunk 22 optimal weight: 5.9990 chunk 4 optimal weight: 0.7980 chunk 16 optimal weight: 0.6980 chunk 25 optimal weight: 5.9990 chunk 46 optimal weight: 7.9990 chunk 5 optimal weight: 7.9990 chunk 27 optimal weight: 4.9990 chunk 35 optimal weight: 1.9990 overall best weight: 1.4986 ------------------------------------------------------------------------------- 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 A 439 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8420 moved from start: 0.1063 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 : 0.536 7.068 5393 Z= 0.285 Chirality : 0.039 0.139 631 Planarity : 0.004 0.032 671 Dihedral : 3.865 14.593 542 Min Nonbonded Distance : 2.233 Molprobity Statistics. All-atom Clashscore : 4.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.02 % Favored : 98.98 % Rotamer: Outliers : 2.14 % Allowed : 13.33 % 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: 2.67 (0.38), residues: 492 helix: 1.88 (0.26), residues: 374 sheet: -0.41 (1.66), 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 0.021 0.002 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 69 residues out of total 420 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 60 time to evaluate : 0.454 Fit side-chains outliers start: 9 outliers final: 6 residues processed: 66 average time/residue: 1.2439 time to fit residues: 85.0534 Evaluate side-chains 65 residues out of total 420 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 59 time to evaluate : 0.340 Switching outliers to nearest non-outliers outliers start: 6 outliers final: 4 residues processed: 2 average time/residue: 0.1180 time to fit residues: 0.7775 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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: 9.9990 chunk 48 optimal weight: 0.8980 chunk 30 optimal weight: 0.4980 chunk 29 optimal weight: 10.0000 chunk 22 optimal weight: 7.9990 chunk 19 optimal weight: 1.9990 chunk 28 optimal weight: 7.9990 chunk 14 optimal weight: 0.7980 chunk 9 optimal weight: 0.9980 chunk 32 optimal weight: 5.9990 overall best weight: 1.0382 ------------------------------------------------------------------------------- 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 A 439 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8392 moved from start: 0.1236 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= 0.156 Angle : 0.506 6.829 5393 Z= 0.269 Chirality : 0.038 0.130 631 Planarity : 0.004 0.031 671 Dihedral : 3.748 14.424 542 Min Nonbonded Distance : 2.224 Molprobity Statistics. All-atom Clashscore : 3.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.02 % Favored : 98.98 % 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: 2.88 (0.38), residues: 492 helix: 2.04 (0.27), residues: 374 sheet: -0.17 (1.68), residues: 10 loop : 1.91 (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 386 TYR 0.019 0.001 TYR A 264 ARG 0.002 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 66 residues out of total 420 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 58 time to evaluate : 0.434 Fit side-chains outliers start: 8 outliers final: 6 residues processed: 63 average time/residue: 1.3276 time to fit residues: 86.4548 Evaluate side-chains 63 residues out of total 420 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 57 time to evaluate : 0.435 Switching outliers to nearest non-outliers outliers start: 6 outliers final: 4 residues processed: 2 average time/residue: 0.5731 time to fit residues: 1.8326 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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: 0.9980 chunk 43 optimal weight: 10.0000 chunk 46 optimal weight: 5.9990 chunk 42 optimal weight: 0.5980 chunk 44 optimal weight: 0.7980 chunk 27 optimal weight: 7.9990 chunk 19 optimal weight: 1.9990 chunk 35 optimal weight: 1.9990 chunk 13 optimal weight: 4.9990 overall best weight: 0.8982 ------------------------------------------------------------------------------- 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 A 419 HIS A 439 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8378 moved from start: 0.1304 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= 0.151 Angle : 0.504 6.748 5393 Z= 0.266 Chirality : 0.038 0.128 631 Planarity : 0.004 0.030 671 Dihedral : 3.689 14.408 542 Min Nonbonded Distance : 2.217 Molprobity Statistics. All-atom Clashscore : 3.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.02 % Favored : 98.98 % Rotamer: Outliers : 1.43 % Allowed : 14.05 % 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: 2.97 (0.39), residues: 492 helix: 2.12 (0.27), residues: 374 sheet: -0.01 (1.70), residues: 10 loop : 1.91 (0.67), residues: 108 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP A 274 HIS 0.003 0.001 HIS A 34 PHE 0.015 0.002 PHE A 386 TYR 0.019 0.001 TYR A 264 ARG 0.002 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 64 residues out of total 420 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 58 time to evaluate : 0.423 Fit side-chains outliers start: 6 outliers final: 6 residues processed: 62 average time/residue: 1.2943 time to fit residues: 82.9268 Evaluate side-chains 63 residues out of total 420 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 57 time to evaluate : 0.414 Switching outliers to nearest non-outliers outliers start: 6 outliers final: 4 residues processed: 2 average time/residue: 0.1830 time to fit residues: 1.0412 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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: 1.9990 chunk 44 optimal weight: 0.7980 chunk 29 optimal weight: 8.9990 chunk 47 optimal weight: 0.0050 chunk 28 optimal weight: 2.9990 chunk 22 optimal weight: 7.9990 chunk 33 optimal weight: 6.9990 chunk 49 optimal weight: 2.9990 chunk 45 optimal weight: 3.9990 chunk 39 optimal weight: 5.9990 overall best weight: 1.7600 ------------------------------------------------------------------------------- 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: 0.8420 moved from start: 0.1202 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= 0.192 Angle : 0.539 6.870 5393 Z= 0.288 Chirality : 0.039 0.142 631 Planarity : 0.004 0.034 671 Dihedral : 3.808 14.397 542 Min Nonbonded Distance : 2.232 Molprobity Statistics. All-atom Clashscore : 3.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.02 % Favored : 98.98 % 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: 2.78 (0.38), residues: 492 helix: 1.95 (0.26), residues: 374 sheet: -0.17 (1.68), residues: 10 loop : 2.01 (0.68), 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 0.016 0.002 PHE A 386 TYR 0.023 0.002 TYR A 264 ARG 0.003 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 66 residues out of total 420 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 58 time to evaluate : 0.465 Fit side-chains outliers start: 8 outliers final: 6 residues processed: 64 average time/residue: 1.2316 time to fit residues: 81.5689 Evaluate side-chains 62 residues out of total 420 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 56 time to evaluate : 0.424 Switching outliers to nearest non-outliers outliers start: 6 outliers final: 5 residues processed: 1 average time/residue: 0.0962 time to fit residues: 0.7412 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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: 5.9990 chunk 24 optimal weight: 3.9990 chunk 31 optimal weight: 4.9990 chunk 42 optimal weight: 0.9980 chunk 12 optimal weight: 2.9990 chunk 36 optimal weight: 6.9990 chunk 5 optimal weight: 0.8980 chunk 11 optimal weight: 0.8980 chunk 39 optimal weight: 6.9990 chunk 16 optimal weight: 0.9990 overall best weight: 0.8982 ------------------------------------------------------------------------------- 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 A 439 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8377 moved from start: 0.1358 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= 0.150 Angle : 0.511 6.834 5393 Z= 0.267 Chirality : 0.038 0.129 631 Planarity : 0.004 0.029 671 Dihedral : 3.690 14.302 542 Min Nonbonded Distance : 2.226 Molprobity Statistics. All-atom Clashscore : 3.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.02 % Favored : 98.98 % Rotamer: Outliers : 1.67 % Allowed : 13.81 % 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: 2.97 (0.39), residues: 492 helix: 2.11 (0.27), residues: 374 sheet: -0.04 (1.68), residues: 10 loop : 1.96 (0.68), residues: 108 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 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 ********************** 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: 7 poor density : 57 time to evaluate : 0.422 Fit side-chains outliers start: 7 outliers final: 6 residues processed: 62 average time/residue: 1.2332 time to fit residues: 79.1388 Evaluate side-chains 62 residues out of total 420 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 56 time to evaluate : 0.508 Switching outliers to nearest non-outliers outliers start: 6 outliers final: 4 residues processed: 2 average time/residue: 0.6337 time to fit residues: 1.9856 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 50 random chunks: chunk 40 optimal weight: 10.0000 chunk 5 optimal weight: 0.0000 chunk 7 optimal weight: 7.9990 chunk 34 optimal weight: 0.0770 chunk 2 optimal weight: 2.9990 chunk 28 optimal weight: 0.0060 chunk 45 optimal weight: 9.9990 chunk 26 optimal weight: 20.0000 chunk 1 optimal weight: 4.9990 chunk 31 optimal weight: 0.5980 chunk 30 optimal weight: 6.9990 overall best weight: 0.7360 ------------------------------------------------------------------------------- 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 = 0.4004 r_free = 0.4004 target = 0.183738 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3638 r_free = 0.3638 target = 0.150068 restraints weight = 2799.297| |-----------------------------------------------------------------------------| r_work (start): 0.3628 rms_B_bonded: 0.92 r_work: 0.3369 rms_B_bonded: 1.87 restraints_weight: 0.5000 r_work: 0.3270 rms_B_bonded: 2.91 restraints_weight: 0.2500 r_work (final): 0.3270 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8443 moved from start: 0.1495 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.027 3964 Z= 0.144 Angle : 0.509 6.703 5393 Z= 0.262 Chirality : 0.037 0.127 631 Planarity : 0.004 0.029 671 Dihedral : 3.627 14.149 542 Min Nonbonded Distance : 2.220 Molprobity Statistics. All-atom Clashscore : 3.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.02 % Favored : 98.98 % Rotamer: Outliers : 1.43 % Allowed : 14.52 % Favored : 84.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 3.00 (0.39), residues: 492 helix: 2.17 (0.27), residues: 375 sheet: 0.05 (1.69), residues: 10 loop : 1.77 (0.67), residues: 107 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 274 HIS 0.002 0.001 HIS A 34 PHE 0.017 0.002 PHE A 386 TYR 0.018 0.001 TYR A 264 ARG 0.003 0.000 ARG A 286 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2059.26 seconds wall clock time: 41 minutes 17.13 seconds (2477.13 seconds total)