Starting phenix.real_space_refine on Wed Mar 5 21:58:27 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8sdu_40352/03_2025/8sdu_40352.cif Found real_map, /net/cci-nas-00/data/ceres_data/8sdu_40352/03_2025/8sdu_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/cci-nas-00/data/ceres_data/8sdu_40352/03_2025/8sdu_40352.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8sdu_40352/03_2025/8sdu_40352.map" model { file = "/net/cci-nas-00/data/ceres_data/8sdu_40352/03_2025/8sdu_40352.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8sdu_40352/03_2025/8sdu_40352.cif" } resolution = 2.05 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.008 sd= 0.092 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 30 5.16 5 C 2520 2.51 5 N 653 2.21 5 O 739 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 6 residue(s): 0.01s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5624/modules/chem_data/mon_lib" Total number of atoms: 3942 Number of models: 1 Model: "" Number of chains: 2 Chain: "A" Number of atoms: 3872 Number of conformers: 1 Conformer: "" Number of residues, atoms: 500, 3872 Classifications: {'peptide': 500} Link IDs: {'PTRANS': 26, 'TRANS': 473} Chain breaks: 3 Chain: "A" Number of atoms: 70 Number of conformers: 1 Conformer: "" Number of residues, atoms: 70, 70 Classifications: {'water': 70} Link IDs: {None: 69} Time building chain proxies: 3.05, per 1000 atoms: 0.77 Number of scatterers: 3942 At special positions: 0 Unit cell: (76.9133, 68.6133, 97.9399, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 30 16.00 O 739 8.00 N 653 7.00 C 2520 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=2, symmetry=0 Simple disulfide: pdb=" SG CYS A 49 " - pdb=" SG CYS A 105 " distance=2.03 Simple disulfide: pdb=" SG CYS A 78 " - pdb=" SG CYS A 128 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 0.99 Conformation dependent library (CDL) restraints added in 468.6 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: 0.40 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: 1.04 Time building geometry restraints manager: 1.18 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.34: 1215 1.34 - 1.46: 935 1.46 - 1.58: 1767 1.58 - 1.70: 0 1.70 - 1.81: 47 Bond restraints: 3964 Sorted by residual: bond pdb=" CB ARG A 158 " pdb=" CG ARG A 158 " ideal model delta sigma weight residual 1.520 1.551 -0.031 3.00e-02 1.11e+03 1.05e+00 bond pdb=" CA ALA A 26 " pdb=" C ALA A 26 " ideal model delta sigma weight residual 1.522 1.534 -0.013 1.29e-02 6.01e+03 9.97e-01 bond pdb=" C PRO A 27 " pdb=" O PRO A 27 " ideal model delta sigma weight residual 1.237 1.249 -0.012 1.32e-02 5.74e+03 8.45e-01 bond pdb=" N PRO A 27 " pdb=" CA PRO A 27 " ideal model delta sigma weight residual 1.471 1.482 -0.012 1.32e-02 5.74e+03 7.83e-01 bond pdb=" CA PRO A 27 " pdb=" C PRO A 27 " ideal model delta sigma weight residual 1.516 1.530 -0.014 1.75e-02 3.27e+03 6.37e-01 ... (remaining 3959 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.41: 5296 1.41 - 2.82: 73 2.82 - 4.23: 12 4.23 - 5.64: 10 5.64 - 7.06: 2 Bond angle restraints: 5393 Sorted by residual: angle pdb=" CA TYR A 264 " pdb=" CB TYR A 264 " pdb=" CG TYR A 264 " ideal model delta sigma weight residual 113.90 119.07 -5.17 1.80e+00 3.09e-01 8.26e+00 angle pdb=" CA ARG A 158 " pdb=" CB ARG A 158 " pdb=" CG ARG A 158 " ideal model delta sigma weight residual 114.10 119.51 -5.41 2.00e+00 2.50e-01 7.31e+00 angle pdb=" CB ARG A 158 " pdb=" CG ARG A 158 " pdb=" CD ARG A 158 " ideal model delta sigma weight residual 111.30 117.20 -5.90 2.30e+00 1.89e-01 6.58e+00 angle pdb=" N VAL A 256 " pdb=" CA VAL A 256 " pdb=" C VAL A 256 " ideal model delta sigma weight residual 108.88 114.27 -5.39 2.16e+00 2.14e-01 6.23e+00 angle pdb=" CA VAL A 256 " pdb=" C VAL A 256 " pdb=" N PRO A 257 " ideal model delta sigma weight residual 118.88 121.99 -3.11 1.54e+00 4.22e-01 4.08e+00 ... (remaining 5388 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.89: 2091 17.89 - 35.78: 204 35.78 - 53.67: 40 53.67 - 71.56: 9 71.56 - 89.44: 3 Dihedral angle restraints: 2347 sinusoidal: 904 harmonic: 1443 Sorted by residual: dihedral pdb=" CB GLU A 270 " pdb=" CG GLU A 270 " pdb=" CD GLU A 270 " pdb=" OE1 GLU A 270 " ideal model delta sinusoidal sigma weight residual 0.00 -88.70 88.70 1 3.00e+01 1.11e-03 1.04e+01 dihedral pdb=" CA CYS A 49 " pdb=" CB CYS A 49 " pdb=" SG CYS A 49 " pdb=" SG CYS A 105 " ideal model delta sinusoidal sigma weight residual -73.00 -19.30 -53.70 1 2.00e+01 2.50e-03 9.79e+00 dihedral pdb=" CG LYS A 382 " pdb=" CD LYS A 382 " pdb=" CE LYS A 382 " pdb=" NZ LYS A 382 " ideal model delta sinusoidal sigma weight residual -60.00 -117.09 57.09 3 1.50e+01 4.44e-03 9.43e+00 ... (remaining 2344 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.027: 398 0.027 - 0.055: 148 0.055 - 0.082: 55 0.082 - 0.110: 25 0.110 - 0.137: 5 Chirality restraints: 631 Sorted by residual: chirality pdb=" CA ILE A 415 " pdb=" N ILE A 415 " pdb=" C ILE A 415 " pdb=" CB ILE A 415 " both_signs ideal model delta sigma weight residual False 2.43 2.57 -0.14 2.00e-01 2.50e+01 4.70e-01 chirality pdb=" CA TYR A 264 " pdb=" N TYR A 264 " pdb=" C TYR A 264 " pdb=" CB TYR A 264 " both_signs ideal model delta sigma weight residual False 2.51 2.38 0.13 2.00e-01 2.50e+01 3.98e-01 chirality pdb=" CA VAL A 110 " pdb=" N VAL A 110 " pdb=" C VAL A 110 " pdb=" CB VAL A 110 " both_signs ideal model delta sigma weight residual False 2.44 2.56 -0.12 2.00e-01 2.50e+01 3.64e-01 ... (remaining 628 not shown) Planarity restraints: 671 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C GLU A 103 " -0.030 5.00e-02 4.00e+02 4.58e-02 3.36e+00 pdb=" N PRO A 104 " 0.079 5.00e-02 4.00e+02 pdb=" CA PRO A 104 " -0.024 5.00e-02 4.00e+02 pdb=" CD PRO A 104 " -0.026 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ALA A 26 " -0.022 5.00e-02 4.00e+02 3.37e-02 1.81e+00 pdb=" N PRO A 27 " 0.058 5.00e-02 4.00e+02 pdb=" CA PRO A 27 " -0.017 5.00e-02 4.00e+02 pdb=" CD PRO A 27 " -0.019 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C VAL A 244 " -0.022 5.00e-02 4.00e+02 3.35e-02 1.79e+00 pdb=" N PRO A 245 " 0.058 5.00e-02 4.00e+02 pdb=" CA PRO A 245 " -0.017 5.00e-02 4.00e+02 pdb=" CD PRO A 245 " -0.019 5.00e-02 4.00e+02 ... (remaining 668 not shown) Histogram of nonbonded interaction distances: 2.23 - 2.76: 733 2.76 - 3.30: 4114 3.30 - 3.83: 7456 3.83 - 4.37: 8554 4.37 - 4.90: 14073 Nonbonded interactions: 34930 Sorted by model distance: nonbonded pdb=" OH TYR A 444 " pdb=" O PRO A 505 " model vdw 2.231 3.040 nonbonded pdb=" OH TYR A 230 " pdb=" O HOH A 601 " model vdw 2.239 3.040 nonbonded pdb=" O LEU A 28 " pdb=" O HOH A 602 " model vdw 2.245 3.040 nonbonded pdb=" O HOH A 603 " pdb=" O HOH A 656 " model vdw 2.253 3.040 nonbonded pdb=" OG SER A 118 " pdb=" O HOH A 603 " model vdw 2.254 3.040 ... (remaining 34925 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.880 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.210 Check model and map are aligned: 0.030 Set scattering table: 0.040 Process input model: 13.760 Find NCS groups from input model: 0.040 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:12.370 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 27.350 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8463 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.031 3964 Z= 0.150 Angle : 0.490 7.056 5393 Z= 0.248 Chirality : 0.037 0.137 631 Planarity : 0.004 0.046 671 Dihedral : 14.855 89.444 1413 Min Nonbonded Distance : 2.231 Molprobity Statistics. All-atom Clashscore : 4.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.02 % Favored : 98.98 % Rotamer: Outliers : 0.71 % Allowed : 13.57 % Favored : 85.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.05 (0.38), residues: 492 helix: 1.37 (0.26), residues: 368 sheet: -0.05 (1.59), residues: 10 loop : 1.90 (0.68), residues: 114 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP A 274 HIS 0.004 0.001 HIS A 34 PHE 0.012 0.001 PHE A 16 TYR 0.017 0.001 TYR A 264 ARG 0.003 0.000 ARG A 219 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 984 Ramachandran restraints generated. 492 Oldfield, 0 Emsley, 492 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 984 Ramachandran restraints generated. 492 Oldfield, 0 Emsley, 492 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 69 residues out of total 420 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 66 time to evaluate : 0.393 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: 1.3941 time to fit residues: 97.7558 Evaluate side-chains 63 residues out of total 420 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 61 time to evaluate : 0.402 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 224 THR Chi-restraints excluded: chain A residue 278 SER Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 50 random chunks: chunk 42 optimal weight: 5.9990 chunk 37 optimal weight: 0.7980 chunk 21 optimal weight: 8.9990 chunk 12 optimal weight: 0.7980 chunk 25 optimal weight: 0.7980 chunk 20 optimal weight: 3.9990 chunk 39 optimal weight: 6.9990 chunk 15 optimal weight: 10.0000 chunk 23 optimal weight: 0.5980 chunk 29 optimal weight: 10.0000 chunk 45 optimal weight: 8.9990 overall best weight: 1.3982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 4 ASN A 9 GLN A 205 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3981 r_free = 0.3981 target = 0.181328 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3595 r_free = 0.3595 target = 0.146221 restraints weight = 2828.247| |-----------------------------------------------------------------------------| r_work (start): 0.3574 rms_B_bonded: 0.85 r_work: 0.3334 rms_B_bonded: 1.74 restraints_weight: 0.5000 r_work: 0.3236 rms_B_bonded: 2.80 restraints_weight: 0.2500 r_work (final): 0.3236 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8488 moved from start: 0.0982 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 3964 Z= 0.188 Angle : 0.554 6.943 5393 Z= 0.297 Chirality : 0.039 0.142 631 Planarity : 0.005 0.035 671 Dihedral : 3.843 15.383 544 Min Nonbonded Distance : 2.540 Molprobity Statistics. All-atom Clashscore : 3.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.81 % Favored : 99.19 % Rotamer: Outliers : 0.95 % Allowed : 12.62 % Favored : 86.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.65 (0.38), residues: 492 helix: 1.85 (0.26), residues: 371 sheet: -0.28 (1.66), residues: 10 loop : 1.98 (0.66), residues: 111 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP A 274 HIS 0.005 0.001 HIS A 34 PHE 0.014 0.002 PHE A 351 TYR 0.020 0.002 TYR A 264 ARG 0.004 0.000 ARG A 134 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 984 Ramachandran restraints generated. 492 Oldfield, 0 Emsley, 492 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 984 Ramachandran restraints generated. 492 Oldfield, 0 Emsley, 492 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 69 residues out of total 420 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 65 time to evaluate : 0.399 Fit side-chains outliers start: 4 outliers final: 3 residues processed: 66 average time/residue: 1.3336 time to fit residues: 90.8253 Evaluate side-chains 65 residues out of total 420 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 62 time to evaluate : 0.403 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 25 VAL Chi-restraints excluded: chain A residue 327 MET Chi-restraints excluded: chain A residue 337 HIS Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 50 random chunks: chunk 22 optimal weight: 7.9990 chunk 4 optimal weight: 0.9980 chunk 39 optimal weight: 9.9990 chunk 13 optimal weight: 4.9990 chunk 33 optimal weight: 4.9990 chunk 40 optimal weight: 5.9990 chunk 20 optimal weight: 7.9990 chunk 10 optimal weight: 6.9990 chunk 7 optimal weight: 7.9990 chunk 29 optimal weight: 10.0000 chunk 32 optimal weight: 5.9990 overall best weight: 4.5988 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3931 r_free = 0.3931 target = 0.176513 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3536 r_free = 0.3536 target = 0.141402 restraints weight = 2766.560| |-----------------------------------------------------------------------------| r_work (start): 0.3523 rms_B_bonded: 0.87 r_work: 0.3253 rms_B_bonded: 1.77 restraints_weight: 0.5000 r_work: 0.3148 rms_B_bonded: 2.90 restraints_weight: 0.2500 r_work (final): 0.3148 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8564 moved from start: 0.0953 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.064 3964 Z= 0.378 Angle : 0.679 7.071 5393 Z= 0.375 Chirality : 0.047 0.164 631 Planarity : 0.006 0.043 671 Dihedral : 4.190 16.424 542 Min Nonbonded Distance : 2.562 Molprobity Statistics. All-atom Clashscore : 3.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.02 % Favored : 98.98 % Rotamer: Outliers : 2.86 % Allowed : 10.71 % Favored : 86.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.01 (0.37), residues: 492 helix: 1.34 (0.25), residues: 370 sheet: -0.73 (1.56), residues: 10 loop : 1.95 (0.65), residues: 112 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.003 TRP A 274 HIS 0.010 0.002 HIS A 34 PHE 0.024 0.003 PHE A 40 TYR 0.028 0.003 TYR A 354 ARG 0.007 0.001 ARG A 134 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 984 Ramachandran restraints generated. 492 Oldfield, 0 Emsley, 492 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 984 Ramachandran restraints generated. 492 Oldfield, 0 Emsley, 492 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 73 residues out of total 420 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 61 time to evaluate : 0.441 Fit side-chains REVERT: A 205 ASN cc_start: 0.8247 (m-40) cc_final: 0.8043 (m110) outliers start: 12 outliers final: 7 residues processed: 67 average time/residue: 1.3139 time to fit residues: 90.9397 Evaluate side-chains 69 residues out of total 420 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 62 time to evaluate : 0.413 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 25 VAL Chi-restraints excluded: chain A residue 31 MET Chi-restraints excluded: chain A residue 206 CYS Chi-restraints excluded: chain A residue 211 VAL Chi-restraints excluded: chain A residue 232 LEU Chi-restraints excluded: chain A residue 297 LYS Chi-restraints excluded: chain A residue 327 MET Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 50 random chunks: chunk 37 optimal weight: 5.9990 chunk 18 optimal weight: 0.8980 chunk 7 optimal weight: 10.0000 chunk 49 optimal weight: 0.8980 chunk 3 optimal weight: 1.9990 chunk 0 optimal weight: 10.0000 chunk 34 optimal weight: 0.2980 chunk 11 optimal weight: 0.8980 chunk 4 optimal weight: 3.9990 chunk 33 optimal weight: 0.7980 chunk 25 optimal weight: 7.9990 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 9 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3981 r_free = 0.3981 target = 0.181483 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3609 r_free = 0.3609 target = 0.147481 restraints weight = 2827.663| |-----------------------------------------------------------------------------| r_work (start): 0.3588 rms_B_bonded: 0.91 r_work: 0.3320 rms_B_bonded: 1.88 restraints_weight: 0.5000 r_work: 0.3214 rms_B_bonded: 3.08 restraints_weight: 0.2500 r_work (final): 0.3214 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8468 moved from start: 0.1237 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= 0.157 Angle : 0.507 6.824 5393 Z= 0.272 Chirality : 0.038 0.131 631 Planarity : 0.004 0.029 671 Dihedral : 3.827 15.115 542 Min Nonbonded Distance : 2.572 Molprobity Statistics. All-atom Clashscore : 2.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.81 % Favored : 99.19 % Rotamer: Outliers : 1.67 % Allowed : 11.90 % Favored : 86.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.67 (0.38), residues: 492 helix: 1.93 (0.27), residues: 374 sheet: -0.21 (1.62), residues: 10 loop : 1.70 (0.66), 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 0.013 0.001 PHE A 351 TYR 0.018 0.001 TYR A 264 ARG 0.004 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 72 residues out of total 420 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 65 time to evaluate : 0.398 Fit side-chains outliers start: 7 outliers final: 5 residues processed: 66 average time/residue: 1.3505 time to fit residues: 91.8948 Evaluate side-chains 66 residues out of total 420 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 61 time to evaluate : 0.445 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 25 VAL Chi-restraints excluded: chain A residue 207 MET Chi-restraints excluded: chain A residue 297 LYS Chi-restraints excluded: chain A residue 327 MET Chi-restraints excluded: chain A residue 337 HIS Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 50 random chunks: chunk 0 optimal weight: 10.0000 chunk 27 optimal weight: 6.9990 chunk 30 optimal weight: 6.9990 chunk 44 optimal weight: 0.8980 chunk 49 optimal weight: 5.9990 chunk 13 optimal weight: 4.9990 chunk 1 optimal weight: 1.9990 chunk 42 optimal weight: 4.9990 chunk 2 optimal weight: 2.9990 chunk 16 optimal weight: 5.9990 chunk 31 optimal weight: 0.7980 overall best weight: 2.3386 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3956 r_free = 0.3956 target = 0.178953 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3564 r_free = 0.3564 target = 0.143604 restraints weight = 2846.906| |-----------------------------------------------------------------------------| r_work (start): 0.3540 rms_B_bonded: 0.85 r_work: 0.3280 rms_B_bonded: 1.79 restraints_weight: 0.5000 r_work: 0.3178 rms_B_bonded: 2.86 restraints_weight: 0.2500 r_work (final): 0.3178 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8522 moved from start: 0.1137 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 3964 Z= 0.236 Angle : 0.570 6.915 5393 Z= 0.311 Chirality : 0.041 0.148 631 Planarity : 0.005 0.033 671 Dihedral : 3.954 15.279 542 Min Nonbonded Distance : 2.583 Molprobity Statistics. All-atom Clashscore : 3.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.81 % Favored : 99.19 % 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: 1.80 (0.26), residues: 371 sheet: -0.31 (1.57), residues: 10 loop : 1.95 (0.66), residues: 111 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP A 274 HIS 0.007 0.001 HIS A 34 PHE 0.017 0.002 PHE A 40 TYR 0.024 0.002 TYR A 264 ARG 0.005 0.000 ARG A 134 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 984 Ramachandran restraints generated. 492 Oldfield, 0 Emsley, 492 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 984 Ramachandran restraints generated. 492 Oldfield, 0 Emsley, 492 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 74 residues out of total 420 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 64 time to evaluate : 0.403 Fit side-chains outliers start: 10 outliers final: 6 residues processed: 69 average time/residue: 1.3188 time to fit residues: 93.9062 Evaluate side-chains 67 residues out of total 420 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 61 time to evaluate : 0.424 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 25 VAL 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 327 MET Chi-restraints excluded: chain A residue 337 HIS Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 50 random chunks: chunk 32 optimal weight: 5.9990 chunk 23 optimal weight: 8.9990 chunk 46 optimal weight: 5.9990 chunk 25 optimal weight: 5.9990 chunk 14 optimal weight: 0.9980 chunk 6 optimal weight: 4.9990 chunk 7 optimal weight: 0.8980 chunk 5 optimal weight: 20.0000 chunk 8 optimal weight: 3.9990 chunk 29 optimal weight: 8.9990 chunk 0 optimal weight: 10.0000 overall best weight: 3.3786 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3941 r_free = 0.3941 target = 0.177478 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3550 r_free = 0.3550 target = 0.142450 restraints weight = 2794.495| |-----------------------------------------------------------------------------| r_work (start): 0.3551 rms_B_bonded: 0.87 r_work: 0.3286 rms_B_bonded: 1.81 restraints_weight: 0.5000 r_work: 0.3186 rms_B_bonded: 2.91 restraints_weight: 0.2500 r_work (final): 0.3186 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8546 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 : 0.005 0.053 3964 Z= 0.300 Angle : 0.623 6.960 5393 Z= 0.342 Chirality : 0.043 0.157 631 Planarity : 0.005 0.036 671 Dihedral : 4.106 15.621 542 Min Nonbonded Distance : 2.578 Molprobity Statistics. All-atom Clashscore : 3.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.02 % Favored : 98.98 % 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: 2.30 (0.37), residues: 492 helix: 1.57 (0.26), residues: 371 sheet: -0.58 (1.54), residues: 10 loop : 1.98 (0.66), residues: 111 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.003 TRP A 274 HIS 0.008 0.001 HIS A 34 PHE 0.021 0.003 PHE A 40 TYR 0.025 0.003 TYR A 264 ARG 0.005 0.001 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 72 residues out of total 420 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 62 time to evaluate : 0.456 Fit side-chains outliers start: 10 outliers final: 7 residues processed: 67 average time/residue: 1.2815 time to fit residues: 88.6282 Evaluate side-chains 69 residues out of total 420 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 62 time to evaluate : 0.405 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 25 VAL Chi-restraints excluded: chain A residue 206 CYS Chi-restraints excluded: chain A residue 207 MET Chi-restraints excluded: chain A residue 211 VAL Chi-restraints excluded: chain A residue 232 LEU Chi-restraints excluded: chain A residue 297 LYS Chi-restraints excluded: chain A residue 327 MET Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 50 random chunks: chunk 35 optimal weight: 2.9990 chunk 29 optimal weight: 3.9990 chunk 15 optimal weight: 6.9990 chunk 6 optimal weight: 2.9990 chunk 46 optimal weight: 0.8980 chunk 13 optimal weight: 4.9990 chunk 45 optimal weight: 0.9990 chunk 22 optimal weight: 5.9990 chunk 5 optimal weight: 20.0000 chunk 31 optimal weight: 6.9990 chunk 24 optimal weight: 0.8980 overall best weight: 1.7586 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3960 r_free = 0.3960 target = 0.179374 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3577 r_free = 0.3577 target = 0.144620 restraints weight = 2853.359| |-----------------------------------------------------------------------------| r_work (start): 0.3550 rms_B_bonded: 0.94 r_work: 0.3265 rms_B_bonded: 1.98 restraints_weight: 0.5000 r_work: 0.3169 rms_B_bonded: 3.04 restraints_weight: 0.2500 r_work (final): 0.3169 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8519 moved from start: 0.1150 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 3964 Z= 0.205 Angle : 0.551 6.906 5393 Z= 0.299 Chirality : 0.040 0.143 631 Planarity : 0.004 0.032 671 Dihedral : 3.945 14.763 542 Min Nonbonded Distance : 2.586 Molprobity Statistics. All-atom Clashscore : 3.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.81 % Favored : 99.19 % Rotamer: Outliers : 1.43 % Allowed : 13.10 % 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: 1.82 (0.26), residues: 371 sheet: -0.40 (1.56), residues: 10 loop : 1.88 (0.66), 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 0.015 0.002 PHE A 40 TYR 0.022 0.002 TYR A 264 ARG 0.004 0.000 ARG A 134 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 984 Ramachandran restraints generated. 492 Oldfield, 0 Emsley, 492 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 984 Ramachandran restraints generated. 492 Oldfield, 0 Emsley, 492 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 68 residues out of total 420 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 62 time to evaluate : 0.423 Fit side-chains outliers start: 6 outliers final: 5 residues processed: 65 average time/residue: 1.2946 time to fit residues: 86.8935 Evaluate side-chains 67 residues out of total 420 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 62 time to evaluate : 0.451 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 25 VAL Chi-restraints excluded: chain A residue 206 CYS Chi-restraints excluded: chain A residue 232 LEU Chi-restraints excluded: chain A residue 297 LYS Chi-restraints excluded: chain A residue 337 HIS Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 50 random chunks: chunk 40 optimal weight: 9.9990 chunk 37 optimal weight: 0.9980 chunk 30 optimal weight: 0.2980 chunk 1 optimal weight: 7.9990 chunk 2 optimal weight: 2.9990 chunk 12 optimal weight: 0.7980 chunk 4 optimal weight: 0.7980 chunk 28 optimal weight: 10.0000 chunk 45 optimal weight: 6.9990 chunk 10 optimal weight: 4.9990 chunk 25 optimal weight: 7.9990 overall best weight: 1.1782 ------------------------------------------------------------------------------- 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 = 0.3981 r_free = 0.3981 target = 0.181512 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3598 r_free = 0.3598 target = 0.146585 restraints weight = 2780.579| |-----------------------------------------------------------------------------| r_work (start): 0.3573 rms_B_bonded: 0.85 r_work: 0.3319 rms_B_bonded: 1.82 restraints_weight: 0.5000 r_work: 0.3221 rms_B_bonded: 2.88 restraints_weight: 0.2500 r_work (final): 0.3221 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8478 moved from start: 0.1301 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 3964 Z= 0.170 Angle : 0.520 6.827 5393 Z= 0.279 Chirality : 0.038 0.134 631 Planarity : 0.004 0.031 671 Dihedral : 3.819 14.352 542 Min Nonbonded Distance : 2.584 Molprobity Statistics. All-atom Clashscore : 2.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.81 % Favored : 99.19 % 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: 2.68 (0.38), residues: 492 helix: 1.96 (0.26), residues: 374 sheet: -0.24 (1.58), residues: 10 loop : 1.61 (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 0.002 TYR A 264 ARG 0.004 0.000 ARG A 134 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 984 Ramachandran restraints generated. 492 Oldfield, 0 Emsley, 492 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 984 Ramachandran restraints generated. 492 Oldfield, 0 Emsley, 492 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 69 residues out of total 420 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 62 time to evaluate : 0.394 Fit side-chains outliers start: 7 outliers final: 6 residues processed: 66 average time/residue: 1.3243 time to fit residues: 90.1725 Evaluate side-chains 64 residues out of total 420 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 58 time to evaluate : 0.431 ------------------------------------------------------------------------------- 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=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 50 random chunks: chunk 5 optimal weight: 0.0030 chunk 38 optimal weight: 0.0570 chunk 14 optimal weight: 3.9990 chunk 40 optimal weight: 0.6980 chunk 1 optimal weight: 8.9990 chunk 26 optimal weight: 0.9980 chunk 0 optimal weight: 10.0000 chunk 9 optimal weight: 9.9990 chunk 37 optimal weight: 0.6980 chunk 16 optimal weight: 5.9990 chunk 7 optimal weight: 6.9990 overall best weight: 0.4908 ------------------------------------------------------------------------------- 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 = 0.4016 r_free = 0.4016 target = 0.184775 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3644 r_free = 0.3644 target = 0.150445 restraints weight = 2858.296| |-----------------------------------------------------------------------------| r_work (start): 0.3627 rms_B_bonded: 0.86 r_work: 0.3388 rms_B_bonded: 1.75 restraints_weight: 0.5000 r_work: 0.3284 rms_B_bonded: 2.95 restraints_weight: 0.2500 r_work (final): 0.3284 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8406 moved from start: 0.1586 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.025 3964 Z= 0.143 Angle : 0.503 6.665 5393 Z= 0.263 Chirality : 0.037 0.123 631 Planarity : 0.004 0.029 671 Dihedral : 3.651 14.168 542 Min Nonbonded Distance : 2.578 Molprobity Statistics. All-atom Clashscore : 2.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.81 % Favored : 99.19 % Rotamer: Outliers : 1.43 % Allowed : 13.81 % 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: 2.92 (0.39), residues: 492 helix: 2.18 (0.27), residues: 374 sheet: 0.21 (1.59), residues: 10 loop : 1.45 (0.65), residues: 108 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP A 346 HIS 0.003 0.001 HIS A 217 PHE 0.015 0.001 PHE A 386 TYR 0.017 0.001 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 64 residues out of total 420 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 58 time to evaluate : 0.397 Fit side-chains REVERT: A 417 LYS cc_start: 0.7877 (mmtm) cc_final: 0.7470 (mmmt) outliers start: 6 outliers final: 3 residues processed: 60 average time/residue: 1.3206 time to fit residues: 81.8512 Evaluate side-chains 60 residues out of total 420 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 57 time to evaluate : 0.422 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 206 CYS Chi-restraints excluded: chain A residue 297 LYS Chi-restraints excluded: chain A residue 337 HIS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 50 random chunks: chunk 33 optimal weight: 0.9990 chunk 21 optimal weight: 10.0000 chunk 37 optimal weight: 0.9980 chunk 24 optimal weight: 2.9990 chunk 15 optimal weight: 4.9990 chunk 4 optimal weight: 0.0870 chunk 12 optimal weight: 0.9990 chunk 28 optimal weight: 0.0370 chunk 20 optimal weight: 3.9990 chunk 1 optimal weight: 7.9990 chunk 6 optimal weight: 3.9990 overall best weight: 0.6240 ------------------------------------------------------------------------------- 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 = 0.4016 r_free = 0.4016 target = 0.184869 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3644 r_free = 0.3644 target = 0.150661 restraints weight = 2861.009| |-----------------------------------------------------------------------------| r_work (start): 0.3615 rms_B_bonded: 0.85 r_work: 0.3377 rms_B_bonded: 1.74 restraints_weight: 0.5000 r_work: 0.3278 rms_B_bonded: 2.84 restraints_weight: 0.2500 r_work (final): 0.3278 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8414 moved from start: 0.1641 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.026 3964 Z= 0.143 Angle : 0.506 6.624 5393 Z= 0.263 Chirality : 0.037 0.124 631 Planarity : 0.004 0.029 671 Dihedral : 3.630 14.029 542 Min Nonbonded Distance : 2.584 Molprobity Statistics. All-atom Clashscore : 2.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.81 % Favored : 99.19 % Rotamer: Outliers : 1.43 % Allowed : 14.29 % 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: 2.90 (0.39), residues: 492 helix: 2.16 (0.27), residues: 374 sheet: 0.39 (1.60), residues: 10 loop : 1.44 (0.65), residues: 108 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP A 346 HIS 0.003 0.001 HIS A 34 PHE 0.016 0.002 PHE A 386 TYR 0.017 0.001 TYR A 264 ARG 0.003 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 66 residues out of total 420 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 60 time to evaluate : 0.424 Fit side-chains outliers start: 6 outliers final: 3 residues processed: 63 average time/residue: 1.3254 time to fit residues: 86.5125 Evaluate side-chains 61 residues out of total 420 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 58 time to evaluate : 0.548 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 206 CYS Chi-restraints excluded: chain A residue 297 LYS Chi-restraints excluded: chain A residue 337 HIS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 50 random chunks: chunk 9 optimal weight: 0.0010 chunk 17 optimal weight: 1.9990 chunk 14 optimal weight: 0.9990 chunk 41 optimal weight: 8.9990 chunk 3 optimal weight: 1.9990 chunk 47 optimal weight: 0.0470 chunk 33 optimal weight: 0.9990 chunk 6 optimal weight: 10.0000 chunk 45 optimal weight: 5.9990 chunk 20 optimal weight: 10.0000 chunk 27 optimal weight: 7.9990 overall best weight: 0.8090 ------------------------------------------------------------------------------- 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 = 0.4008 r_free = 0.4008 target = 0.184072 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3635 r_free = 0.3635 target = 0.149782 restraints weight = 2845.694| |-----------------------------------------------------------------------------| r_work (start): 0.3607 rms_B_bonded: 0.85 r_work: 0.3361 rms_B_bonded: 1.77 restraints_weight: 0.5000 r_work: 0.3259 rms_B_bonded: 2.88 restraints_weight: 0.2500 r_work (final): 0.3259 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8436 moved from start: 0.1622 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.028 3964 Z= 0.153 Angle : 0.518 6.704 5393 Z= 0.271 Chirality : 0.038 0.126 631 Planarity : 0.004 0.029 671 Dihedral : 3.661 14.019 542 Min Nonbonded Distance : 2.584 Molprobity Statistics. All-atom Clashscore : 2.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.02 % Favored : 98.98 % Rotamer: Outliers : 1.67 % Allowed : 14.29 % 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: 2.87 (0.38), residues: 492 helix: 2.13 (0.27), residues: 374 sheet: 0.37 (1.64), residues: 10 loop : 1.45 (0.65), 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 0.016 0.002 PHE A 386 TYR 0.018 0.001 TYR A 264 ARG 0.003 0.000 ARG A 134 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4665.93 seconds wall clock time: 80 minutes 1.59 seconds (4801.59 seconds total)