Starting phenix.real_space_refine on Tue Feb 11 02:50:00 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8sdu_40352/02_2025/8sdu_40352.cif Found real_map, /net/cci-nas-00/data/ceres_data/8sdu_40352/02_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_40352/02_2025/8sdu_40352.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8sdu_40352/02_2025/8sdu_40352.map" model { file = "/net/cci-nas-00/data/ceres_data/8sdu_40352/02_2025/8sdu_40352.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8sdu_40352/02_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-5592/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: 2.99, per 1000 atoms: 0.76 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: 0.80 Conformation dependent library (CDL) restraints added in 428.6 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: 0.39 Creating SS restraints... Processing helix chain 'A' and resid 2 through 10 removed outlier: 3.559A pdb=" N LEU A 6 " --> pdb=" O ALA A 2 " (cutoff:3.500A) Processing helix chain 'A' and resid 14 through 26 Processing helix chain 'A' and resid 27 through 36 removed outlier: 4.059A pdb=" N ALA A 32 " --> pdb=" O LEU A 28 " (cutoff:3.500A) removed outlier: 4.567A pdb=" N SER A 33 " --> pdb=" O LEU A 29 " (cutoff:3.500A) Processing helix chain 'A' and resid 37 through 42 Processing helix chain 'A' and resid 119 through 125 Processing helix chain 'A' and resid 127 through 130 Processing helix chain 'A' and resid 131 through 160 removed outlier: 4.185A pdb=" N GLN A 135 " --> pdb=" O ARG A 131 " (cutoff:3.500A) removed outlier: 3.636A pdb=" N ASP A 157 " --> pdb=" O GLY A 153 " (cutoff:3.500A) Processing helix chain 'A' and resid 160 through 181 Processing helix chain 'A' and resid 184 through 213 removed outlier: 3.640A pdb=" N MET A 207 " --> pdb=" O ALA A 203 " (cutoff:3.500A) Processing helix chain 'A' and resid 214 through 217 removed outlier: 6.055A pdb=" N HIS A 217 " --> pdb=" O MET A 214 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 214 through 217' Processing helix chain 'A' and resid 218 through 244 removed outlier: 3.613A pdb=" N VAL A 222 " --> pdb=" O THR A 218 " (cutoff:3.500A) removed outlier: 3.542A pdb=" N GLY A 223 " --> pdb=" O ARG A 219 " (cutoff:3.500A) removed outlier: 3.801A pdb=" N PHE A 235 " --> pdb=" O SER A 231 " (cutoff:3.500A) Processing helix chain 'A' and resid 246 through 256 Processing helix chain 'A' and resid 256 through 266 removed outlier: 3.936A pdb=" N ILE A 260 " --> pdb=" O VAL A 256 " (cutoff:3.500A) removed outlier: 4.009A pdb=" N TRP A 266 " --> pdb=" O PHE A 262 " (cutoff:3.500A) Processing helix chain 'A' and resid 271 through 278 Processing helix chain 'A' and resid 280 through 296 Processing helix chain 'A' and resid 297 through 303 Processing helix chain 'A' and resid 305 through 313 Processing helix chain 'A' and resid 327 through 332 Processing helix chain 'A' and resid 332 through 358 removed outlier: 3.914A pdb=" N LEU A 338 " --> pdb=" O THR A 334 " (cutoff:3.500A) Processing helix chain 'A' and resid 359 through 364 removed outlier: 3.600A pdb=" N PHE A 363 " --> pdb=" O LEU A 360 " (cutoff:3.500A) removed outlier: 3.973A pdb=" N GLY A 364 " --> pdb=" O GLN A 361 " (cutoff:3.500A) Processing helix chain 'A' and resid 366 through 392 removed outlier: 3.866A pdb=" N ASP A 378 " --> pdb=" O PHE A 374 " (cutoff:3.500A) removed outlier: 4.533A pdb=" N LEU A 379 " --> pdb=" O GLY A 375 " (cutoff:3.500A) Proline residue: A 380 - end of helix Processing helix chain 'A' and resid 393 through 415 removed outlier: 3.520A pdb=" N ILE A 414 " --> pdb=" O LEU A 410 " (cutoff:3.500A) Processing helix chain 'A' and resid 419 through 449 removed outlier: 3.650A pdb=" N LEU A 443 " --> pdb=" O ASN A 439 " (cutoff:3.500A) Processing helix chain 'A' and resid 453 through 477 Proline residue: A 473 - end of helix Processing helix chain 'A' and resid 478 through 481 Processing helix chain 'A' and resid 484 through 501 Proline residue: A 494 - end of helix Processing helix chain 'A' and resid 502 through 504 No H-bonds generated for 'chain 'A' and resid 502 through 504' Processing helix chain 'A' and resid 515 through 524 Processing sheet with id=AA1, first strand: chain 'A' and resid 47 through 49 Processing sheet with id=AA2, first strand: chain 'A' and resid 80 through 81 274 hydrogen bonds defined for protein. 810 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 1.12 Time building geometry restraints manager: 0.94 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: 0.570 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: 0.220 Check model and map are aligned: 0.030 Set scattering table: 0.030 Process input model: 13.600 Find NCS groups from input model: 0.030 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:11.820 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 26.320 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8463 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.031 3964 Z= 0.150 Angle : 0.490 7.056 5393 Z= 0.248 Chirality : 0.037 0.137 631 Planarity : 0.004 0.046 671 Dihedral : 14.855 89.444 1413 Min Nonbonded Distance : 2.231 Molprobity Statistics. All-atom Clashscore : 4.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.02 % Favored : 98.98 % Rotamer: Outliers : 0.71 % Allowed : 13.57 % Favored : 85.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.05 (0.38), residues: 492 helix: 1.37 (0.26), residues: 368 sheet: -0.05 (1.59), residues: 10 loop : 1.90 (0.68), residues: 114 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP A 274 HIS 0.004 0.001 HIS A 34 PHE 0.012 0.001 PHE A 16 TYR 0.017 0.001 TYR A 264 ARG 0.003 0.000 ARG A 219 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 984 Ramachandran restraints generated. 492 Oldfield, 0 Emsley, 492 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 984 Ramachandran restraints generated. 492 Oldfield, 0 Emsley, 492 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 69 residues out of total 420 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 66 time to evaluate : 0.369 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: 1.3953 time to fit residues: 97.5733 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 : 0.434 ------------------------------------------------------------------------------- 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 = 0.3979 r_free = 0.3979 target = 0.181068 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3598 r_free = 0.3598 target = 0.146377 restraints weight = 2835.154| |-----------------------------------------------------------------------------| r_work (start): 0.3568 rms_B_bonded: 0.83 r_work: 0.3322 rms_B_bonded: 1.75 restraints_weight: 0.5000 r_work: 0.3226 rms_B_bonded: 2.75 restraints_weight: 0.2500 r_work (final): 0.3226 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8486 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 : 0.431 Fit side-chains outliers start: 4 outliers final: 3 residues processed: 66 average time/residue: 1.3676 time to fit residues: 93.2269 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 : 0.458 ------------------------------------------------------------------------------- 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: 1.9990 chunk 33 optimal weight: 4.9990 chunk 40 optimal weight: 5.9990 chunk 20 optimal weight: 8.9990 chunk 10 optimal weight: 6.9990 chunk 7 optimal weight: 9.9990 chunk 29 optimal weight: 6.9990 chunk 32 optimal weight: 5.9990 overall best weight: 3.9988 ------------------------------------------------------------------------------- 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 = 0.3944 r_free = 0.3944 target = 0.177630 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3547 r_free = 0.3547 target = 0.142055 restraints weight = 2778.926| |-----------------------------------------------------------------------------| r_work (start): 0.3525 rms_B_bonded: 0.85 r_work: 0.3275 rms_B_bonded: 1.74 restraints_weight: 0.5000 r_work: 0.3172 rms_B_bonded: 2.84 restraints_weight: 0.2500 r_work (final): 0.3172 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8553 moved from start: 0.0956 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.058 3964 Z= 0.339 Angle : 0.650 7.042 5393 Z= 0.358 Chirality : 0.045 0.160 631 Planarity : 0.006 0.041 671 Dihedral : 4.131 16.393 542 Min Nonbonded Distance : 2.563 Molprobity Statistics. All-atom Clashscore : 3.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.02 % Favored : 98.98 % Rotamer: Outliers : 2.62 % Allowed : 10.95 % 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: 2.14 (0.37), residues: 492 helix: 1.45 (0.25), residues: 370 sheet: -0.67 (1.57), residues: 10 loop : 1.98 (0.66), residues: 112 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.003 TRP A 274 HIS 0.010 0.002 HIS A 34 PHE 0.022 0.003 PHE A 40 TYR 0.026 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 74 residues out of total 420 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 63 time to evaluate : 0.447 Fit side-chains outliers start: 11 outliers final: 6 residues processed: 67 average time/residue: 1.3655 time to fit residues: 94.5449 Evaluate side-chains 70 residues out of total 420 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 64 time to evaluate : 0.460 ------------------------------------------------------------------------------- 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 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: 6.9990 chunk 18 optimal weight: 0.9990 chunk 7 optimal weight: 10.0000 chunk 49 optimal weight: 5.9990 chunk 3 optimal weight: 0.5980 chunk 0 optimal weight: 10.0000 chunk 34 optimal weight: 0.8980 chunk 11 optimal weight: 2.9990 chunk 4 optimal weight: 4.9990 chunk 33 optimal weight: 1.9990 chunk 25 optimal weight: 0.9990 overall best weight: 1.0986 ------------------------------------------------------------------------------- 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 = 0.3975 r_free = 0.3975 target = 0.180902 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3600 r_free = 0.3600 target = 0.146850 restraints weight = 2812.227| |-----------------------------------------------------------------------------| r_work (start): 0.3578 rms_B_bonded: 0.82 r_work: 0.3319 rms_B_bonded: 1.75 restraints_weight: 0.5000 r_work: 0.3213 rms_B_bonded: 2.91 restraints_weight: 0.2500 r_work (final): 0.3213 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8482 moved from start: 0.1158 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 3964 Z= 0.169 Angle : 0.520 6.843 5393 Z= 0.281 Chirality : 0.038 0.133 631 Planarity : 0.004 0.032 671 Dihedral : 3.859 15.289 542 Min Nonbonded Distance : 2.574 Molprobity Statistics. All-atom Clashscore : 2.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.81 % Favored : 99.19 % Rotamer: Outliers : 2.14 % Allowed : 11.67 % Favored : 86.19 % 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: 1.86 (0.26), residues: 374 sheet: -0.35 (1.60), residues: 10 loop : 1.71 (0.66), 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 386 TYR 0.020 0.001 TYR A 264 ARG 0.003 0.000 ARG A 134 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 984 Ramachandran restraints generated. 492 Oldfield, 0 Emsley, 492 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 984 Ramachandran restraints generated. 492 Oldfield, 0 Emsley, 492 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 72 residues out of total 420 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 63 time to evaluate : 0.461 Fit side-chains outliers start: 9 outliers final: 6 residues processed: 66 average time/residue: 1.3584 time to fit residues: 92.6095 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 : 0.405 ------------------------------------------------------------------------------- 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 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: 5.9990 chunk 30 optimal weight: 5.9990 chunk 44 optimal weight: 0.9980 chunk 49 optimal weight: 4.9990 chunk 13 optimal weight: 4.9990 chunk 1 optimal weight: 2.9990 chunk 42 optimal weight: 1.9990 chunk 2 optimal weight: 2.9990 chunk 16 optimal weight: 5.9990 chunk 31 optimal weight: 3.9990 overall best weight: 2.5988 ------------------------------------------------------------------------------- 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 = 0.3949 r_free = 0.3949 target = 0.178353 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3559 r_free = 0.3559 target = 0.143361 restraints weight = 2842.454| |-----------------------------------------------------------------------------| r_work (start): 0.3560 rms_B_bonded: 0.88 r_work: 0.3297 rms_B_bonded: 1.80 restraints_weight: 0.5000 r_work: 0.3196 rms_B_bonded: 2.92 restraints_weight: 0.2500 r_work (final): 0.3196 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8531 moved from start: 0.1080 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.046 3964 Z= 0.252 Angle : 0.584 6.982 5393 Z= 0.319 Chirality : 0.042 0.149 631 Planarity : 0.005 0.035 671 Dihedral : 3.994 15.515 542 Min Nonbonded Distance : 2.584 Molprobity Statistics. All-atom Clashscore : 3.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.02 % Favored : 98.98 % Rotamer: Outliers : 2.14 % Allowed : 12.38 % 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: 2.47 (0.38), residues: 492 helix: 1.71 (0.26), residues: 371 sheet: -0.52 (1.58), 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 0.007 0.001 HIS A 34 PHE 0.018 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 71 residues out of total 420 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 62 time to evaluate : 0.418 Fit side-chains outliers start: 9 outliers final: 6 residues processed: 67 average time/residue: 1.2684 time to fit residues: 87.8768 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 : 0.477 ------------------------------------------------------------------------------- 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 327 MET 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: 7.9990 chunk 25 optimal weight: 1.9990 chunk 14 optimal weight: 1.9990 chunk 6 optimal weight: 1.9990 chunk 7 optimal weight: 0.9980 chunk 5 optimal weight: 20.0000 chunk 8 optimal weight: 7.9990 chunk 29 optimal weight: 7.9990 chunk 0 optimal weight: 10.0000 overall best weight: 2.5988 ------------------------------------------------------------------------------- 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 = 0.3946 r_free = 0.3946 target = 0.178064 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3553 r_free = 0.3553 target = 0.142761 restraints weight = 2799.685| |-----------------------------------------------------------------------------| r_work (start): 0.3563 rms_B_bonded: 0.84 r_work: 0.3312 rms_B_bonded: 1.75 restraints_weight: 0.5000 r_work: 0.3213 rms_B_bonded: 2.79 restraints_weight: 0.2500 r_work (final): 0.3213 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8523 moved from start: 0.1103 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.046 3964 Z= 0.251 Angle : 0.585 6.938 5393 Z= 0.320 Chirality : 0.042 0.149 631 Planarity : 0.005 0.035 671 Dihedral : 4.025 15.471 542 Min Nonbonded Distance : 2.584 Molprobity Statistics. All-atom Clashscore : 3.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.81 % Favored : 99.19 % Rotamer: Outliers : 2.62 % Allowed : 12.14 % 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: 2.43 (0.37), residues: 492 helix: 1.67 (0.26), residues: 371 sheet: -0.46 (1.57), residues: 10 loop : 1.97 (0.66), residues: 111 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP A 274 HIS 0.007 0.001 HIS A 34 PHE 0.018 0.002 PHE A 40 TYR 0.023 0.002 TYR A 264 ARG 0.005 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 71 residues out of total 420 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 60 time to evaluate : 0.461 Fit side-chains outliers start: 11 outliers final: 6 residues processed: 66 average time/residue: 1.3467 time to fit residues: 91.8619 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 : 0.432 ------------------------------------------------------------------------------- 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 211 VAL Chi-restraints excluded: chain A residue 232 LEU Chi-restraints excluded: chain A residue 297 LYS Chi-restraints excluded: chain A residue 391 SER Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 50 random chunks: chunk 35 optimal weight: 3.9990 chunk 29 optimal weight: 4.9990 chunk 15 optimal weight: 8.9990 chunk 6 optimal weight: 30.0000 chunk 46 optimal weight: 0.9990 chunk 13 optimal weight: 0.0050 chunk 45 optimal weight: 0.7980 chunk 22 optimal weight: 3.9990 chunk 5 optimal weight: 0.9980 chunk 31 optimal weight: 6.9990 chunk 24 optimal weight: 1.9990 overall best weight: 0.9598 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 4 ASN A 9 GLN A 205 ASN A 419 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3988 r_free = 0.3988 target = 0.182152 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3606 r_free = 0.3606 target = 0.147312 restraints weight = 2872.488| |-----------------------------------------------------------------------------| r_work (start): 0.3581 rms_B_bonded: 0.86 r_work: 0.3330 rms_B_bonded: 1.84 restraints_weight: 0.5000 r_work: 0.3231 rms_B_bonded: 2.89 restraints_weight: 0.2500 r_work (final): 0.3231 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8463 moved from start: 0.1327 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= 0.159 Angle : 0.510 6.824 5393 Z= 0.274 Chirality : 0.038 0.130 631 Planarity : 0.004 0.029 671 Dihedral : 3.792 14.344 542 Min Nonbonded Distance : 2.582 Molprobity Statistics. All-atom Clashscore : 2.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.81 % Favored : 99.19 % Rotamer: Outliers : 1.67 % Allowed : 13.10 % Favored : 85.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.75 (0.38), residues: 492 helix: 2.00 (0.27), residues: 374 sheet: 0.06 (1.55), residues: 10 loop : 1.65 (0.67), residues: 108 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP A 274 HIS 0.004 0.001 HIS A 34 PHE 0.015 0.002 PHE A 386 TYR 0.019 0.001 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 65 residues out of total 420 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 58 time to evaluate : 0.485 Fit side-chains outliers start: 7 outliers final: 5 residues processed: 62 average time/residue: 1.3488 time to fit residues: 86.3510 Evaluate side-chains 62 residues out of total 420 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 57 time to evaluate : 0.475 ------------------------------------------------------------------------------- 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 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: 1.9990 chunk 37 optimal weight: 0.9990 chunk 30 optimal weight: 0.9980 chunk 1 optimal weight: 0.3980 chunk 2 optimal weight: 2.9990 chunk 12 optimal weight: 0.9980 chunk 4 optimal weight: 0.0970 chunk 28 optimal weight: 5.9990 chunk 45 optimal weight: 6.9990 chunk 10 optimal weight: 5.9990 chunk 25 optimal weight: 7.9990 overall best weight: 0.6980 ------------------------------------------------------------------------------- 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 = 0.4012 r_free = 0.4012 target = 0.184404 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3639 r_free = 0.3639 target = 0.150132 restraints weight = 2810.321| |-----------------------------------------------------------------------------| r_work (start): 0.3605 rms_B_bonded: 0.85 r_work: 0.3358 rms_B_bonded: 1.78 restraints_weight: 0.5000 r_work: 0.3258 rms_B_bonded: 2.88 restraints_weight: 0.2500 r_work (final): 0.3258 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8430 moved from start: 0.1489 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= 0.145 Angle : 0.496 6.702 5393 Z= 0.262 Chirality : 0.037 0.125 631 Planarity : 0.004 0.027 671 Dihedral : 3.668 14.146 542 Min Nonbonded Distance : 2.582 Molprobity Statistics. All-atom Clashscore : 2.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.81 % Favored : 99.19 % Rotamer: Outliers : 1.19 % Allowed : 13.57 % 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: 2.91 (0.39), residues: 492 helix: 2.15 (0.27), residues: 374 sheet: 0.29 (1.61), residues: 10 loop : 1.55 (0.66), 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 0.018 0.001 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: 5 poor density : 64 time to evaluate : 0.435 Fit side-chains REVERT: A 417 LYS cc_start: 0.7878 (mmtm) cc_final: 0.7467 (mmmt) outliers start: 5 outliers final: 3 residues processed: 67 average time/residue: 1.3890 time to fit residues: 95.9923 Evaluate side-chains 64 residues out of total 420 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 61 time to evaluate : 0.452 ------------------------------------------------------------------------------- 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=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 50 random chunks: chunk 5 optimal weight: 0.8980 chunk 38 optimal weight: 10.0000 chunk 14 optimal weight: 3.9990 chunk 40 optimal weight: 0.8980 chunk 1 optimal weight: 0.0040 chunk 26 optimal weight: 0.0060 chunk 0 optimal weight: 9.9990 chunk 9 optimal weight: 0.0070 chunk 37 optimal weight: 0.9980 chunk 16 optimal weight: 5.9990 chunk 7 optimal weight: 0.5980 overall best weight: 0.3026 ------------------------------------------------------------------------------- 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 Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4061 r_free = 0.4061 target = 0.189092 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3705 r_free = 0.3705 target = 0.155740 restraints weight = 2901.106| |-----------------------------------------------------------------------------| r_work (start): 0.3683 rms_B_bonded: 0.86 r_work: 0.3455 rms_B_bonded: 1.78 restraints_weight: 0.5000 r_work: 0.3361 rms_B_bonded: 2.91 restraints_weight: 0.2500 r_work (final): 0.3361 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8341 moved from start: 0.1842 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.022 3964 Z= 0.131 Angle : 0.479 6.543 5393 Z= 0.249 Chirality : 0.037 0.121 631 Planarity : 0.004 0.027 671 Dihedral : 3.526 13.940 542 Min Nonbonded Distance : 2.589 Molprobity Statistics. All-atom Clashscore : 2.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.81 % Favored : 99.19 % Rotamer: Outliers : 0.95 % Allowed : 13.81 % 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: 2.95 (0.39), residues: 492 helix: 2.24 (0.27), residues: 375 sheet: 0.37 (1.66), residues: 10 loop : 1.27 (0.65), residues: 107 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 274 HIS 0.003 0.001 HIS A 217 PHE 0.017 0.001 PHE A 386 TYR 0.017 0.001 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 69 residues out of total 420 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 65 time to evaluate : 0.431 Fit side-chains outliers start: 4 outliers final: 2 residues processed: 66 average time/residue: 1.3799 time to fit residues: 93.9896 Evaluate side-chains 62 residues out of total 420 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 60 time to evaluate : 0.446 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 206 CYS Chi-restraints excluded: chain A residue 297 LYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 50 random chunks: chunk 33 optimal weight: 9.9990 chunk 21 optimal weight: 4.9990 chunk 37 optimal weight: 0.9990 chunk 24 optimal weight: 2.9990 chunk 15 optimal weight: 10.0000 chunk 4 optimal weight: 0.0980 chunk 12 optimal weight: 0.7980 chunk 28 optimal weight: 10.0000 chunk 20 optimal weight: 3.9990 chunk 1 optimal weight: 7.9990 chunk 6 optimal weight: 6.9990 overall best weight: 1.7786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 4 ASN 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 = 0.3982 r_free = 0.3982 target = 0.181603 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3594 r_free = 0.3594 target = 0.146353 restraints weight = 2820.069| |-----------------------------------------------------------------------------| r_work (start): 0.3558 rms_B_bonded: 0.86 r_work: 0.3307 rms_B_bonded: 1.80 restraints_weight: 0.5000 r_work: 0.3208 rms_B_bonded: 2.83 restraints_weight: 0.2500 r_work (final): 0.3208 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8488 moved from start: 0.1384 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 3964 Z= 0.201 Angle : 0.550 6.737 5393 Z= 0.293 Chirality : 0.040 0.138 631 Planarity : 0.004 0.034 671 Dihedral : 3.786 14.808 542 Min Nonbonded Distance : 2.585 Molprobity Statistics. All-atom Clashscore : 2.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.02 % Favored : 98.98 % Rotamer: Outliers : 0.71 % Allowed : 14.05 % 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: 2.82 (0.38), residues: 492 helix: 2.03 (0.26), residues: 371 sheet: 0.35 (1.59), residues: 10 loop : 1.72 (0.64), residues: 111 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP A 274 HIS 0.006 0.001 HIS A 34 PHE 0.016 0.002 PHE A 386 TYR 0.022 0.002 TYR A 264 ARG 0.004 0.000 ARG A 134 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 984 Ramachandran restraints generated. 492 Oldfield, 0 Emsley, 492 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 984 Ramachandran restraints generated. 492 Oldfield, 0 Emsley, 492 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 62 residues out of total 420 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 59 time to evaluate : 0.424 Fit side-chains outliers start: 3 outliers final: 2 residues processed: 62 average time/residue: 1.3869 time to fit residues: 88.8749 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 : 0.457 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 206 CYS Chi-restraints excluded: chain A residue 297 LYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 50 random chunks: chunk 9 optimal weight: 0.0770 chunk 17 optimal weight: 0.5980 chunk 14 optimal weight: 3.9990 chunk 41 optimal weight: 0.9990 chunk 3 optimal weight: 5.9990 chunk 47 optimal weight: 3.9990 chunk 33 optimal weight: 4.9990 chunk 6 optimal weight: 9.9990 chunk 45 optimal weight: 0.7980 chunk 20 optimal weight: 3.9990 chunk 27 optimal weight: 0.9980 overall best weight: 0.6940 ------------------------------------------------------------------------------- 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 = 0.184029 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3642 r_free = 0.3642 target = 0.150368 restraints weight = 2852.916| |-----------------------------------------------------------------------------| r_work (start): 0.3616 rms_B_bonded: 0.92 r_work: 0.3322 rms_B_bonded: 2.26 restraints_weight: 0.5000 r_work: 0.3215 rms_B_bonded: 3.78 restraints_weight: 0.2500 r_work (final): 0.3215 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8473 moved from start: 0.1581 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= 0.149 Angle : 0.508 6.718 5393 Z= 0.267 Chirality : 0.038 0.126 631 Planarity : 0.004 0.028 671 Dihedral : 3.657 14.371 542 Min Nonbonded Distance : 2.578 Molprobity Statistics. All-atom Clashscore : 2.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.81 % Favored : 99.19 % Rotamer: Outliers : 0.71 % Allowed : 14.05 % 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: 2.92 (0.38), residues: 492 helix: 2.16 (0.27), residues: 374 sheet: 0.44 (1.60), residues: 10 loop : 1.51 (0.65), residues: 108 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 274 HIS 0.003 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 134 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4568.62 seconds wall clock time: 80 minutes 52.46 seconds (4852.46 seconds total)