Starting phenix.real_space_refine on Tue Feb 11 06:50:24 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7yim_33861/02_2025/7yim_33861.cif Found real_map, /net/cci-nas-00/data/ceres_data/7yim_33861/02_2025/7yim_33861.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.6 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/7yim_33861/02_2025/7yim_33861.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7yim_33861/02_2025/7yim_33861.map" model { file = "/net/cci-nas-00/data/ceres_data/7yim_33861/02_2025/7yim_33861.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7yim_33861/02_2025/7yim_33861.cif" } resolution = 2.6 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= -0.006 sd= 0.095 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 40 5.16 5 C 2925 2.51 5 N 791 2.21 5 O 901 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 43 residue(s): 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5592/modules/chem_data/mon_lib" Total number of atoms: 4657 Number of models: 1 Model: "" Number of chains: 1 Chain: "A" Number of atoms: 4657 Number of conformers: 1 Conformer: "" Number of residues, atoms: 592, 4657 Classifications: {'peptide': 592} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 21, 'TRANS': 570} Time building chain proxies: 3.12, per 1000 atoms: 0.67 Number of scatterers: 4657 At special positions: 0 Unit cell: (69.5594, 91.3616, 103.82, 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 40 16.00 O 901 8.00 N 791 7.00 C 2925 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=16, symmetry=0 Simple disulfide: pdb=" SG CYS A 37 " - pdb=" SG CYS A 86 " distance=2.03 Simple disulfide: pdb=" SG CYS A 99 " - pdb=" SG CYS A 114 " distance=2.02 Simple disulfide: pdb=" SG CYS A 113 " - pdb=" SG CYS A 124 " distance=2.02 Simple disulfide: pdb=" SG CYS A 148 " - pdb=" SG CYS A 193 " distance=2.03 Simple disulfide: pdb=" SG CYS A 192 " - pdb=" SG CYS A 201 " distance=2.03 Simple disulfide: pdb=" SG CYS A 224 " - pdb=" SG CYS A 270 " distance=2.01 Simple disulfide: pdb=" SG CYS A 269 " - pdb=" SG CYS A 277 " distance=2.00 Simple disulfide: pdb=" SG CYS A 289 " - pdb=" SG CYS A 303 " distance=2.03 Simple disulfide: pdb=" SG CYS A 302 " - pdb=" SG CYS A 313 " distance=2.04 Simple disulfide: pdb=" SG CYS A 384 " - pdb=" SG CYS A 393 " distance=2.02 Simple disulfide: pdb=" SG CYS A 416 " - pdb=" SG CYS A 462 " distance=2.01 Simple disulfide: pdb=" SG CYS A 461 " - pdb=" SG CYS A 472 " distance=2.01 Simple disulfide: pdb=" SG CYS A 485 " - pdb=" SG CYS A 501 " distance=2.01 Simple disulfide: pdb=" SG CYS A 500 " - pdb=" SG CYS A 511 " distance=2.05 Simple disulfide: pdb=" SG CYS A 538 " - pdb=" SG CYS A 583 " distance=2.03 Simple disulfide: pdb=" SG CYS A 582 " - pdb=" SG CYS A 591 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 1.03 Conformation dependent library (CDL) restraints added in 609.7 milliseconds 1180 Ramachandran restraints generated. 590 Oldfield, 0 Emsley, 590 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1132 Finding SS restraints... Secondary structure from input PDB file: 28 helices and 0 sheets defined 75.0% alpha, 0.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.44 Creating SS restraints... Processing helix chain 'A' and resid 30 through 34 removed outlier: 4.209A pdb=" N ASP A 33 " --> pdb=" O SER A 30 " (cutoff:3.500A) Processing helix chain 'A' and resid 42 through 55 removed outlier: 3.750A pdb=" N LEU A 46 " --> pdb=" O SER A 42 " (cutoff:3.500A) Processing helix chain 'A' and resid 59 through 75 removed outlier: 3.573A pdb=" N GLU A 75 " --> pdb=" O LEU A 71 " (cutoff:3.500A) Processing helix chain 'A' and resid 90 through 101 Processing helix chain 'A' and resid 101 through 108 removed outlier: 3.546A pdb=" N LEU A 105 " --> pdb=" O GLU A 101 " (cutoff:3.500A) Processing helix chain 'A' and resid 111 through 116 removed outlier: 3.613A pdb=" N SER A 115 " --> pdb=" O ASP A 112 " (cutoff:3.500A) removed outlier: 3.511A pdb=" N GLN A 116 " --> pdb=" O CYS A 113 " (cutoff:3.500A) Processing helix chain 'A' and resid 117 through 128 Processing helix chain 'A' and resid 143 through 154 removed outlier: 3.629A pdb=" N ASP A 154 " --> pdb=" O ALA A 150 " (cutoff:3.500A) Processing helix chain 'A' and resid 154 through 168 Processing helix chain 'A' and resid 174 through 193 Proline residue: A 190 - end of helix Processing helix chain 'A' and resid 197 through 231 removed outlier: 3.915A pdb=" N THR A 208 " --> pdb=" O THR A 204 " (cutoff:3.500A) removed outlier: 4.883A pdb=" N VAL A 209 " --> pdb=" O LYS A 205 " (cutoff:3.500A) Processing helix chain 'A' and resid 231 through 247 Processing helix chain 'A' and resid 251 through 271 Processing helix chain 'A' and resid 273 through 290 Processing helix chain 'A' and resid 301 through 305 removed outlier: 4.018A pdb=" N LEU A 305 " --> pdb=" O CYS A 302 " (cutoff:3.500A) Processing helix chain 'A' and resid 306 through 317 Processing helix chain 'A' and resid 343 through 361 Processing helix chain 'A' and resid 366 through 385 removed outlier: 3.746A pdb=" N PHE A 385 " --> pdb=" O LEU A 381 " (cutoff:3.500A) Processing helix chain 'A' and resid 389 through 399 removed outlier: 4.181A pdb=" N CYS A 393 " --> pdb=" O ASN A 389 " (cutoff:3.500A) Processing helix chain 'A' and resid 402 through 439 removed outlier: 7.982A pdb=" N GLU A 424 " --> pdb=" O GLN A 420 " (cutoff:3.500A) removed outlier: 9.376A pdb=" N TYR A 425 " --> pdb=" O LYS A 421 " (cutoff:3.500A) removed outlier: 4.204A pdb=" N TYR A 426 " --> pdb=" O LEU A 422 " (cutoff:3.500A) Processing helix chain 'A' and resid 443 through 462 Processing helix chain 'A' and resid 467 through 491 removed outlier: 4.204A pdb=" N ALA A 471 " --> pdb=" O ASP A 467 " (cutoff:3.500A) Processing helix chain 'A' and resid 494 through 503 removed outlier: 3.527A pdb=" N GLY A 498 " --> pdb=" O ASN A 494 " (cutoff:3.500A) Processing helix chain 'A' and resid 507 through 514 Processing helix chain 'A' and resid 527 through 531 removed outlier: 3.999A pdb=" N LYS A 530 " --> pdb=" O SER A 527 " (cutoff:3.500A) Processing helix chain 'A' and resid 542 through 560 Processing helix chain 'A' and resid 565 through 582 Processing helix chain 'A' and resid 587 through 608 removed outlier: 3.913A pdb=" N CYS A 591 " --> pdb=" O GLU A 587 " (cutoff:3.500A) removed outlier: 4.586A pdb=" N GLN A 597 " --> pdb=" O ALA A 593 " (cutoff:3.500A) removed outlier: 4.094A pdb=" N LYS A 598 " --> pdb=" O GLU A 594 " (cutoff:3.500A) 312 hydrogen bonds defined for protein. 924 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: 1.28 Time building geometry restraints manager: 1.25 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.33: 1072 1.33 - 1.46: 1193 1.46 - 1.58: 2428 1.58 - 1.71: 0 1.71 - 1.84: 48 Bond restraints: 4741 Sorted by residual: bond pdb=" CB VAL A 355 " pdb=" CG2 VAL A 355 " ideal model delta sigma weight residual 1.521 1.408 0.113 3.30e-02 9.18e+02 1.17e+01 bond pdb=" C TYR A 174 " pdb=" N ALA A 175 " ideal model delta sigma weight residual 1.332 1.297 0.035 1.09e-02 8.42e+03 1.04e+01 bond pdb=" CG GLN A 245 " pdb=" CD GLN A 245 " ideal model delta sigma weight residual 1.516 1.439 0.077 2.50e-02 1.60e+03 9.56e+00 bond pdb=" CB GLN A 245 " pdb=" CG GLN A 245 " ideal model delta sigma weight residual 1.520 1.427 0.093 3.00e-02 1.11e+03 9.55e+00 bond pdb=" CG1 ILE A 314 " pdb=" CD1 ILE A 314 " ideal model delta sigma weight residual 1.513 1.400 0.113 3.90e-02 6.57e+02 8.40e+00 ... (remaining 4736 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.87: 6228 2.87 - 5.74: 147 5.74 - 8.61: 23 8.61 - 11.48: 1 11.48 - 14.36: 1 Bond angle restraints: 6400 Sorted by residual: angle pdb=" CA CYS A 591 " pdb=" CB CYS A 591 " pdb=" SG CYS A 591 " ideal model delta sigma weight residual 114.40 128.76 -14.36 2.30e+00 1.89e-01 3.90e+01 angle pdb=" C CYS A 591 " pdb=" CA CYS A 591 " pdb=" CB CYS A 591 " ideal model delta sigma weight residual 110.88 103.82 7.06 1.57e+00 4.06e-01 2.02e+01 angle pdb=" CA GLU A 81 " pdb=" CB GLU A 81 " pdb=" CG GLU A 81 " ideal model delta sigma weight residual 114.10 122.78 -8.68 2.00e+00 2.50e-01 1.88e+01 angle pdb=" C GLU A 398 " pdb=" N GLU A 399 " pdb=" CA GLU A 399 " ideal model delta sigma weight residual 122.60 116.29 6.31 1.56e+00 4.11e-01 1.64e+01 angle pdb=" C LYS A 581 " pdb=" N CYS A 582 " pdb=" CA CYS A 582 " ideal model delta sigma weight residual 122.54 115.64 6.90 1.82e+00 3.02e-01 1.44e+01 ... (remaining 6395 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.11: 2536 17.11 - 34.21: 342 34.21 - 51.31: 60 51.31 - 68.42: 19 68.42 - 85.52: 5 Dihedral angle restraints: 2962 sinusoidal: 1222 harmonic: 1740 Sorted by residual: dihedral pdb=" CB CYS A 582 " pdb=" SG CYS A 582 " pdb=" SG CYS A 591 " pdb=" CB CYS A 591 " ideal model delta sinusoidal sigma weight residual 93.00 173.66 -80.66 1 1.00e+01 1.00e-02 8.04e+01 dihedral pdb=" CA LYS A 76 " pdb=" C LYS A 76 " pdb=" N PRO A 77 " pdb=" CA PRO A 77 " ideal model delta harmonic sigma weight residual -180.00 -144.61 -35.39 0 5.00e+00 4.00e-02 5.01e+01 dihedral pdb=" CA SER A 117 " pdb=" C SER A 117 " pdb=" N GLU A 118 " pdb=" CA GLU A 118 " ideal model delta harmonic sigma weight residual -180.00 -146.39 -33.61 0 5.00e+00 4.00e-02 4.52e+01 ... (remaining 2959 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.070: 519 0.070 - 0.139: 176 0.139 - 0.209: 19 0.209 - 0.278: 4 0.278 - 0.348: 1 Chirality restraints: 719 Sorted by residual: chirality pdb=" CB ILE A 481 " pdb=" CA ILE A 481 " pdb=" CG1 ILE A 481 " pdb=" CG2 ILE A 481 " both_signs ideal model delta sigma weight residual False 2.64 2.30 0.35 2.00e-01 2.50e+01 3.02e+00 chirality pdb=" CB VAL A 355 " pdb=" CA VAL A 355 " pdb=" CG1 VAL A 355 " pdb=" CG2 VAL A 355 " both_signs ideal model delta sigma weight residual False -2.63 -2.37 -0.26 2.00e-01 2.50e+01 1.72e+00 chirality pdb=" CA PRO A 510 " pdb=" N PRO A 510 " pdb=" C PRO A 510 " pdb=" CB PRO A 510 " both_signs ideal model delta sigma weight residual False 2.72 2.46 0.25 2.00e-01 2.50e+01 1.61e+00 ... (remaining 716 not shown) Planarity restraints: 837 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ARG A 509 " 0.059 5.00e-02 4.00e+02 8.92e-02 1.27e+01 pdb=" N PRO A 510 " -0.154 5.00e-02 4.00e+02 pdb=" CA PRO A 510 " 0.045 5.00e-02 4.00e+02 pdb=" CD PRO A 510 " 0.050 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA PHE A 592 " -0.013 2.00e-02 2.50e+03 2.69e-02 7.25e+00 pdb=" C PHE A 592 " 0.047 2.00e-02 2.50e+03 pdb=" O PHE A 592 " -0.017 2.00e-02 2.50e+03 pdb=" N ALA A 593 " -0.016 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C ALA A 175 " 0.045 5.00e-02 4.00e+02 6.65e-02 7.07e+00 pdb=" N PRO A 176 " -0.115 5.00e-02 4.00e+02 pdb=" CA PRO A 176 " 0.032 5.00e-02 4.00e+02 pdb=" CD PRO A 176 " 0.038 5.00e-02 4.00e+02 ... (remaining 834 not shown) Histogram of nonbonded interaction distances: 2.27 - 2.80: 1194 2.80 - 3.32: 4406 3.32 - 3.85: 7985 3.85 - 4.37: 9276 4.37 - 4.90: 15248 Nonbonded interactions: 38109 Sorted by model distance: nonbonded pdb=" OE1 GLU A 165 " pdb=" NH1 ARG A 169 " model vdw 2.272 3.120 nonbonded pdb=" O ARG A 509 " pdb=" OG SER A 513 " model vdw 2.276 3.040 nonbonded pdb=" OE1 GLU A 62 " pdb=" OH TYR A 108 " model vdw 2.284 3.040 nonbonded pdb=" OG SER A 42 " pdb=" OD2 ASP A 45 " model vdw 2.294 3.040 nonbonded pdb=" O ALA A 44 " pdb=" OG1 THR A 48 " model vdw 2.311 3.040 ... (remaining 38104 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: 0.200 Set stop_for_unknowns flag: 0.010 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: 0.170 Check model and map are aligned: 0.040 Set scattering table: 0.040 Process input model: 14.680 Find NCS groups from input model: 0.050 Set up NCS constraints: 0.030 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:11.310 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 26.530 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6532 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 : 0.013 0.113 4741 Z= 0.829 Angle : 1.136 14.355 6400 Z= 0.635 Chirality : 0.068 0.348 719 Planarity : 0.009 0.089 837 Dihedral : 15.893 85.522 1782 Min Nonbonded Distance : 2.272 Molprobity Statistics. All-atom Clashscore : 6.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.92 % Favored : 95.08 % Rotamer: Outliers : 0.78 % Allowed : 6.59 % Favored : 92.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 4.76 % Twisted General : 0.18 % 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: -4.17 (0.25), residues: 590 helix: -2.57 (0.18), residues: 420 sheet: None (None), residues: 0 loop : -2.74 (0.38), residues: 170 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.007 TRP A 181 HIS 0.012 0.003 HIS A 483 PHE 0.031 0.005 PHE A 235 TYR 0.043 0.005 TYR A 185 ARG 0.008 0.001 ARG A 509 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1180 Ramachandran restraints generated. 590 Oldfield, 0 Emsley, 590 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1180 Ramachandran restraints generated. 590 Oldfield, 0 Emsley, 590 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 70 residues out of total 516 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 66 time to evaluate : 0.480 Fit side-chains revert: symmetry clash REVERT: A 519 GLU cc_start: 0.7173 (tm-30) cc_final: 0.6959 (tm-30) outliers start: 4 outliers final: 0 residues processed: 68 average time/residue: 1.6446 time to fit residues: 115.4169 Evaluate side-chains 37 residues out of total 516 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 37 time to evaluate : 0.518 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 59 random chunks: chunk 49 optimal weight: 0.8980 chunk 44 optimal weight: 1.9990 chunk 24 optimal weight: 0.9980 chunk 15 optimal weight: 0.7980 chunk 30 optimal weight: 1.9990 chunk 23 optimal weight: 0.9990 chunk 46 optimal weight: 1.9990 chunk 17 optimal weight: 0.9990 chunk 28 optimal weight: 0.8980 chunk 34 optimal weight: 0.8980 chunk 53 optimal weight: 0.9980 overall best weight: 0.8980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 116 GLN A 220 ASN A 389 ASN A 420 GLN A 534 HIS A 555 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4791 r_free = 0.4791 target = 0.205496 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.4378 r_free = 0.4378 target = 0.161462 restraints weight = 5301.662| |-----------------------------------------------------------------------------| r_work (start): 0.4378 rms_B_bonded: 2.40 r_work: 0.4249 rms_B_bonded: 3.19 restraints_weight: 0.5000 r_work: 0.4114 rms_B_bonded: 4.99 restraints_weight: 0.2500 r_work (final): 0.4114 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6484 moved from start: 0.2154 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 4741 Z= 0.211 Angle : 0.577 7.347 6400 Z= 0.312 Chirality : 0.040 0.154 719 Planarity : 0.005 0.051 837 Dihedral : 5.332 30.320 631 Min Nonbonded Distance : 2.461 Molprobity Statistics. All-atom Clashscore : 7.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.39 % Favored : 96.61 % Rotamer: Outliers : 1.16 % Allowed : 13.37 % Favored : 85.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 4.76 % 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: -1.61 (0.31), residues: 590 helix: -0.47 (0.23), residues: 429 sheet: None (None), residues: 0 loop : -2.47 (0.41), residues: 161 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.003 TRP A 181 HIS 0.008 0.001 HIS A 534 PHE 0.016 0.002 PHE A 235 TYR 0.019 0.001 TYR A 185 ARG 0.005 0.000 ARG A 168 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1180 Ramachandran restraints generated. 590 Oldfield, 0 Emsley, 590 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1180 Ramachandran restraints generated. 590 Oldfield, 0 Emsley, 590 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 66 residues out of total 516 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 60 time to evaluate : 0.498 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 43 LEU cc_start: 0.7037 (tp) cc_final: 0.6827 (tp) REVERT: A 96 GLU cc_start: 0.7051 (tm-30) cc_final: 0.6850 (tm-30) REVERT: A 228 LYS cc_start: 0.7752 (tttt) cc_final: 0.7109 (mppt) REVERT: A 548 MET cc_start: 0.6299 (mtp) cc_final: 0.6011 (tpt) outliers start: 6 outliers final: 1 residues processed: 63 average time/residue: 1.3259 time to fit residues: 86.8676 Evaluate side-chains 48 residues out of total 516 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 47 time to evaluate : 0.558 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 393 CYS Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 59 random chunks: chunk 43 optimal weight: 4.9990 chunk 55 optimal weight: 1.9990 chunk 57 optimal weight: 0.9990 chunk 5 optimal weight: 5.9990 chunk 15 optimal weight: 3.9990 chunk 3 optimal weight: 0.9980 chunk 44 optimal weight: 6.9990 chunk 24 optimal weight: 0.8980 chunk 53 optimal weight: 2.9990 chunk 34 optimal weight: 4.9990 chunk 40 optimal weight: 1.9990 overall best weight: 1.3786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 362 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4784 r_free = 0.4784 target = 0.204507 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.4340 r_free = 0.4340 target = 0.158571 restraints weight = 5392.987| |-----------------------------------------------------------------------------| r_work (start): 0.4337 rms_B_bonded: 2.45 r_work: 0.4204 rms_B_bonded: 3.28 restraints_weight: 0.5000 r_work (final): 0.4204 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6398 moved from start: 0.2532 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 4741 Z= 0.229 Angle : 0.582 8.447 6400 Z= 0.306 Chirality : 0.041 0.148 719 Planarity : 0.004 0.042 837 Dihedral : 4.883 27.109 631 Min Nonbonded Distance : 2.475 Molprobity Statistics. All-atom Clashscore : 8.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.90 % Favored : 96.10 % Rotamer: Outliers : 2.71 % Allowed : 14.34 % Favored : 82.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.64 (0.32), residues: 590 helix: 0.25 (0.23), residues: 430 sheet: None (None), residues: 0 loop : -2.14 (0.45), residues: 160 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.002 TRP A 181 HIS 0.007 0.001 HIS A 483 PHE 0.027 0.002 PHE A 50 TYR 0.021 0.002 TYR A 164 ARG 0.008 0.000 ARG A 332 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1180 Ramachandran restraints generated. 590 Oldfield, 0 Emsley, 590 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1180 Ramachandran restraints generated. 590 Oldfield, 0 Emsley, 590 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 62 residues out of total 516 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 48 time to evaluate : 0.553 Fit side-chains revert: symmetry clash REVERT: A 43 LEU cc_start: 0.7108 (tp) cc_final: 0.6869 (tp) REVERT: A 228 LYS cc_start: 0.7842 (tttt) cc_final: 0.7138 (mppt) REVERT: A 534 HIS cc_start: 0.7132 (OUTLIER) cc_final: 0.6911 (p-80) outliers start: 14 outliers final: 3 residues processed: 57 average time/residue: 1.1741 time to fit residues: 70.1976 Evaluate side-chains 42 residues out of total 516 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 38 time to evaluate : 0.617 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 88 GLU Chi-restraints excluded: chain A residue 393 CYS Chi-restraints excluded: chain A residue 534 HIS Chi-restraints excluded: chain A residue 583 CYS Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 59 random chunks: chunk 23 optimal weight: 7.9990 chunk 14 optimal weight: 4.9990 chunk 29 optimal weight: 1.9990 chunk 2 optimal weight: 8.9990 chunk 38 optimal weight: 5.9990 chunk 20 optimal weight: 1.9990 chunk 51 optimal weight: 0.0980 chunk 53 optimal weight: 0.8980 chunk 3 optimal weight: 0.6980 chunk 21 optimal weight: 0.9980 chunk 5 optimal weight: 1.9990 overall best weight: 0.9382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4807 r_free = 0.4807 target = 0.206455 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.4371 r_free = 0.4371 target = 0.161123 restraints weight = 5354.501| |-----------------------------------------------------------------------------| r_work (start): 0.4372 rms_B_bonded: 2.43 r_work: 0.4240 rms_B_bonded: 3.26 restraints_weight: 0.5000 r_work (final): 0.4240 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6364 moved from start: 0.2907 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 4741 Z= 0.202 Angle : 0.553 7.513 6400 Z= 0.294 Chirality : 0.040 0.134 719 Planarity : 0.004 0.037 837 Dihedral : 4.604 23.586 631 Min Nonbonded Distance : 2.453 Molprobity Statistics. All-atom Clashscore : 8.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.22 % Favored : 96.78 % Rotamer: Outliers : 3.10 % Allowed : 16.09 % Favored : 80.81 % 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: -0.03 (0.33), residues: 590 helix: 0.74 (0.24), residues: 431 sheet: None (None), residues: 0 loop : -2.07 (0.45), residues: 159 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.002 TRP A 181 HIS 0.006 0.001 HIS A 483 PHE 0.032 0.002 PHE A 50 TYR 0.016 0.001 TYR A 164 ARG 0.004 0.000 ARG A 169 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1180 Ramachandran restraints generated. 590 Oldfield, 0 Emsley, 590 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1180 Ramachandran restraints generated. 590 Oldfield, 0 Emsley, 590 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 62 residues out of total 516 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 46 time to evaluate : 0.562 Fit side-chains revert: symmetry clash REVERT: A 43 LEU cc_start: 0.7105 (tp) cc_final: 0.6866 (tp) REVERT: A 97 GLU cc_start: 0.6195 (tp30) cc_final: 0.5726 (tp30) REVERT: A 228 LYS cc_start: 0.7794 (tttt) cc_final: 0.7090 (mppt) REVERT: A 291 GLN cc_start: 0.5695 (OUTLIER) cc_final: 0.5387 (mt0) REVERT: A 448 MET cc_start: 0.6758 (mtp) cc_final: 0.6319 (mtt) REVERT: A 536 ASP cc_start: 0.6135 (p0) cc_final: 0.5863 (p0) outliers start: 16 outliers final: 6 residues processed: 55 average time/residue: 0.9301 time to fit residues: 54.0701 Evaluate side-chains 42 residues out of total 516 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 35 time to evaluate : 0.519 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 88 GLU Chi-restraints excluded: chain A residue 276 ASP Chi-restraints excluded: chain A residue 291 GLN Chi-restraints excluded: chain A residue 365 LEU Chi-restraints excluded: chain A residue 384 CYS Chi-restraints excluded: chain A residue 393 CYS Chi-restraints excluded: chain A residue 583 CYS Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 59 random chunks: chunk 3 optimal weight: 0.9980 chunk 40 optimal weight: 1.9990 chunk 16 optimal weight: 0.6980 chunk 33 optimal weight: 1.9990 chunk 34 optimal weight: 0.5980 chunk 18 optimal weight: 4.9990 chunk 15 optimal weight: 2.9990 chunk 7 optimal weight: 2.9990 chunk 48 optimal weight: 5.9990 chunk 17 optimal weight: 0.6980 chunk 58 optimal weight: 8.9990 overall best weight: 0.9982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4800 r_free = 0.4800 target = 0.205968 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.4368 r_free = 0.4368 target = 0.160729 restraints weight = 5401.003| |-----------------------------------------------------------------------------| r_work (start): 0.4370 rms_B_bonded: 2.42 r_work: 0.4235 rms_B_bonded: 3.27 restraints_weight: 0.5000 r_work (final): 0.4235 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6394 moved from start: 0.3006 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 4741 Z= 0.200 Angle : 0.534 7.684 6400 Z= 0.286 Chirality : 0.040 0.133 719 Planarity : 0.004 0.035 837 Dihedral : 4.470 22.104 631 Min Nonbonded Distance : 2.446 Molprobity Statistics. All-atom Clashscore : 7.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.05 % Favored : 96.95 % Rotamer: Outliers : 2.52 % Allowed : 17.64 % Favored : 79.84 % 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: 0.26 (0.34), residues: 590 helix: 0.93 (0.24), residues: 431 sheet: None (None), residues: 0 loop : -1.88 (0.47), residues: 159 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.002 TRP A 181 HIS 0.006 0.001 HIS A 483 PHE 0.031 0.002 PHE A 54 TYR 0.010 0.001 TYR A 185 ARG 0.003 0.000 ARG A 169 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1180 Ramachandran restraints generated. 590 Oldfield, 0 Emsley, 590 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1180 Ramachandran restraints generated. 590 Oldfield, 0 Emsley, 590 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 58 residues out of total 516 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 45 time to evaluate : 0.542 Fit side-chains revert: symmetry clash REVERT: A 43 LEU cc_start: 0.7113 (tp) cc_final: 0.6862 (tp) REVERT: A 124 CYS cc_start: 0.6412 (t) cc_final: 0.5930 (t) REVERT: A 228 LYS cc_start: 0.7789 (tttt) cc_final: 0.7144 (mppt) REVERT: A 403 LYS cc_start: 0.6616 (pttt) cc_final: 0.5948 (tptp) REVERT: A 448 MET cc_start: 0.6840 (mtp) cc_final: 0.6313 (mtt) outliers start: 13 outliers final: 5 residues processed: 56 average time/residue: 1.1126 time to fit residues: 65.2658 Evaluate side-chains 42 residues out of total 516 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 37 time to evaluate : 0.582 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 276 ASP Chi-restraints excluded: chain A residue 365 LEU Chi-restraints excluded: chain A residue 384 CYS Chi-restraints excluded: chain A residue 393 CYS Chi-restraints excluded: chain A residue 583 CYS Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 59 random chunks: chunk 13 optimal weight: 8.9990 chunk 36 optimal weight: 0.8980 chunk 40 optimal weight: 2.9990 chunk 26 optimal weight: 0.8980 chunk 33 optimal weight: 2.9990 chunk 6 optimal weight: 4.9990 chunk 53 optimal weight: 5.9990 chunk 21 optimal weight: 1.9990 chunk 30 optimal weight: 0.9980 chunk 3 optimal weight: 0.6980 chunk 23 optimal weight: 6.9990 overall best weight: 1.0982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 24 ASN A 428 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4796 r_free = 0.4796 target = 0.205111 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.4363 r_free = 0.4363 target = 0.160084 restraints weight = 5349.930| |-----------------------------------------------------------------------------| r_work (start): 0.4361 rms_B_bonded: 2.43 r_work: 0.4224 rms_B_bonded: 3.28 restraints_weight: 0.5000 r_work (final): 0.4224 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6377 moved from start: 0.3189 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 4741 Z= 0.209 Angle : 0.555 8.462 6400 Z= 0.296 Chirality : 0.040 0.132 719 Planarity : 0.004 0.036 837 Dihedral : 4.449 21.999 631 Min Nonbonded Distance : 2.433 Molprobity Statistics. All-atom Clashscore : 7.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.22 % Favored : 96.78 % Rotamer: Outliers : 1.94 % Allowed : 18.99 % Favored : 79.07 % 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: 0.35 (0.34), residues: 590 helix: 0.98 (0.24), residues: 431 sheet: None (None), residues: 0 loop : -1.79 (0.47), residues: 159 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.002 TRP A 181 HIS 0.009 0.001 HIS A 534 PHE 0.024 0.002 PHE A 54 TYR 0.015 0.002 TYR A 151 ARG 0.003 0.000 ARG A 169 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1180 Ramachandran restraints generated. 590 Oldfield, 0 Emsley, 590 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1180 Ramachandran restraints generated. 590 Oldfield, 0 Emsley, 590 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 49 residues out of total 516 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 39 time to evaluate : 0.534 Fit side-chains revert: symmetry clash REVERT: A 43 LEU cc_start: 0.7123 (tp) cc_final: 0.6867 (tp) REVERT: A 124 CYS cc_start: 0.6417 (t) cc_final: 0.5930 (t) REVERT: A 228 LYS cc_start: 0.7802 (tttt) cc_final: 0.7118 (mppt) REVERT: A 291 GLN cc_start: 0.5726 (OUTLIER) cc_final: 0.5441 (mt0) REVERT: A 403 LYS cc_start: 0.6552 (pttt) cc_final: 0.5941 (tptp) REVERT: A 448 MET cc_start: 0.6902 (mtp) cc_final: 0.6516 (mtt) outliers start: 10 outliers final: 6 residues processed: 47 average time/residue: 1.1213 time to fit residues: 55.4422 Evaluate side-chains 42 residues out of total 516 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 35 time to evaluate : 0.624 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 99 CYS Chi-restraints excluded: chain A residue 276 ASP Chi-restraints excluded: chain A residue 291 GLN Chi-restraints excluded: chain A residue 365 LEU Chi-restraints excluded: chain A residue 384 CYS Chi-restraints excluded: chain A residue 393 CYS Chi-restraints excluded: chain A residue 583 CYS Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 59 random chunks: chunk 20 optimal weight: 5.9990 chunk 48 optimal weight: 4.9990 chunk 57 optimal weight: 0.8980 chunk 58 optimal weight: 9.9990 chunk 29 optimal weight: 0.0980 chunk 54 optimal weight: 0.0020 chunk 37 optimal weight: 10.0000 chunk 22 optimal weight: 1.9990 chunk 45 optimal weight: 0.9980 chunk 8 optimal weight: 1.9990 chunk 7 optimal weight: 1.9990 overall best weight: 0.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4813 r_free = 0.4813 target = 0.206844 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.4388 r_free = 0.4388 target = 0.162183 restraints weight = 5346.029| |-----------------------------------------------------------------------------| r_work (start): 0.4377 rms_B_bonded: 2.43 r_work: 0.4240 rms_B_bonded: 3.28 restraints_weight: 0.5000 r_work (final): 0.4240 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6359 moved from start: 0.3370 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 4741 Z= 0.187 Angle : 0.536 9.257 6400 Z= 0.286 Chirality : 0.039 0.128 719 Planarity : 0.004 0.034 837 Dihedral : 4.287 22.970 631 Min Nonbonded Distance : 2.423 Molprobity Statistics. All-atom Clashscore : 6.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.22 % Favored : 96.78 % Rotamer: Outliers : 1.74 % Allowed : 19.77 % Favored : 78.49 % 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: 0.63 (0.34), residues: 590 helix: 1.19 (0.25), residues: 431 sheet: None (None), residues: 0 loop : -1.68 (0.48), residues: 159 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.002 TRP A 181 HIS 0.007 0.001 HIS A 534 PHE 0.023 0.002 PHE A 50 TYR 0.013 0.001 TYR A 151 ARG 0.002 0.000 ARG A 169 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1180 Ramachandran restraints generated. 590 Oldfield, 0 Emsley, 590 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1180 Ramachandran restraints generated. 590 Oldfield, 0 Emsley, 590 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 50 residues out of total 516 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 41 time to evaluate : 0.599 Fit side-chains revert: symmetry clash REVERT: A 43 LEU cc_start: 0.7097 (tp) cc_final: 0.6840 (tp) REVERT: A 124 CYS cc_start: 0.6345 (t) cc_final: 0.5880 (t) REVERT: A 228 LYS cc_start: 0.7788 (tttt) cc_final: 0.7097 (mppt) REVERT: A 291 GLN cc_start: 0.5622 (OUTLIER) cc_final: 0.5310 (mt0) REVERT: A 403 LYS cc_start: 0.6419 (pttt) cc_final: 0.5964 (tptp) REVERT: A 552 PHE cc_start: 0.5660 (t80) cc_final: 0.4508 (m-80) outliers start: 9 outliers final: 6 residues processed: 48 average time/residue: 1.2603 time to fit residues: 63.2114 Evaluate side-chains 44 residues out of total 516 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 37 time to evaluate : 0.541 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 99 CYS Chi-restraints excluded: chain A residue 276 ASP Chi-restraints excluded: chain A residue 291 GLN Chi-restraints excluded: chain A residue 365 LEU Chi-restraints excluded: chain A residue 384 CYS Chi-restraints excluded: chain A residue 393 CYS Chi-restraints excluded: chain A residue 583 CYS Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 59 random chunks: chunk 0 optimal weight: 10.0000 chunk 16 optimal weight: 3.9990 chunk 57 optimal weight: 4.9990 chunk 40 optimal weight: 2.9990 chunk 38 optimal weight: 3.9990 chunk 3 optimal weight: 0.9990 chunk 54 optimal weight: 0.9980 chunk 19 optimal weight: 0.6980 chunk 44 optimal weight: 0.9990 chunk 28 optimal weight: 0.9980 chunk 5 optimal weight: 1.9990 overall best weight: 0.9384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4807 r_free = 0.4807 target = 0.206088 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.4376 r_free = 0.4376 target = 0.161114 restraints weight = 5393.632| |-----------------------------------------------------------------------------| r_work (start): 0.4368 rms_B_bonded: 2.44 r_work: 0.4234 rms_B_bonded: 3.27 restraints_weight: 0.5000 r_work (final): 0.4234 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6362 moved from start: 0.3409 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 4741 Z= 0.197 Angle : 0.546 9.777 6400 Z= 0.291 Chirality : 0.040 0.127 719 Planarity : 0.004 0.035 837 Dihedral : 4.254 23.244 631 Min Nonbonded Distance : 2.428 Molprobity Statistics. All-atom Clashscore : 7.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.39 % Favored : 96.61 % Rotamer: Outliers : 1.55 % Allowed : 20.16 % Favored : 78.29 % 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: 0.67 (0.34), residues: 590 helix: 1.20 (0.25), residues: 432 sheet: None (None), residues: 0 loop : -1.62 (0.49), residues: 158 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.002 TRP A 181 HIS 0.006 0.001 HIS A 534 PHE 0.020 0.002 PHE A 50 TYR 0.016 0.001 TYR A 164 ARG 0.003 0.000 ARG A 169 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1180 Ramachandran restraints generated. 590 Oldfield, 0 Emsley, 590 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1180 Ramachandran restraints generated. 590 Oldfield, 0 Emsley, 590 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 45 residues out of total 516 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 37 time to evaluate : 0.536 Fit side-chains REVERT: A 43 LEU cc_start: 0.7114 (tp) cc_final: 0.6864 (tp) REVERT: A 124 CYS cc_start: 0.6348 (t) cc_final: 0.5899 (t) REVERT: A 228 LYS cc_start: 0.7728 (tttt) cc_final: 0.7069 (mppt) REVERT: A 291 GLN cc_start: 0.5614 (OUTLIER) cc_final: 0.5308 (mt0) REVERT: A 403 LYS cc_start: 0.6395 (pttt) cc_final: 0.6007 (tptp) REVERT: A 490 MET cc_start: 0.6496 (mpt) cc_final: 0.5563 (mpt) outliers start: 8 outliers final: 4 residues processed: 43 average time/residue: 1.0947 time to fit residues: 49.6731 Evaluate side-chains 38 residues out of total 516 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 33 time to evaluate : 0.488 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 99 CYS Chi-restraints excluded: chain A residue 276 ASP Chi-restraints excluded: chain A residue 291 GLN Chi-restraints excluded: chain A residue 365 LEU Chi-restraints excluded: chain A residue 384 CYS Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 59 random chunks: chunk 21 optimal weight: 1.9990 chunk 19 optimal weight: 4.9990 chunk 3 optimal weight: 1.9990 chunk 7 optimal weight: 0.8980 chunk 31 optimal weight: 0.8980 chunk 2 optimal weight: 7.9990 chunk 52 optimal weight: 0.3980 chunk 25 optimal weight: 0.5980 chunk 37 optimal weight: 0.0070 chunk 12 optimal weight: 2.9990 chunk 11 optimal weight: 0.9980 overall best weight: 0.5598 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4830 r_free = 0.4830 target = 0.208618 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.4413 r_free = 0.4413 target = 0.164423 restraints weight = 5380.406| |-----------------------------------------------------------------------------| r_work (start): 0.4398 rms_B_bonded: 2.42 r_work: 0.4267 rms_B_bonded: 3.26 restraints_weight: 0.5000 r_work (final): 0.4267 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6355 moved from start: 0.3629 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 4741 Z= 0.179 Angle : 0.542 10.561 6400 Z= 0.288 Chirality : 0.039 0.125 719 Planarity : 0.004 0.033 837 Dihedral : 4.130 22.472 631 Min Nonbonded Distance : 2.448 Molprobity Statistics. All-atom Clashscore : 7.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.39 % Favored : 96.61 % Rotamer: Outliers : 1.55 % Allowed : 20.16 % Favored : 78.29 % 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: 0.95 (0.35), residues: 590 helix: 1.39 (0.25), residues: 432 sheet: None (None), residues: 0 loop : -1.47 (0.50), residues: 158 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.002 TRP A 181 HIS 0.005 0.001 HIS A 534 PHE 0.023 0.002 PHE A 54 TYR 0.014 0.001 TYR A 151 ARG 0.002 0.000 ARG A 169 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1180 Ramachandran restraints generated. 590 Oldfield, 0 Emsley, 590 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1180 Ramachandran restraints generated. 590 Oldfield, 0 Emsley, 590 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 46 residues out of total 516 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 38 time to evaluate : 0.582 Fit side-chains REVERT: A 43 LEU cc_start: 0.7082 (tp) cc_final: 0.6842 (tp) REVERT: A 124 CYS cc_start: 0.6376 (t) cc_final: 0.5943 (t) REVERT: A 228 LYS cc_start: 0.7754 (tttt) cc_final: 0.7108 (mppt) REVERT: A 403 LYS cc_start: 0.6391 (pttt) cc_final: 0.6105 (tptp) outliers start: 8 outliers final: 5 residues processed: 43 average time/residue: 1.0189 time to fit residues: 46.3665 Evaluate side-chains 37 residues out of total 516 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 32 time to evaluate : 0.480 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 99 CYS Chi-restraints excluded: chain A residue 276 ASP Chi-restraints excluded: chain A residue 384 CYS Chi-restraints excluded: chain A residue 462 CYS Chi-restraints excluded: chain A residue 583 CYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 59 random chunks: chunk 29 optimal weight: 0.9980 chunk 38 optimal weight: 0.9980 chunk 54 optimal weight: 0.5980 chunk 35 optimal weight: 0.8980 chunk 55 optimal weight: 3.9990 chunk 26 optimal weight: 1.9990 chunk 5 optimal weight: 3.9990 chunk 12 optimal weight: 2.9990 chunk 45 optimal weight: 2.9990 chunk 23 optimal weight: 0.7980 chunk 15 optimal weight: 0.9980 overall best weight: 0.8580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4816 r_free = 0.4816 target = 0.207280 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.4391 r_free = 0.4391 target = 0.162563 restraints weight = 5380.780| |-----------------------------------------------------------------------------| r_work (start): 0.4376 rms_B_bonded: 2.42 r_work: 0.4244 rms_B_bonded: 3.24 restraints_weight: 0.5000 r_work (final): 0.4244 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6347 moved from start: 0.3657 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 4741 Z= 0.198 Angle : 0.568 10.821 6400 Z= 0.303 Chirality : 0.040 0.124 719 Planarity : 0.004 0.033 837 Dihedral : 4.145 22.214 631 Min Nonbonded Distance : 2.464 Molprobity Statistics. All-atom Clashscore : 7.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.05 % Favored : 96.95 % Rotamer: Outliers : 1.16 % Allowed : 21.51 % Favored : 77.33 % 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: 0.90 (0.35), residues: 590 helix: 1.36 (0.25), residues: 432 sheet: None (None), residues: 0 loop : -1.51 (0.49), residues: 158 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.002 TRP A 181 HIS 0.006 0.001 HIS A 483 PHE 0.032 0.002 PHE A 54 TYR 0.017 0.001 TYR A 164 ARG 0.007 0.000 ARG A 310 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1180 Ramachandran restraints generated. 590 Oldfield, 0 Emsley, 590 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1180 Ramachandran restraints generated. 590 Oldfield, 0 Emsley, 590 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 42 residues out of total 516 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 36 time to evaluate : 0.502 Fit side-chains REVERT: A 43 LEU cc_start: 0.7111 (tp) cc_final: 0.6854 (tp) REVERT: A 124 CYS cc_start: 0.6562 (t) cc_final: 0.6045 (t) REVERT: A 228 LYS cc_start: 0.7706 (tttt) cc_final: 0.7067 (mppt) REVERT: A 403 LYS cc_start: 0.6351 (pttt) cc_final: 0.6100 (tptp) REVERT: A 490 MET cc_start: 0.6475 (mpt) cc_final: 0.5600 (mpt) outliers start: 6 outliers final: 5 residues processed: 41 average time/residue: 1.0127 time to fit residues: 43.8915 Evaluate side-chains 37 residues out of total 516 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 32 time to evaluate : 0.494 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 99 CYS Chi-restraints excluded: chain A residue 276 ASP Chi-restraints excluded: chain A residue 384 CYS Chi-restraints excluded: chain A residue 462 CYS Chi-restraints excluded: chain A residue 583 CYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 59 random chunks: chunk 4 optimal weight: 6.9990 chunk 7 optimal weight: 1.9990 chunk 26 optimal weight: 0.8980 chunk 50 optimal weight: 7.9990 chunk 36 optimal weight: 8.9990 chunk 8 optimal weight: 4.9990 chunk 58 optimal weight: 9.9990 chunk 34 optimal weight: 0.0670 chunk 18 optimal weight: 3.9990 chunk 56 optimal weight: 7.9990 chunk 53 optimal weight: 6.9990 overall best weight: 2.3924 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 122 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 197 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4760 r_free = 0.4760 target = 0.202193 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.4318 r_free = 0.4318 target = 0.156291 restraints weight = 5415.724| |-----------------------------------------------------------------------------| r_work (start): 0.4321 rms_B_bonded: 2.42 r_work: 0.4186 rms_B_bonded: 3.22 restraints_weight: 0.5000 r_work: 0.4050 rms_B_bonded: 4.99 restraints_weight: 0.2500 r_work (final): 0.4050 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6549 moved from start: 0.3270 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.044 4741 Z= 0.312 Angle : 0.649 10.565 6400 Z= 0.348 Chirality : 0.045 0.162 719 Planarity : 0.004 0.040 837 Dihedral : 4.526 21.519 631 Min Nonbonded Distance : 2.426 Molprobity Statistics. All-atom Clashscore : 10.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.39 % Favored : 96.61 % Rotamer: Outliers : 1.74 % Allowed : 20.93 % Favored : 77.33 % 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: 0.32 (0.34), residues: 590 helix: 0.92 (0.24), residues: 425 sheet: None (None), residues: 0 loop : -1.58 (0.49), residues: 165 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.002 TRP A 181 HIS 0.007 0.002 HIS A 534 PHE 0.025 0.002 PHE A 54 TYR 0.016 0.002 TYR A 185 ARG 0.005 0.000 ARG A 310 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4496.11 seconds wall clock time: 79 minutes 43.72 seconds (4783.72 seconds total)