Starting phenix.real_space_refine on Mon Jul 28 05:49:13 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7k8d_22728/07_2025/7k8d_22728.cif Found real_map, /net/cci-nas-00/data/ceres_data/7k8d_22728/07_2025/7k8d_22728.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.33 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/7k8d_22728/07_2025/7k8d_22728.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7k8d_22728/07_2025/7k8d_22728.map" model { file = "/net/cci-nas-00/data/ceres_data/7k8d_22728/07_2025/7k8d_22728.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7k8d_22728/07_2025/7k8d_22728.cif" } resolution = 4.33 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 ------------------------------------------------------------------------------- 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= -0.000 sd= 0.134 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Anisotropic ADP refinement not supported. Converting 5528 atoms to isotropic. 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 28 5.16 5 C 3577 2.51 5 N 918 2.21 5 O 1006 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 10 residue(s): 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5711/modules/chem_data/mon_lib" Total number of atoms: 5529 Number of models: 1 Model: "" Number of chains: 1 Chain: "A" Number of atoms: 5529 Number of conformers: 1 Conformer: "" Number of residues, atoms: 725, 5529 Classifications: {'peptide': 725} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 36, 'TRANS': 688} Chain breaks: 1 Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 5 Unresolved non-hydrogen dihedrals: 2 Unresolved non-hydrogen chiralities: 1 Time building chain proxies: 3.47, per 1000 atoms: 0.63 Number of scatterers: 5529 At special positions: 0 Unit cell: (76.96, 74.88, 111.28, 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 28 16.00 O 1006 8.00 N 918 7.00 C 3577 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 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: 1.24 Conformation dependent library (CDL) restraints added in 765.7 milliseconds 1442 Ramachandran restraints generated. 721 Oldfield, 0 Emsley, 721 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1326 Finding SS restraints... Secondary structure from input PDB file: 33 helices and 2 sheets defined 75.6% alpha, 3.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.80 Creating SS restraints... Processing helix chain 'A' and resid 1 through 12 removed outlier: 4.156A pdb=" N TYR A 10 " --> pdb=" O GLY A 6 " (cutoff:3.500A) Processing helix chain 'A' and resid 12 through 34 removed outlier: 3.502A pdb=" N LEU A 25 " --> pdb=" O VAL A 21 " (cutoff:3.500A) Processing helix chain 'A' and resid 47 through 62 removed outlier: 3.886A pdb=" N VAL A 51 " --> pdb=" O GLY A 47 " (cutoff:3.500A) removed outlier: 3.633A pdb=" N ALA A 52 " --> pdb=" O SER A 48 " (cutoff:3.500A) Processing helix chain 'A' and resid 83 through 101 Processing helix chain 'A' and resid 110 through 114 Processing helix chain 'A' and resid 119 through 124 Processing helix chain 'A' and resid 143 through 160 Proline residue: A 156 - end of helix Processing helix chain 'A' and resid 161 through 165 Processing helix chain 'A' and resid 170 through 205 removed outlier: 3.883A pdb=" N ILE A 194 " --> pdb=" O GLU A 190 " (cutoff:3.500A) Proline residue: A 195 - end of helix Processing helix chain 'A' and resid 207 through 233 removed outlier: 3.667A pdb=" N ALA A 211 " --> pdb=" O THR A 207 " (cutoff:3.500A) Proline residue: A 214 - end of helix Processing helix chain 'A' and resid 241 through 272 removed outlier: 3.705A pdb=" N VAL A 245 " --> pdb=" O PHE A 241 " (cutoff:3.500A) removed outlier: 3.536A pdb=" N GLY A 272 " --> pdb=" O GLU A 268 " (cutoff:3.500A) Processing helix chain 'A' and resid 274 through 307 removed outlier: 3.690A pdb=" N THR A 289 " --> pdb=" O THR A 285 " (cutoff:3.500A) Proline residue: A 303 - end of helix Processing helix chain 'A' and resid 310 through 332 Processing helix chain 'A' and resid 332 through 342 removed outlier: 3.697A pdb=" N LEU A 341 " --> pdb=" O ALA A 337 " (cutoff:3.500A) Processing helix chain 'A' and resid 343 through 347 removed outlier: 3.805A pdb=" N ALA A 347 " --> pdb=" O ARG A 344 " (cutoff:3.500A) Processing helix chain 'A' and resid 383 through 400 Processing helix chain 'A' and resid 401 through 416 Proline residue: A 407 - end of helix removed outlier: 3.738A pdb=" N VAL A 413 " --> pdb=" O LEU A 409 " (cutoff:3.500A) removed outlier: 4.196A pdb=" N LEU A 414 " --> pdb=" O VAL A 410 " (cutoff:3.500A) removed outlier: 3.798A pdb=" N LEU A 415 " --> pdb=" O VAL A 411 " (cutoff:3.500A) removed outlier: 4.200A pdb=" N ILE A 416 " --> pdb=" O MET A 412 " (cutoff:3.500A) Processing helix chain 'A' and resid 418 through 422 Processing helix chain 'A' and resid 428 through 432 removed outlier: 3.726A pdb=" N LEU A 432 " --> pdb=" O GLU A 429 " (cutoff:3.500A) Processing helix chain 'A' and resid 436 through 449 Processing helix chain 'A' and resid 470 through 483 Processing helix chain 'A' and resid 493 through 497 Processing helix chain 'A' and resid 524 through 535 removed outlier: 4.584A pdb=" N LYS A 528 " --> pdb=" O ASN A 524 " (cutoff:3.500A) Processing helix chain 'A' and resid 548 through 583 Proline residue: A 565 - end of helix Processing helix chain 'A' and resid 586 through 612 removed outlier: 4.035A pdb=" N ILE A 590 " --> pdb=" O VAL A 586 " (cutoff:3.500A) Processing helix chain 'A' and resid 616 through 621 removed outlier: 3.647A pdb=" N MET A 620 " --> pdb=" O GLY A 616 " (cutoff:3.500A) Processing helix chain 'A' and resid 628 through 660 removed outlier: 3.557A pdb=" N ILE A 632 " --> pdb=" O MET A 628 " (cutoff:3.500A) Processing helix chain 'A' and resid 663 through 675 Processing helix chain 'A' and resid 675 through 695 Processing helix chain 'A' and resid 698 through 718 Processing helix chain 'A' and resid 718 through 732 Proline residue: A 725 - end of helix Processing helix chain 'A' and resid 733 through 737 Processing helix chain 'A' and resid 739 through 748 Processing sheet with id=AA1, first strand: chain 'A' and resid 70 through 73 removed outlier: 3.617A pdb=" N LEU A 73 " --> pdb=" O THR A 133 " (cutoff:3.500A) removed outlier: 4.498A pdb=" N THR A 133 " --> pdb=" O LEU A 73 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 513 through 518 396 hydrogen bonds defined for protein. 1149 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: 1.70 Time building geometry restraints manager: 1.48 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 1324 1.33 - 1.45: 1034 1.45 - 1.57: 3227 1.57 - 1.69: 0 1.69 - 1.81: 54 Bond restraints: 5639 Sorted by residual: bond pdb=" C ILE A 417 " pdb=" O ILE A 417 " ideal model delta sigma weight residual 1.242 1.224 0.018 8.60e-03 1.35e+04 4.33e+00 bond pdb=" N ALA A 526 " pdb=" CA ALA A 526 " ideal model delta sigma weight residual 1.459 1.435 0.024 1.19e-02 7.06e+03 4.23e+00 bond pdb=" C VAL A 411 " pdb=" O VAL A 411 " ideal model delta sigma weight residual 1.237 1.214 0.023 1.23e-02 6.61e+03 3.57e+00 bond pdb=" CA ASP A 525 " pdb=" C ASP A 525 " ideal model delta sigma weight residual 1.523 1.497 0.026 1.41e-02 5.03e+03 3.39e+00 bond pdb=" CB MET A 461 " pdb=" CG MET A 461 " ideal model delta sigma weight residual 1.520 1.467 0.053 3.00e-02 1.11e+03 3.10e+00 ... (remaining 5634 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.70: 7399 2.70 - 5.41: 225 5.41 - 8.11: 39 8.11 - 10.82: 5 10.82 - 13.52: 4 Bond angle restraints: 7672 Sorted by residual: angle pdb=" C LEU A 422 " pdb=" N SER A 423 " pdb=" CA SER A 423 " ideal model delta sigma weight residual 122.81 136.33 -13.52 1.57e+00 4.06e-01 7.42e+01 angle pdb=" N LEU A 422 " pdb=" CA LEU A 422 " pdb=" C LEU A 422 " ideal model delta sigma weight residual 110.23 122.19 -11.96 1.45e+00 4.76e-01 6.80e+01 angle pdb=" C ILE A 417 " pdb=" N PRO A 418 " pdb=" CA PRO A 418 " ideal model delta sigma weight residual 119.56 127.53 -7.97 1.01e+00 9.80e-01 6.23e+01 angle pdb=" CA ILE A 417 " pdb=" C ILE A 417 " pdb=" N PRO A 418 " ideal model delta sigma weight residual 120.83 116.10 4.73 6.10e-01 2.69e+00 6.01e+01 angle pdb=" CA LEU A 422 " pdb=" C LEU A 422 " pdb=" N SER A 423 " ideal model delta sigma weight residual 115.85 108.31 7.54 1.29e+00 6.01e-01 3.41e+01 ... (remaining 7667 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.48: 3111 17.48 - 34.97: 188 34.97 - 52.45: 61 52.45 - 69.93: 4 69.93 - 87.42: 3 Dihedral angle restraints: 3367 sinusoidal: 1305 harmonic: 2062 Sorted by residual: dihedral pdb=" CA HIS A 239 " pdb=" C HIS A 239 " pdb=" N PHE A 240 " pdb=" CA PHE A 240 " ideal model delta harmonic sigma weight residual 180.00 159.63 20.37 0 5.00e+00 4.00e-02 1.66e+01 dihedral pdb=" CA SER A 33 " pdb=" C SER A 33 " pdb=" N LEU A 34 " pdb=" CA LEU A 34 " ideal model delta harmonic sigma weight residual -180.00 -160.64 -19.36 0 5.00e+00 4.00e-02 1.50e+01 dihedral pdb=" N TYR A 703 " pdb=" C TYR A 703 " pdb=" CA TYR A 703 " pdb=" CB TYR A 703 " ideal model delta harmonic sigma weight residual 122.80 131.52 -8.72 0 2.50e+00 1.60e-01 1.22e+01 ... (remaining 3364 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.085: 808 0.085 - 0.171: 91 0.171 - 0.256: 11 0.256 - 0.341: 6 0.341 - 0.426: 1 Chirality restraints: 917 Sorted by residual: chirality pdb=" CA LEU A 422 " pdb=" N LEU A 422 " pdb=" C LEU A 422 " pdb=" CB LEU A 422 " both_signs ideal model delta sigma weight residual False 2.51 2.08 0.43 2.00e-01 2.50e+01 4.54e+00 chirality pdb=" CG LEU A 415 " pdb=" CB LEU A 415 " pdb=" CD1 LEU A 415 " pdb=" CD2 LEU A 415 " both_signs ideal model delta sigma weight residual False -2.59 -2.25 -0.34 2.00e-01 2.50e+01 2.87e+00 chirality pdb=" CA TYR A 703 " pdb=" N TYR A 703 " pdb=" C TYR A 703 " pdb=" CB TYR A 703 " both_signs ideal model delta sigma weight residual False 2.51 2.22 0.29 2.00e-01 2.50e+01 2.09e+00 ... (remaining 914 not shown) Planarity restraints: 969 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TYR A 703 " -0.041 2.00e-02 2.50e+03 3.70e-02 2.73e+01 pdb=" CG TYR A 703 " 0.091 2.00e-02 2.50e+03 pdb=" CD1 TYR A 703 " -0.021 2.00e-02 2.50e+03 pdb=" CD2 TYR A 703 " -0.007 2.00e-02 2.50e+03 pdb=" CE1 TYR A 703 " -0.005 2.00e-02 2.50e+03 pdb=" CE2 TYR A 703 " -0.019 2.00e-02 2.50e+03 pdb=" CZ TYR A 703 " -0.005 2.00e-02 2.50e+03 pdb=" OH TYR A 703 " 0.005 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ARG A 720 " -0.024 2.00e-02 2.50e+03 4.80e-02 2.31e+01 pdb=" C ARG A 720 " 0.083 2.00e-02 2.50e+03 pdb=" O ARG A 720 " -0.031 2.00e-02 2.50e+03 pdb=" N MET A 721 " -0.028 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA GLY A 691 " -0.024 2.00e-02 2.50e+03 4.79e-02 2.30e+01 pdb=" C GLY A 691 " 0.083 2.00e-02 2.50e+03 pdb=" O GLY A 691 " -0.031 2.00e-02 2.50e+03 pdb=" N ALA A 692 " -0.028 2.00e-02 2.50e+03 ... (remaining 966 not shown) Histogram of nonbonded interaction distances: 2.20 - 2.74: 699 2.74 - 3.28: 5997 3.28 - 3.82: 8923 3.82 - 4.36: 10012 4.36 - 4.90: 16562 Nonbonded interactions: 42193 Sorted by model distance: nonbonded pdb=" CD1 LEU A 422 " pdb=" O SER A 423 " model vdw 2.205 3.460 nonbonded pdb=" O LEU A 432 " pdb=" NH1 ARG A 439 " model vdw 2.224 3.120 nonbonded pdb=" O PRO A 407 " pdb=" CG2 VAL A 411 " model vdw 2.227 3.460 nonbonded pdb=" O LEU A 414 " pdb=" CD1 ILE A 417 " model vdw 2.243 3.460 nonbonded pdb=" NH1 ARG A 65 " pdb=" OD1 ASN A 504 " model vdw 2.254 3.120 ... (remaining 42188 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 group one per residue 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: 0.040 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.060 Construct map_model_manager: 0.010 Extract box with map and model: 0.180 Check model and map are aligned: 0.030 Set scattering table: 0.050 Process input model: 16.530 Find NCS groups from input model: 0.070 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:2.690 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 19.680 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.4091 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 : 0.004 0.053 5639 Z= 0.236 Angle : 1.121 13.520 7672 Z= 0.691 Chirality : 0.061 0.426 917 Planarity : 0.009 0.080 969 Dihedral : 12.529 87.415 2041 Min Nonbonded Distance : 2.205 Molprobity Statistics. All-atom Clashscore : 23.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.30 % Favored : 95.70 % Rotamer: Outliers : 1.86 % Allowed : 9.15 % Favored : 88.98 % 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: -2.98 (0.27), residues: 721 helix: -1.95 (0.19), residues: 494 sheet: -1.26 (0.95), residues: 21 loop : -1.56 (0.42), residues: 206 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.036 0.002 TRP A 736 HIS 0.007 0.001 HIS A 68 PHE 0.042 0.003 PHE A 12 TYR 0.091 0.005 TYR A 703 ARG 0.003 0.000 ARG A 501 Details of bonding type rmsd hydrogen bonds : bond 0.14872 ( 396) hydrogen bonds : angle 7.37256 ( 1149) covalent geometry : bond 0.00389 ( 5639) covalent geometry : angle 1.12074 ( 7672) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1442 Ramachandran restraints generated. 721 Oldfield, 0 Emsley, 721 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1442 Ramachandran restraints generated. 721 Oldfield, 0 Emsley, 721 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 167 residues out of total 591 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 156 time to evaluate : 0.562 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash TARDY: cannot create tardy model for: "LYS A 748 " (corrupted residue). Skipping it. REVERT: A 20 MET cc_start: 0.5777 (tmm) cc_final: 0.4769 (tpp) REVERT: A 79 LYS cc_start: 0.7398 (mmpt) cc_final: 0.7192 (mmpt) REVERT: A 307 PHE cc_start: 0.4082 (m-10) cc_final: 0.3830 (m-80) REVERT: A 325 LEU cc_start: 0.7733 (OUTLIER) cc_final: 0.7492 (pp) REVERT: A 414 LEU cc_start: 0.0394 (OUTLIER) cc_final: -0.1126 (mp) REVERT: A 555 ASP cc_start: 0.7868 (m-30) cc_final: 0.7652 (m-30) REVERT: A 559 SER cc_start: 0.8509 (m) cc_final: 0.8097 (p) REVERT: A 580 PHE cc_start: 0.6584 (t80) cc_final: 0.6160 (t80) REVERT: A 640 TRP cc_start: 0.6175 (t-100) cc_final: 0.5698 (t-100) REVERT: A 668 ILE cc_start: 0.4527 (tp) cc_final: 0.4168 (mm) outliers start: 11 outliers final: 4 residues processed: 165 average time/residue: 0.1608 time to fit residues: 34.6313 Evaluate side-chains 117 residues out of total 591 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 111 time to evaluate : 0.518 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 72 random chunks: chunk 60 optimal weight: 1.9990 chunk 54 optimal weight: 6.9990 chunk 30 optimal weight: 0.0470 chunk 18 optimal weight: 8.9990 chunk 36 optimal weight: 4.9990 chunk 29 optimal weight: 30.0000 chunk 56 optimal weight: 10.0000 chunk 21 optimal weight: 7.9990 chunk 34 optimal weight: 0.0070 chunk 42 optimal weight: 2.9990 chunk 65 optimal weight: 6.9990 overall best weight: 2.0102 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 37 HIS A 395 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.5165 r_free = 0.5165 target = 0.315117 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 63)----------------| | r_work = 0.4926 r_free = 0.4926 target = 0.286581 restraints weight = 11501.307| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 41)----------------| | r_work = 0.4969 r_free = 0.4969 target = 0.292110 restraints weight = 8612.028| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.5004 r_free = 0.5004 target = 0.296578 restraints weight = 6558.142| |-----------------------------------------------------------------------------| r_work (final): 0.5010 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.4367 moved from start: 0.2552 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.059 5639 Z= 0.170 Angle : 0.754 7.460 7672 Z= 0.398 Chirality : 0.047 0.208 917 Planarity : 0.006 0.050 969 Dihedral : 4.355 24.993 770 Min Nonbonded Distance : 2.525 Molprobity Statistics. All-atom Clashscore : 13.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.22 % Favored : 97.78 % Rotamer: Outliers : 0.17 % Allowed : 2.88 % Favored : 96.95 % 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: -0.11 (0.30), residues: 721 helix: 0.32 (0.22), residues: 489 sheet: -0.29 (0.96), residues: 21 loop : -0.71 (0.43), residues: 211 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP A 737 HIS 0.007 0.001 HIS A 239 PHE 0.023 0.002 PHE A 12 TYR 0.040 0.003 TYR A 703 ARG 0.003 0.000 ARG A 13 Details of bonding type rmsd hydrogen bonds : bond 0.04807 ( 396) hydrogen bonds : angle 5.26899 ( 1149) covalent geometry : bond 0.00346 ( 5639) covalent geometry : angle 0.75423 ( 7672) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1442 Ramachandran restraints generated. 721 Oldfield, 0 Emsley, 721 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1442 Ramachandran restraints generated. 721 Oldfield, 0 Emsley, 721 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 129 residues out of total 591 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 128 time to evaluate : 0.530 Fit side-chains revert: symmetry clash revert: symmetry clash TARDY: cannot create tardy model for: "LYS A 748 " (corrupted residue). Skipping it. REVERT: A 20 MET cc_start: 0.5893 (tmm) cc_final: 0.5455 (tmm) REVERT: A 125 MET cc_start: 0.1189 (tpt) cc_final: 0.0959 (mtm) REVERT: A 131 ARG cc_start: 0.4915 (ttt180) cc_final: 0.4586 (ttt180) REVERT: A 171 LEU cc_start: 0.7738 (mp) cc_final: 0.7502 (mp) REVERT: A 307 PHE cc_start: 0.5359 (m-80) cc_final: 0.5096 (m-80) REVERT: A 412 MET cc_start: 0.2986 (ptt) cc_final: 0.2641 (ptt) REVERT: A 477 MET cc_start: 0.4006 (mtp) cc_final: 0.3768 (mtp) REVERT: A 580 PHE cc_start: 0.6764 (t80) cc_final: 0.6303 (t80) REVERT: A 640 TRP cc_start: 0.6355 (t-100) cc_final: 0.6006 (t-100) REVERT: A 649 PHE cc_start: 0.6516 (m-10) cc_final: 0.6154 (m-80) REVERT: A 701 MET cc_start: 0.9097 (tpp) cc_final: 0.8582 (tpp) REVERT: A 704 LEU cc_start: 0.8348 (mt) cc_final: 0.7982 (mt) REVERT: A 715 ASP cc_start: 0.6657 (m-30) cc_final: 0.6413 (m-30) outliers start: 1 outliers final: 0 residues processed: 128 average time/residue: 0.1430 time to fit residues: 24.7274 Evaluate side-chains 112 residues out of total 591 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 112 time to evaluate : 0.542 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 72 random chunks: chunk 51 optimal weight: 0.2980 chunk 61 optimal weight: 9.9990 chunk 7 optimal weight: 5.9990 chunk 29 optimal weight: 9.9990 chunk 23 optimal weight: 5.9990 chunk 14 optimal weight: 9.9990 chunk 66 optimal weight: 5.9990 chunk 56 optimal weight: 7.9990 chunk 11 optimal weight: 6.9990 chunk 43 optimal weight: 2.9990 chunk 59 optimal weight: 10.0000 overall best weight: 4.2588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 37 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.5124 r_free = 0.5124 target = 0.309947 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 60)----------------| | r_work = 0.4825 r_free = 0.4825 target = 0.275050 restraints weight = 10943.635| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 43)----------------| | r_work = 0.4870 r_free = 0.4870 target = 0.280651 restraints weight = 8028.498| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 46)----------------| | r_work = 0.4902 r_free = 0.4902 target = 0.284901 restraints weight = 6251.830| |-----------------------------------------------------------------------------| r_work (final): 0.4925 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.4791 moved from start: 0.3708 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.034 5639 Z= 0.179 Angle : 0.732 8.404 7672 Z= 0.383 Chirality : 0.045 0.183 917 Planarity : 0.006 0.055 969 Dihedral : 4.393 24.233 770 Min Nonbonded Distance : 2.473 Molprobity Statistics. All-atom Clashscore : 13.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.88 % Favored : 96.12 % Rotamer: Outliers : 0.00 % Allowed : 4.58 % Favored : 95.42 % 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: 0.76 (0.31), residues: 721 helix: 1.12 (0.23), residues: 482 sheet: 0.29 (0.90), residues: 21 loop : -0.73 (0.45), residues: 218 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.029 0.002 TRP A 737 HIS 0.003 0.001 HIS A 239 PHE 0.026 0.002 PHE A 311 TYR 0.030 0.002 TYR A 703 ARG 0.005 0.001 ARG A 514 Details of bonding type rmsd hydrogen bonds : bond 0.04546 ( 396) hydrogen bonds : angle 4.87646 ( 1149) covalent geometry : bond 0.00370 ( 5639) covalent geometry : angle 0.73209 ( 7672) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1442 Ramachandran restraints generated. 721 Oldfield, 0 Emsley, 721 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1442 Ramachandran restraints generated. 721 Oldfield, 0 Emsley, 721 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 123 residues out of total 591 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 123 time to evaluate : 0.532 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash TARDY: cannot create tardy model for: "LYS A 748 " (corrupted residue). Skipping it. REVERT: A 131 ARG cc_start: 0.5217 (ttt180) cc_final: 0.5009 (ttt180) REVERT: A 171 LEU cc_start: 0.7748 (mp) cc_final: 0.7533 (mp) REVERT: A 284 MET cc_start: 0.2864 (ppp) cc_final: 0.2513 (ppp) REVERT: A 461 MET cc_start: -0.0840 (tpt) cc_final: -0.1689 (tpt) REVERT: A 580 PHE cc_start: 0.7247 (t80) cc_final: 0.6630 (t80) REVERT: A 631 MET cc_start: 0.8002 (ttp) cc_final: 0.7724 (ttp) REVERT: A 640 TRP cc_start: 0.6731 (t-100) cc_final: 0.6216 (t-100) REVERT: A 649 PHE cc_start: 0.7062 (m-10) cc_final: 0.6687 (m-80) REVERT: A 700 MET cc_start: 0.6892 (tmm) cc_final: 0.6667 (tmm) REVERT: A 751 LEU cc_start: 0.8490 (pp) cc_final: 0.7804 (tp) outliers start: 0 outliers final: 0 residues processed: 123 average time/residue: 0.1478 time to fit residues: 24.4806 Evaluate side-chains 107 residues out of total 591 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 107 time to evaluate : 0.518 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 72 random chunks: chunk 51 optimal weight: 0.0870 chunk 14 optimal weight: 4.9990 chunk 34 optimal weight: 10.0000 chunk 22 optimal weight: 40.0000 chunk 24 optimal weight: 1.9990 chunk 45 optimal weight: 4.9990 chunk 10 optimal weight: 8.9990 chunk 19 optimal weight: 20.0000 chunk 39 optimal weight: 0.0050 chunk 13 optimal weight: 3.9990 chunk 67 optimal weight: 5.9990 overall best weight: 2.2178 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 37 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.5135 r_free = 0.5135 target = 0.311949 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 63)----------------| | r_work = 0.4847 r_free = 0.4847 target = 0.277186 restraints weight = 11103.937| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 42)----------------| | r_work = 0.4893 r_free = 0.4893 target = 0.282892 restraints weight = 8191.346| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 52)----------------| | r_work = 0.4926 r_free = 0.4926 target = 0.287180 restraints weight = 6376.569| |-----------------------------------------------------------------------------| r_work (final): 0.4930 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.4745 moved from start: 0.4231 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 5639 Z= 0.145 Angle : 0.675 6.825 7672 Z= 0.351 Chirality : 0.043 0.196 917 Planarity : 0.005 0.061 969 Dihedral : 4.407 25.642 770 Min Nonbonded Distance : 2.495 Molprobity Statistics. All-atom Clashscore : 12.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.19 % Favored : 96.81 % Rotamer: Outliers : 0.00 % Allowed : 3.39 % Favored : 96.61 % 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: 0.81 (0.32), residues: 721 helix: 1.14 (0.23), residues: 487 sheet: -0.06 (0.79), residues: 21 loop : -0.66 (0.45), residues: 213 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.034 0.002 TRP A 111 HIS 0.007 0.001 HIS A 239 PHE 0.015 0.002 PHE A 611 TYR 0.031 0.002 TYR A 703 ARG 0.010 0.000 ARG A 281 Details of bonding type rmsd hydrogen bonds : bond 0.04197 ( 396) hydrogen bonds : angle 4.69146 ( 1149) covalent geometry : bond 0.00288 ( 5639) covalent geometry : angle 0.67533 ( 7672) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1442 Ramachandran restraints generated. 721 Oldfield, 0 Emsley, 721 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1442 Ramachandran restraints generated. 721 Oldfield, 0 Emsley, 721 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 118 residues out of total 591 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 118 time to evaluate : 0.502 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash TARDY: cannot create tardy model for: "LYS A 748 " (corrupted residue). Skipping it. REVERT: A 84 LYS cc_start: 0.7855 (pptt) cc_final: 0.7214 (pttt) REVERT: A 131 ARG cc_start: 0.5075 (ttt180) cc_final: 0.4489 (ttt180) REVERT: A 171 LEU cc_start: 0.7732 (mp) cc_final: 0.7495 (mp) REVERT: A 477 MET cc_start: 0.3774 (mtp) cc_final: 0.3515 (mtp) REVERT: A 563 LYS cc_start: 0.8897 (mmpt) cc_final: 0.8583 (mmmt) REVERT: A 580 PHE cc_start: 0.7261 (t80) cc_final: 0.6806 (t80) REVERT: A 640 TRP cc_start: 0.6655 (t-100) cc_final: 0.6146 (t-100) REVERT: A 649 PHE cc_start: 0.7059 (m-10) cc_final: 0.6698 (m-80) REVERT: A 715 ASP cc_start: 0.7207 (m-30) cc_final: 0.6897 (m-30) REVERT: A 751 LEU cc_start: 0.8458 (pp) cc_final: 0.7848 (tp) outliers start: 0 outliers final: 0 residues processed: 118 average time/residue: 0.1511 time to fit residues: 23.7011 Evaluate side-chains 103 residues out of total 591 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 103 time to evaluate : 0.534 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 72 random chunks: chunk 14 optimal weight: 9.9990 chunk 27 optimal weight: 20.0000 chunk 61 optimal weight: 10.0000 chunk 62 optimal weight: 9.9990 chunk 42 optimal weight: 0.1980 chunk 18 optimal weight: 50.0000 chunk 49 optimal weight: 8.9990 chunk 34 optimal weight: 10.0000 chunk 55 optimal weight: 5.9990 chunk 39 optimal weight: 6.9990 chunk 68 optimal weight: 5.9990 overall best weight: 5.6388 ------------------------------------------------------------------------------- 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 = 0.5069 r_free = 0.5069 target = 0.304270 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 87)----------------| | r_work = 0.4780 r_free = 0.4780 target = 0.270261 restraints weight = 11149.224| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.4816 r_free = 0.4816 target = 0.274882 restraints weight = 8398.378| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 60)----------------| | r_work = 0.4850 r_free = 0.4850 target = 0.278762 restraints weight = 6683.421| |-----------------------------------------------------------------------------| r_work (final): 0.4862 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5036 moved from start: 0.5118 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.046 5639 Z= 0.206 Angle : 0.768 9.076 7672 Z= 0.406 Chirality : 0.045 0.193 917 Planarity : 0.006 0.059 969 Dihedral : 4.788 29.699 770 Min Nonbonded Distance : 2.417 Molprobity Statistics. All-atom Clashscore : 14.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.58 % Favored : 95.42 % Rotamer: Outliers : 0.00 % Allowed : 4.07 % Favored : 95.93 % 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: 0.69 (0.32), residues: 721 helix: 1.09 (0.24), residues: 486 sheet: -0.43 (0.88), residues: 21 loop : -0.78 (0.45), residues: 214 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.030 0.002 TRP A 111 HIS 0.013 0.003 HIS A 132 PHE 0.025 0.002 PHE A 311 TYR 0.032 0.003 TYR A 703 ARG 0.019 0.001 ARG A 281 Details of bonding type rmsd hydrogen bonds : bond 0.04706 ( 396) hydrogen bonds : angle 4.87578 ( 1149) covalent geometry : bond 0.00428 ( 5639) covalent geometry : angle 0.76753 ( 7672) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1442 Ramachandran restraints generated. 721 Oldfield, 0 Emsley, 721 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1442 Ramachandran restraints generated. 721 Oldfield, 0 Emsley, 721 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 111 residues out of total 591 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 111 time to evaluate : 0.624 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash TARDY: cannot create tardy model for: "LYS A 748 " (corrupted residue). Skipping it. REVERT: A 131 ARG cc_start: 0.5426 (ttt180) cc_final: 0.4880 (ttt180) REVERT: A 171 LEU cc_start: 0.7910 (mp) cc_final: 0.7689 (mp) REVERT: A 563 LYS cc_start: 0.8879 (mmpt) cc_final: 0.8562 (mmmt) REVERT: A 579 MET cc_start: 0.8020 (mmt) cc_final: 0.7789 (tpt) REVERT: A 580 PHE cc_start: 0.7426 (t80) cc_final: 0.6997 (t80) REVERT: A 640 TRP cc_start: 0.6817 (t-100) cc_final: 0.6240 (t-100) REVERT: A 649 PHE cc_start: 0.7220 (m-10) cc_final: 0.6929 (m-80) REVERT: A 654 MET cc_start: 0.1407 (mmp) cc_final: 0.1045 (mmm) outliers start: 0 outliers final: 0 residues processed: 111 average time/residue: 0.1527 time to fit residues: 22.7293 Evaluate side-chains 97 residues out of total 591 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 97 time to evaluate : 0.596 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 72 random chunks: chunk 41 optimal weight: 5.9990 chunk 43 optimal weight: 5.9990 chunk 18 optimal weight: 40.0000 chunk 13 optimal weight: 3.9990 chunk 67 optimal weight: 9.9990 chunk 40 optimal weight: 0.1980 chunk 25 optimal weight: 20.0000 chunk 63 optimal weight: 6.9990 chunk 39 optimal weight: 8.9990 chunk 16 optimal weight: 0.6980 chunk 52 optimal weight: 30.0000 overall best weight: 3.3786 ------------------------------------------------------------------------------- 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 = 0.5027 r_free = 0.5027 target = 0.299944 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 66)----------------| | r_work = 0.4742 r_free = 0.4742 target = 0.265585 restraints weight = 10294.251| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 43)----------------| | r_work = 0.4785 r_free = 0.4785 target = 0.270934 restraints weight = 7577.488| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 46)----------------| | r_work = 0.4818 r_free = 0.4818 target = 0.275041 restraints weight = 5872.834| |-----------------------------------------------------------------------------| r_work (final): 0.4819 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.4960 moved from start: 0.5485 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 5639 Z= 0.157 Angle : 0.719 7.795 7672 Z= 0.371 Chirality : 0.045 0.231 917 Planarity : 0.005 0.069 969 Dihedral : 4.692 27.418 770 Min Nonbonded Distance : 2.469 Molprobity Statistics. All-atom Clashscore : 12.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.74 % Favored : 96.26 % Rotamer: Outliers : 0.17 % Allowed : 1.53 % Favored : 98.31 % 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: 0.85 (0.32), residues: 721 helix: 1.23 (0.24), residues: 484 sheet: -1.00 (0.84), residues: 21 loop : -0.67 (0.46), residues: 216 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.002 TRP A 111 HIS 0.005 0.001 HIS A 239 PHE 0.021 0.002 PHE A 12 TYR 0.027 0.002 TYR A 703 ARG 0.012 0.001 ARG A 281 Details of bonding type rmsd hydrogen bonds : bond 0.04347 ( 396) hydrogen bonds : angle 4.64084 ( 1149) covalent geometry : bond 0.00306 ( 5639) covalent geometry : angle 0.71893 ( 7672) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1442 Ramachandran restraints generated. 721 Oldfield, 0 Emsley, 721 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1442 Ramachandran restraints generated. 721 Oldfield, 0 Emsley, 721 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 118 residues out of total 591 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 117 time to evaluate : 0.587 Fit side-chains revert: symmetry clash revert: symmetry clash TARDY: cannot create tardy model for: "LYS A 748 " (corrupted residue). Skipping it. REVERT: A 131 ARG cc_start: 0.5184 (ttt180) cc_final: 0.4337 (ttt180) REVERT: A 463 ARG cc_start: 0.4730 (OUTLIER) cc_final: 0.4025 (mtp-110) REVERT: A 555 ASP cc_start: 0.8302 (m-30) cc_final: 0.8054 (m-30) REVERT: A 563 LYS cc_start: 0.8929 (mmpt) cc_final: 0.8672 (mmmt) REVERT: A 566 LEU cc_start: 0.8451 (mt) cc_final: 0.8096 (mp) REVERT: A 631 MET cc_start: 0.8029 (ttp) cc_final: 0.7809 (ttp) REVERT: A 640 TRP cc_start: 0.6640 (t-100) cc_final: 0.6056 (t-100) REVERT: A 649 PHE cc_start: 0.7094 (m-10) cc_final: 0.6879 (m-80) REVERT: A 751 LEU cc_start: 0.8258 (pp) cc_final: 0.7472 (tp) outliers start: 1 outliers final: 0 residues processed: 117 average time/residue: 0.1590 time to fit residues: 24.7010 Evaluate side-chains 105 residues out of total 591 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 104 time to evaluate : 0.573 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 72 random chunks: chunk 70 optimal weight: 5.9990 chunk 64 optimal weight: 9.9990 chunk 45 optimal weight: 8.9990 chunk 50 optimal weight: 3.9990 chunk 48 optimal weight: 5.9990 chunk 53 optimal weight: 30.0000 chunk 68 optimal weight: 20.0000 chunk 35 optimal weight: 1.9990 chunk 18 optimal weight: 5.9990 chunk 66 optimal weight: 10.0000 chunk 3 optimal weight: 20.0000 overall best weight: 4.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 49 GLN A 162 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.5012 r_free = 0.5012 target = 0.298981 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.4797 r_free = 0.4797 target = 0.272886 restraints weight = 9765.112| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.4814 r_free = 0.4814 target = 0.275486 restraints weight = 7611.724| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 51)----------------| | r_work = 0.4845 r_free = 0.4845 target = 0.278928 restraints weight = 5725.741| |-----------------------------------------------------------------------------| r_work (final): 0.4824 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.4982 moved from start: 0.6167 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.047 5639 Z= 0.188 Angle : 0.780 7.836 7672 Z= 0.403 Chirality : 0.045 0.188 917 Planarity : 0.006 0.077 969 Dihedral : 4.923 29.381 770 Min Nonbonded Distance : 2.429 Molprobity Statistics. All-atom Clashscore : 14.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.27 % Favored : 94.73 % Rotamer: Outliers : 0.00 % Allowed : 2.37 % Favored : 97.63 % 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: 0.65 (0.32), residues: 721 helix: 1.14 (0.24), residues: 482 sheet: -0.93 (0.94), residues: 21 loop : -0.93 (0.45), residues: 218 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.002 TRP A 111 HIS 0.007 0.002 HIS A 239 PHE 0.027 0.002 PHE A 311 TYR 0.029 0.003 TYR A 703 ARG 0.009 0.001 ARG A 653 Details of bonding type rmsd hydrogen bonds : bond 0.04723 ( 396) hydrogen bonds : angle 4.79917 ( 1149) covalent geometry : bond 0.00382 ( 5639) covalent geometry : angle 0.78006 ( 7672) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1442 Ramachandran restraints generated. 721 Oldfield, 0 Emsley, 721 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1442 Ramachandran restraints generated. 721 Oldfield, 0 Emsley, 721 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 110 residues out of total 591 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 110 time to evaluate : 0.539 Fit side-chains revert: symmetry clash revert: symmetry clash TARDY: cannot create tardy model for: "LYS A 748 " (corrupted residue). Skipping it. REVERT: A 1 MET cc_start: 0.7564 (tmm) cc_final: 0.7186 (tmm) REVERT: A 400 ARG cc_start: 0.6928 (mmm160) cc_final: 0.4245 (mmt180) REVERT: A 563 LYS cc_start: 0.9075 (mmpt) cc_final: 0.8800 (mmmt) REVERT: A 566 LEU cc_start: 0.8421 (mt) cc_final: 0.8100 (mp) REVERT: A 640 TRP cc_start: 0.6477 (t-100) cc_final: 0.5888 (t-100) REVERT: A 751 LEU cc_start: 0.7810 (pp) cc_final: 0.7170 (tp) outliers start: 0 outliers final: 0 residues processed: 110 average time/residue: 0.1477 time to fit residues: 21.9296 Evaluate side-chains 97 residues out of total 591 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 97 time to evaluate : 0.517 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 72 random chunks: chunk 25 optimal weight: 9.9990 chunk 31 optimal weight: 7.9990 chunk 1 optimal weight: 0.6980 chunk 35 optimal weight: 0.4980 chunk 69 optimal weight: 50.0000 chunk 20 optimal weight: 0.0020 chunk 6 optimal weight: 8.9990 chunk 17 optimal weight: 10.0000 chunk 0 optimal weight: 9.9990 chunk 19 optimal weight: 10.0000 chunk 68 optimal weight: 20.0000 overall best weight: 3.6392 ------------------------------------------------------------------------------- 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 = 0.4999 r_free = 0.4999 target = 0.299923 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.4777 r_free = 0.4777 target = 0.271083 restraints weight = 11187.519| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.4800 r_free = 0.4800 target = 0.274622 restraints weight = 8387.183| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.4818 r_free = 0.4818 target = 0.277569 restraints weight = 6098.413| |-----------------------------------------------------------------------------| r_work (final): 0.4823 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5025 moved from start: 0.6356 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 5639 Z= 0.159 Angle : 0.746 7.223 7672 Z= 0.385 Chirality : 0.045 0.243 917 Planarity : 0.006 0.073 969 Dihedral : 4.900 29.185 770 Min Nonbonded Distance : 2.435 Molprobity Statistics. All-atom Clashscore : 12.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.02 % Favored : 95.98 % Rotamer: Outliers : 0.00 % Allowed : 0.34 % Favored : 99.66 % 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: 0.65 (0.32), residues: 721 helix: 1.18 (0.24), residues: 477 sheet: -1.39 (0.98), residues: 21 loop : -0.93 (0.44), residues: 223 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.002 TRP A 111 HIS 0.006 0.001 HIS A 239 PHE 0.030 0.002 PHE A 649 TYR 0.015 0.002 TYR A 703 ARG 0.014 0.001 ARG A 281 Details of bonding type rmsd hydrogen bonds : bond 0.04537 ( 396) hydrogen bonds : angle 4.75828 ( 1149) covalent geometry : bond 0.00321 ( 5639) covalent geometry : angle 0.74614 ( 7672) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1442 Ramachandran restraints generated. 721 Oldfield, 0 Emsley, 721 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1442 Ramachandran restraints generated. 721 Oldfield, 0 Emsley, 721 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 104 residues out of total 591 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 104 time to evaluate : 0.557 Fit side-chains revert: symmetry clash TARDY: cannot create tardy model for: "LYS A 748 " (corrupted residue). Skipping it. REVERT: A 463 ARG cc_start: 0.6045 (mtm110) cc_final: 0.3856 (ttp80) REVERT: A 563 LYS cc_start: 0.8998 (mmpt) cc_final: 0.8740 (mmmt) REVERT: A 566 LEU cc_start: 0.8370 (mt) cc_final: 0.8046 (mp) REVERT: A 640 TRP cc_start: 0.6739 (t-100) cc_final: 0.6133 (t-100) REVERT: A 662 MET cc_start: -0.4077 (mmt) cc_final: -0.5015 (mmt) REVERT: A 751 LEU cc_start: 0.7828 (pp) cc_final: 0.7194 (tp) outliers start: 0 outliers final: 0 residues processed: 104 average time/residue: 0.1506 time to fit residues: 21.1234 Evaluate side-chains 95 residues out of total 591 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 95 time to evaluate : 0.557 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 72 random chunks: chunk 32 optimal weight: 1.9990 chunk 66 optimal weight: 20.0000 chunk 64 optimal weight: 7.9990 chunk 43 optimal weight: 7.9990 chunk 8 optimal weight: 0.5980 chunk 68 optimal weight: 30.0000 chunk 5 optimal weight: 40.0000 chunk 44 optimal weight: 5.9990 chunk 16 optimal weight: 0.2980 chunk 0 optimal weight: 10.0000 chunk 53 optimal weight: 40.0000 overall best weight: 3.3786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 162 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 625 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4989 r_free = 0.4989 target = 0.298159 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.4810 r_free = 0.4810 target = 0.274294 restraints weight = 10980.770| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.4822 r_free = 0.4822 target = 0.276866 restraints weight = 10982.073| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.4840 r_free = 0.4840 target = 0.279212 restraints weight = 7545.285| |-----------------------------------------------------------------------------| r_work (final): 0.4814 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.4942 moved from start: 0.6650 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 5639 Z= 0.152 Angle : 0.746 8.847 7672 Z= 0.381 Chirality : 0.044 0.204 917 Planarity : 0.006 0.077 969 Dihedral : 4.881 26.340 770 Min Nonbonded Distance : 2.475 Molprobity Statistics. All-atom Clashscore : 13.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.85 % Favored : 95.15 % Rotamer: Outliers : 0.00 % Allowed : 1.02 % Favored : 98.98 % 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: 0.58 (0.32), residues: 721 helix: 1.12 (0.24), residues: 485 sheet: -1.41 (1.02), residues: 21 loop : -1.02 (0.45), residues: 215 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.002 TRP A 111 HIS 0.006 0.001 HIS A 239 PHE 0.051 0.002 PHE A 649 TYR 0.020 0.002 TYR A 703 ARG 0.009 0.001 ARG A 281 Details of bonding type rmsd hydrogen bonds : bond 0.04247 ( 396) hydrogen bonds : angle 4.67818 ( 1149) covalent geometry : bond 0.00306 ( 5639) covalent geometry : angle 0.74579 ( 7672) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1442 Ramachandran restraints generated. 721 Oldfield, 0 Emsley, 721 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1442 Ramachandran restraints generated. 721 Oldfield, 0 Emsley, 721 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 101 residues out of total 591 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 101 time to evaluate : 0.480 Fit side-chains revert: symmetry clash revert: symmetry clash TARDY: cannot create tardy model for: "LYS A 748 " (corrupted residue). Skipping it. REVERT: A 20 MET cc_start: 0.6830 (tmm) cc_final: 0.6272 (tpt) REVERT: A 566 LEU cc_start: 0.8353 (mt) cc_final: 0.8024 (mp) REVERT: A 625 GLN cc_start: 0.7308 (mp-120) cc_final: 0.7078 (mp10) REVERT: A 640 TRP cc_start: 0.6411 (t-100) cc_final: 0.5873 (t-100) REVERT: A 649 PHE cc_start: 0.7260 (m-80) cc_final: 0.6867 (m-80) outliers start: 0 outliers final: 0 residues processed: 101 average time/residue: 0.1369 time to fit residues: 19.0179 Evaluate side-chains 95 residues out of total 591 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 95 time to evaluate : 0.598 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 72 random chunks: chunk 45 optimal weight: 9.9990 chunk 12 optimal weight: 6.9990 chunk 65 optimal weight: 20.0000 chunk 17 optimal weight: 5.9990 chunk 35 optimal weight: 7.9990 chunk 0 optimal weight: 10.0000 chunk 60 optimal weight: 8.9990 chunk 18 optimal weight: 7.9990 chunk 47 optimal weight: 6.9990 chunk 42 optimal weight: 10.0000 chunk 8 optimal weight: 1.9990 overall best weight: 5.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 162 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 = 0.4981 r_free = 0.4981 target = 0.293458 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.4790 r_free = 0.4790 target = 0.269830 restraints weight = 9468.197| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.4814 r_free = 0.4814 target = 0.273517 restraints weight = 9749.342| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.4837 r_free = 0.4837 target = 0.276066 restraints weight = 6459.925| |-----------------------------------------------------------------------------| r_work (final): 0.4836 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5055 moved from start: 0.7248 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 5639 Z= 0.201 Angle : 0.812 9.018 7672 Z= 0.421 Chirality : 0.047 0.253 917 Planarity : 0.007 0.077 969 Dihedral : 5.355 31.130 770 Min Nonbonded Distance : 2.467 Molprobity Statistics. All-atom Clashscore : 16.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.99 % Favored : 95.01 % Rotamer: Outliers : 0.00 % Allowed : 1.19 % Favored : 98.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.15 % 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: 0.38 (0.32), residues: 721 helix: 1.02 (0.24), residues: 477 sheet: -1.59 (1.01), residues: 21 loop : -1.17 (0.44), residues: 223 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.002 TRP A 111 HIS 0.008 0.002 HIS A 239 PHE 0.038 0.003 PHE A 649 TYR 0.014 0.002 TYR A 703 ARG 0.007 0.001 ARG A 281 Details of bonding type rmsd hydrogen bonds : bond 0.04842 ( 396) hydrogen bonds : angle 4.93820 ( 1149) covalent geometry : bond 0.00415 ( 5639) covalent geometry : angle 0.81203 ( 7672) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1442 Ramachandran restraints generated. 721 Oldfield, 0 Emsley, 721 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1442 Ramachandran restraints generated. 721 Oldfield, 0 Emsley, 721 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 107 residues out of total 591 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 107 time to evaluate : 0.510 Fit side-chains revert: symmetry clash revert: symmetry clash TARDY: cannot create tardy model for: "LYS A 748 " (corrupted residue). Skipping it. REVERT: A 130 LEU cc_start: 0.7939 (mp) cc_final: 0.7191 (tp) REVERT: A 463 ARG cc_start: 0.6119 (mtm110) cc_final: 0.5593 (mtp180) REVERT: A 566 LEU cc_start: 0.8058 (mt) cc_final: 0.7774 (mp) REVERT: A 631 MET cc_start: 0.8006 (ttp) cc_final: 0.7806 (ttp) REVERT: A 640 TRP cc_start: 0.6322 (t-100) cc_final: 0.5782 (t-100) REVERT: A 649 PHE cc_start: 0.7107 (m-80) cc_final: 0.6834 (m-80) REVERT: A 737 TRP cc_start: 0.5337 (t60) cc_final: 0.4611 (t60) outliers start: 0 outliers final: 0 residues processed: 107 average time/residue: 0.1549 time to fit residues: 22.3385 Evaluate side-chains 95 residues out of total 591 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 95 time to evaluate : 0.599 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 72 random chunks: chunk 34 optimal weight: 9.9990 chunk 46 optimal weight: 0.0070 chunk 71 optimal weight: 0.8980 chunk 30 optimal weight: 0.9990 chunk 15 optimal weight: 2.9990 chunk 67 optimal weight: 20.0000 chunk 26 optimal weight: 20.0000 chunk 5 optimal weight: 2.9990 chunk 65 optimal weight: 5.9990 chunk 60 optimal weight: 0.0060 chunk 11 optimal weight: 1.9990 overall best weight: 0.7818 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 625 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.5034 r_free = 0.5034 target = 0.299518 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.4832 r_free = 0.4832 target = 0.273559 restraints weight = 11316.958| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.4846 r_free = 0.4846 target = 0.277148 restraints weight = 9197.001| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.4870 r_free = 0.4870 target = 0.280440 restraints weight = 6613.975| |-----------------------------------------------------------------------------| r_work (final): 0.4853 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.4920 moved from start: 0.7175 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 5639 Z= 0.142 Angle : 0.755 9.321 7672 Z= 0.381 Chirality : 0.045 0.254 917 Planarity : 0.006 0.072 969 Dihedral : 4.822 24.816 770 Min Nonbonded Distance : 2.499 Molprobity Statistics. All-atom Clashscore : 13.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.88 % Favored : 96.12 % Rotamer: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.59 (0.32), residues: 721 helix: 1.19 (0.24), residues: 481 sheet: -1.70 (1.03), residues: 21 loop : -1.13 (0.44), residues: 219 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.001 TRP A 111 HIS 0.002 0.001 HIS A 239 PHE 0.036 0.002 PHE A 649 TYR 0.018 0.001 TYR A 703 ARG 0.008 0.001 ARG A 463 Details of bonding type rmsd hydrogen bonds : bond 0.04154 ( 396) hydrogen bonds : angle 4.63724 ( 1149) covalent geometry : bond 0.00285 ( 5639) covalent geometry : angle 0.75476 ( 7672) =============================================================================== Job complete usr+sys time: 1951.63 seconds wall clock time: 34 minutes 31.15 seconds (2071.15 seconds total)