Starting phenix.real_space_refine on Fri May 9 16:59:21 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8qtd_18649/05_2025/8qtd_18649.cif Found real_map, /net/cci-nas-00/data/ceres_data/8qtd_18649/05_2025/8qtd_18649.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.6 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8qtd_18649/05_2025/8qtd_18649.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8qtd_18649/05_2025/8qtd_18649.map" model { file = "/net/cci-nas-00/data/ceres_data/8qtd_18649/05_2025/8qtd_18649.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8qtd_18649/05_2025/8qtd_18649.cif" } resolution = 3.6 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= -0.000 sd= 0.016 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 16 5.16 5 C 2058 2.51 5 N 541 2.21 5 O 604 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 10 residue(s): 0.01s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/chem_data/mon_lib" Total number of atoms: 3219 Number of models: 1 Model: "" Number of chains: 3 Chain: "A" Number of atoms: 1566 Number of conformers: 1 Conformer: "" Number of residues, atoms: 195, 1566 Classifications: {'peptide': 195} Link IDs: {'PTRANS': 13, 'TRANS': 181} Chain: "H" Number of atoms: 1021 Number of conformers: 1 Conformer: "" Number of residues, atoms: 130, 1021 Classifications: {'peptide': 130} Link IDs: {'PTRANS': 3, 'TRANS': 126} Chain: "L" Number of atoms: 632 Number of conformers: 1 Conformer: "" Number of residues, atoms: 88, 632 Classifications: {'peptide': 88} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 4, 'TRANS': 83} Chain breaks: 2 Unresolved non-hydrogen bonds: 10 Unresolved non-hydrogen angles: 11 Unresolved non-hydrogen dihedrals: 9 Planarities with less than four sites: {'GLU:plan': 1} Unresolved non-hydrogen planarities: 4 Time building chain proxies: 3.83, per 1000 atoms: 1.19 Number of scatterers: 3219 At special positions: 0 Unit cell: (70.8391, 58.424, 97.8602, 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 16 16.00 O 604 8.00 N 541 7.00 C 2058 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=6, symmetry=0 Simple disulfide: pdb=" SG CYS A 333 " - pdb=" SG CYS A 358 " distance=2.03 Simple disulfide: pdb=" SG CYS A 376 " - pdb=" SG CYS A 429 " distance=2.03 Simple disulfide: pdb=" SG CYS A 388 " - pdb=" SG CYS A 521 " distance=2.03 Simple disulfide: pdb=" SG CYS A 477 " - pdb=" SG CYS A 484 " distance=2.03 Simple disulfide: pdb=" SG CYS H 22 " - pdb=" SG CYS H 96 " distance=2.03 Simple disulfide: pdb=" SG CYS L 22 " - pdb=" SG CYS L 90 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 0.75 Conformation dependent library (CDL) restraints added in 429.6 milliseconds 806 Ramachandran restraints generated. 403 Oldfield, 0 Emsley, 403 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 746 Finding SS restraints... Secondary structure from input PDB file: 10 helices and 10 sheets defined 13.1% alpha, 37.5% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.42 Creating SS restraints... Processing helix chain 'A' and resid 334 through 339 removed outlier: 4.331A pdb=" N VAL A 338 " --> pdb=" O PRO A 334 " (cutoff:3.500A) Processing helix chain 'A' and resid 361 through 363 No H-bonds generated for 'chain 'A' and resid 361 through 363' Processing helix chain 'A' and resid 364 through 369 removed outlier: 3.896A pdb=" N ALA A 369 " --> pdb=" O LEU A 365 " (cutoff:3.500A) Processing helix chain 'A' and resid 380 through 387 removed outlier: 4.951A pdb=" N ASN A 385 " --> pdb=" O THR A 382 " (cutoff:3.500A) removed outlier: 3.811A pdb=" N LEU A 387 " --> pdb=" O LEU A 384 " (cutoff:3.500A) Processing helix chain 'A' and resid 401 through 405 removed outlier: 3.854A pdb=" N SER A 405 " --> pdb=" O ASN A 402 " (cutoff:3.500A) Processing helix chain 'A' and resid 414 through 419 Processing helix chain 'H' and resid 62 through 65 Processing helix chain 'H' and resid 87 through 91 removed outlier: 3.785A pdb=" N THR H 91 " --> pdb=" O ALA H 88 " (cutoff:3.500A) Processing helix chain 'H' and resid 105 through 110 removed outlier: 3.802A pdb=" N GLY H 108 " --> pdb=" O ASP H 105 " (cutoff:3.500A) removed outlier: 3.951A pdb=" N TYR H 109 " --> pdb=" O SER H 106 " (cutoff:3.500A) removed outlier: 3.801A pdb=" N TYR H 110 " --> pdb=" O ALA H 107 " (cutoff:3.500A) No H-bonds generated for 'chain 'H' and resid 105 through 110' Processing helix chain 'L' and resid 81 through 85 Processing sheet with id=AA1, first strand: chain 'A' and resid 351 through 355 Processing sheet with id=AA2, first strand: chain 'A' and resid 358 through 359 removed outlier: 7.322A pdb=" N CYS A 358 " --> pdb=" O CYS A 521 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA2 Processing sheet with id=AA3, first strand: chain 'A' and resid 449 through 451 Processing sheet with id=AA4, first strand: chain 'A' and resid 470 through 471 Processing sheet with id=AA5, first strand: chain 'H' and resid 3 through 7 removed outlier: 3.827A pdb=" N SER H 78 " --> pdb=" O ASP H 73 " (cutoff:3.500A) removed outlier: 3.531A pdb=" N ASP H 73 " --> pdb=" O SER H 78 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'H' and resid 10 through 12 removed outlier: 6.381A pdb=" N GLY H 10 " --> pdb=" O THR H 128 " (cutoff:3.500A) removed outlier: 4.454A pdb=" N SER H 33 " --> pdb=" O VAL H 99 " (cutoff:3.500A) removed outlier: 5.529A pdb=" N ARG H 38 " --> pdb=" O TRP H 47 " (cutoff:3.500A) removed outlier: 5.004A pdb=" N TRP H 47 " --> pdb=" O ARG H 38 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'H' and resid 10 through 12 removed outlier: 6.381A pdb=" N GLY H 10 " --> pdb=" O THR H 128 " (cutoff:3.500A) removed outlier: 6.969A pdb=" N CYS H 96 " --> pdb=" O TRP H 121 " (cutoff:3.500A) removed outlier: 4.902A pdb=" N TRP H 121 " --> pdb=" O CYS H 96 " (cutoff:3.500A) removed outlier: 7.089A pdb=" N ARG H 98 " --> pdb=" O ASP H 119 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'L' and resid 9 through 12 removed outlier: 6.452A pdb=" N VAL L 10 " --> pdb=" O THR L 107 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'L' and resid 9 through 12 removed outlier: 6.452A pdb=" N VAL L 10 " --> pdb=" O THR L 107 " (cutoff:3.500A) removed outlier: 3.796A pdb=" N VAL L 99 " --> pdb=" O SER L 92 " (cutoff:3.500A) removed outlier: 3.688A pdb=" N THR L 94 " --> pdb=" O VAL L 97 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'L' and resid 18 through 23 108 hydrogen bonds defined for protein. 237 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: 0.86 Time building geometry restraints manager: 0.90 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.34: 1016 1.34 - 1.46: 888 1.46 - 1.58: 1386 1.58 - 1.69: 0 1.69 - 1.81: 20 Bond restraints: 3310 Sorted by residual: bond pdb=" C GLY L 12 " pdb=" N SER L 13 " ideal model delta sigma weight residual 1.330 1.348 -0.018 1.47e-02 4.63e+03 1.49e+00 bond pdb=" N LYS H 65 " pdb=" CA LYS H 65 " ideal model delta sigma weight residual 1.457 1.470 -0.013 1.29e-02 6.01e+03 9.79e-01 bond pdb=" C THR A 412 " pdb=" N GLY A 413 " ideal model delta sigma weight residual 1.331 1.319 0.011 1.46e-02 4.69e+03 5.78e-01 bond pdb=" CA VAL A 379 " pdb=" CB VAL A 379 " ideal model delta sigma weight residual 1.540 1.550 -0.010 1.36e-02 5.41e+03 4.96e-01 bond pdb=" CA LYS A 478 " pdb=" CB LYS A 478 " ideal model delta sigma weight residual 1.530 1.542 -0.011 1.69e-02 3.50e+03 4.57e-01 ... (remaining 3305 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.10: 4344 1.10 - 2.20: 112 2.20 - 3.30: 29 3.30 - 4.41: 7 4.41 - 5.51: 2 Bond angle restraints: 4494 Sorted by residual: angle pdb=" C GLY L 12 " pdb=" N SER L 13 " pdb=" CA SER L 13 " ideal model delta sigma weight residual 120.68 124.94 -4.26 1.52e+00 4.33e-01 7.87e+00 angle pdb=" C LYS H 65 " pdb=" CA LYS H 65 " pdb=" CB LYS H 65 " ideal model delta sigma weight residual 110.42 115.55 -5.13 1.99e+00 2.53e-01 6.64e+00 angle pdb=" N ASN L 33 " pdb=" CA ASN L 33 " pdb=" C ASN L 33 " ideal model delta sigma weight residual 114.56 111.40 3.16 1.27e+00 6.20e-01 6.19e+00 angle pdb=" CA LYS A 478 " pdb=" CB LYS A 478 " pdb=" CG LYS A 478 " ideal model delta sigma weight residual 114.10 117.99 -3.89 2.00e+00 2.50e-01 3.79e+00 angle pdb=" C CYS A 477 " pdb=" N LYS A 478 " pdb=" CA LYS A 478 " ideal model delta sigma weight residual 121.54 125.24 -3.70 1.91e+00 2.74e-01 3.76e+00 ... (remaining 4489 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 11.94: 1750 11.94 - 23.87: 119 23.87 - 35.81: 41 35.81 - 47.74: 6 47.74 - 59.68: 3 Dihedral angle restraints: 1919 sinusoidal: 733 harmonic: 1186 Sorted by residual: dihedral pdb=" CA ARG H 112 " pdb=" CB ARG H 112 " pdb=" CG ARG H 112 " pdb=" CD ARG H 112 " ideal model delta sinusoidal sigma weight residual 180.00 127.06 52.94 3 1.50e+01 4.44e-03 9.16e+00 dihedral pdb=" N TYR H 104 " pdb=" CA TYR H 104 " pdb=" CB TYR H 104 " pdb=" CG TYR H 104 " ideal model delta sinusoidal sigma weight residual -60.00 -112.60 52.60 3 1.50e+01 4.44e-03 9.13e+00 dihedral pdb=" N MET H 83 " pdb=" CA MET H 83 " pdb=" CB MET H 83 " pdb=" CG MET H 83 " ideal model delta sinusoidal sigma weight residual -180.00 -132.62 -47.38 3 1.50e+01 4.44e-03 8.48e+00 ... (remaining 1916 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.027: 256 0.027 - 0.053: 137 0.053 - 0.080: 34 0.080 - 0.106: 23 0.106 - 0.133: 18 Chirality restraints: 468 Sorted by residual: chirality pdb=" CA ILE A 355 " pdb=" N ILE A 355 " pdb=" C ILE A 355 " pdb=" CB ILE A 355 " both_signs ideal model delta sigma weight residual False 2.43 2.57 -0.13 2.00e-01 2.50e+01 4.39e-01 chirality pdb=" CA VAL A 392 " pdb=" N VAL A 392 " pdb=" C VAL A 392 " pdb=" CB VAL A 392 " both_signs ideal model delta sigma weight residual False 2.44 2.56 -0.12 2.00e-01 2.50e+01 3.79e-01 chirality pdb=" CA VAL H 79 " pdb=" N VAL H 79 " pdb=" C VAL H 79 " pdb=" CB VAL H 79 " both_signs ideal model delta sigma weight residual False 2.44 2.56 -0.12 2.00e-01 2.50e+01 3.75e-01 ... (remaining 465 not shown) Planarity restraints: 579 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ALA L 45 " 0.015 5.00e-02 4.00e+02 2.33e-02 8.72e-01 pdb=" N PRO L 46 " -0.040 5.00e-02 4.00e+02 pdb=" CA PRO L 46 " 0.012 5.00e-02 4.00e+02 pdb=" CD PRO L 46 " 0.013 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C GLN H 13 " 0.015 5.00e-02 4.00e+02 2.27e-02 8.22e-01 pdb=" N PRO H 14 " -0.039 5.00e-02 4.00e+02 pdb=" CA PRO H 14 " 0.012 5.00e-02 4.00e+02 pdb=" CD PRO H 14 " 0.013 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ALA A 369 " -0.014 5.00e-02 4.00e+02 2.10e-02 7.06e-01 pdb=" N PRO A 370 " 0.036 5.00e-02 4.00e+02 pdb=" CA PRO A 370 " -0.011 5.00e-02 4.00e+02 pdb=" CD PRO A 370 " -0.012 5.00e-02 4.00e+02 ... (remaining 576 not shown) Histogram of nonbonded interaction distances: 2.30 - 2.82: 998 2.82 - 3.34: 2668 3.34 - 3.86: 5033 3.86 - 4.38: 6031 4.38 - 4.90: 10562 Nonbonded interactions: 25292 Sorted by model distance: nonbonded pdb=" OD1 ASP L 84 " pdb=" OH TYR L 88 " model vdw 2.298 3.040 nonbonded pdb=" O PHE H 29 " pdb=" NH2 ARG H 72 " model vdw 2.336 3.120 nonbonded pdb=" OD1 ASP A 361 " pdb=" OG SER A 363 " model vdw 2.342 3.040 nonbonded pdb=" OG SER A 490 " pdb=" O ARG H 112 " model vdw 2.352 3.040 nonbonded pdb=" OG SER L 69 " pdb=" OG1 THR L 72 " model vdw 2.378 3.040 ... (remaining 25287 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 ========== 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: 5.790 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.140 Check model and map are aligned: 0.020 Set scattering table: 0.050 Process input model: 13.810 Find NCS groups from input model: 0.030 Set up NCS constraints: 0.010 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.790 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 22.660 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7704 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.018 3316 Z= 0.103 Angle : 0.488 5.508 4506 Z= 0.265 Chirality : 0.042 0.133 468 Planarity : 0.003 0.023 579 Dihedral : 9.320 59.680 1155 Min Nonbonded Distance : 2.298 Molprobity Statistics. All-atom Clashscore : 6.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.47 % Favored : 95.53 % Rotamer: Outliers : 2.63 % Allowed : 5.56 % Favored : 91.81 % 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: 0.45 (0.44), residues: 403 helix: -3.83 (0.67), residues: 20 sheet: 0.62 (0.43), residues: 133 loop : 0.63 (0.44), residues: 250 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP A 433 HIS 0.001 0.000 HIS H 113 PHE 0.004 0.001 PHE H 27 TYR 0.008 0.001 TYR H 95 ARG 0.001 0.000 ARG H 87 Details of bonding type rmsd hydrogen bonds : bond 0.15611 ( 102) hydrogen bonds : angle 6.95054 ( 237) SS BOND : bond 0.00164 ( 6) SS BOND : angle 0.48717 ( 12) covalent geometry : bond 0.00190 ( 3310) covalent geometry : angle 0.48752 ( 4494) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 806 Ramachandran restraints generated. 403 Oldfield, 0 Emsley, 403 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 806 Ramachandran restraints generated. 403 Oldfield, 0 Emsley, 403 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 91 residues out of total 345 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 82 time to evaluate : 0.322 Fit side-chains revert: symmetry clash REVERT: H 64 VAL cc_start: 0.7737 (m) cc_final: 0.7352 (m) REVERT: L 91 SER cc_start: 0.9076 (t) cc_final: 0.8731 (p) outliers start: 9 outliers final: 3 residues processed: 87 average time/residue: 0.1879 time to fit residues: 19.1162 Evaluate side-chains 62 residues out of total 345 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 59 time to evaluate : 0.386 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 514 LEU Chi-restraints excluded: chain H residue 104 TYR Chi-restraints excluded: chain L residue 98 THR Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 40 random chunks: chunk 33 optimal weight: 10.0000 chunk 30 optimal weight: 5.9990 chunk 16 optimal weight: 0.7980 chunk 10 optimal weight: 3.9990 chunk 20 optimal weight: 0.0000 chunk 31 optimal weight: 5.9990 chunk 12 optimal weight: 0.9990 chunk 19 optimal weight: 0.9980 chunk 23 optimal weight: 2.9990 chunk 36 optimal weight: 3.9990 chunk 11 optimal weight: 0.9990 overall best weight: 0.7588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 471 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3835 r_free = 0.3835 target = 0.143556 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3475 r_free = 0.3475 target = 0.115155 restraints weight = 5068.082| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3516 r_free = 0.3516 target = 0.118284 restraints weight = 3535.974| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.3547 r_free = 0.3547 target = 0.120630 restraints weight = 2764.892| |-----------------------------------------------------------------------------| r_work (final): 0.3538 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7753 moved from start: 0.1510 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.033 3316 Z= 0.108 Angle : 0.481 5.239 4506 Z= 0.249 Chirality : 0.044 0.126 468 Planarity : 0.003 0.023 579 Dihedral : 5.218 50.667 463 Min Nonbonded Distance : 2.546 Molprobity Statistics. All-atom Clashscore : 6.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.72 % Favored : 96.28 % Rotamer: Outliers : 1.75 % Allowed : 11.70 % Favored : 86.55 % 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: 0.39 (0.43), residues: 403 helix: -3.72 (0.74), residues: 19 sheet: 0.67 (0.44), residues: 126 loop : 0.50 (0.42), residues: 258 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A 433 HIS 0.001 0.000 HIS A 336 PHE 0.019 0.001 PHE H 68 TYR 0.016 0.001 TYR H 109 ARG 0.005 0.000 ARG H 67 Details of bonding type rmsd hydrogen bonds : bond 0.03163 ( 102) hydrogen bonds : angle 5.29335 ( 237) SS BOND : bond 0.00115 ( 6) SS BOND : angle 0.45474 ( 12) covalent geometry : bond 0.00244 ( 3310) covalent geometry : angle 0.48150 ( 4494) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 806 Ramachandran restraints generated. 403 Oldfield, 0 Emsley, 403 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 806 Ramachandran restraints generated. 403 Oldfield, 0 Emsley, 403 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 68 residues out of total 345 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 62 time to evaluate : 0.329 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: H 83 MET cc_start: 0.6646 (tpp) cc_final: 0.6357 (tpp) REVERT: L 91 SER cc_start: 0.9232 (t) cc_final: 0.9013 (p) outliers start: 6 outliers final: 3 residues processed: 67 average time/residue: 0.1821 time to fit residues: 14.4814 Evaluate side-chains 59 residues out of total 345 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 56 time to evaluate : 0.330 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 514 LEU Chi-restraints excluded: chain H residue 104 TYR Chi-restraints excluded: chain L residue 98 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 40 random chunks: chunk 11 optimal weight: 8.9990 chunk 27 optimal weight: 10.0000 chunk 8 optimal weight: 5.9990 chunk 36 optimal weight: 6.9990 chunk 18 optimal weight: 4.9990 chunk 17 optimal weight: 0.4980 chunk 29 optimal weight: 3.9990 chunk 34 optimal weight: 0.9980 chunk 32 optimal weight: 5.9990 chunk 5 optimal weight: 4.9990 chunk 38 optimal weight: 4.9990 overall best weight: 3.0986 ------------------------------------------------------------------------------- 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 = 0.3728 r_free = 0.3728 target = 0.136086 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3342 r_free = 0.3342 target = 0.107400 restraints weight = 5165.445| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3381 r_free = 0.3381 target = 0.110210 restraints weight = 3708.783| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 40)----------------| | r_work = 0.3409 r_free = 0.3409 target = 0.112281 restraints weight = 2972.422| |-----------------------------------------------------------------------------| r_work (final): 0.3400 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7907 moved from start: 0.2194 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.044 3316 Z= 0.305 Angle : 0.633 7.486 4506 Z= 0.330 Chirality : 0.048 0.136 468 Planarity : 0.004 0.023 579 Dihedral : 5.781 56.814 463 Min Nonbonded Distance : 2.432 Molprobity Statistics. All-atom Clashscore : 8.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.20 % Favored : 93.80 % Rotamer: Outliers : 2.92 % Allowed : 13.74 % Favored : 83.33 % 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: -0.54 (0.41), residues: 403 helix: -4.03 (0.54), residues: 28 sheet: -0.24 (0.40), residues: 147 loop : 0.22 (0.43), residues: 228 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.002 TRP H 121 HIS 0.003 0.001 HIS H 113 PHE 0.035 0.003 PHE H 68 TYR 0.018 0.002 TYR A 450 ARG 0.003 0.001 ARG A 352 Details of bonding type rmsd hydrogen bonds : bond 0.04103 ( 102) hydrogen bonds : angle 5.81270 ( 237) SS BOND : bond 0.00210 ( 6) SS BOND : angle 0.61281 ( 12) covalent geometry : bond 0.00702 ( 3310) covalent geometry : angle 0.63339 ( 4494) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 806 Ramachandran restraints generated. 403 Oldfield, 0 Emsley, 403 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 806 Ramachandran restraints generated. 403 Oldfield, 0 Emsley, 403 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 62 residues out of total 345 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 52 time to evaluate : 0.360 Fit side-chains REVERT: H 83 MET cc_start: 0.6908 (OUTLIER) cc_final: 0.6585 (tpp) REVERT: H 109 TYR cc_start: 0.8042 (t80) cc_final: 0.7820 (t80) REVERT: L 91 SER cc_start: 0.9312 (t) cc_final: 0.8981 (p) outliers start: 10 outliers final: 8 residues processed: 59 average time/residue: 0.1647 time to fit residues: 11.8033 Evaluate side-chains 59 residues out of total 345 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 50 time to evaluate : 0.332 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 329 VAL Chi-restraints excluded: chain A residue 458 LEU Chi-restraints excluded: chain A residue 496 THR Chi-restraints excluded: chain A residue 514 LEU Chi-restraints excluded: chain H residue 37 VAL Chi-restraints excluded: chain H residue 83 MET Chi-restraints excluded: chain H residue 104 TYR Chi-restraints excluded: chain H residue 119 ASP Chi-restraints excluded: chain L residue 98 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 40 random chunks: chunk 26 optimal weight: 3.9990 chunk 10 optimal weight: 0.9980 chunk 0 optimal weight: 5.9990 chunk 33 optimal weight: 5.9990 chunk 21 optimal weight: 0.9990 chunk 35 optimal weight: 0.5980 chunk 12 optimal weight: 0.9980 chunk 1 optimal weight: 1.9990 chunk 20 optimal weight: 2.9990 chunk 23 optimal weight: 0.0170 chunk 9 optimal weight: 0.9990 overall best weight: 0.7220 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 402 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3792 r_free = 0.3792 target = 0.141271 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3398 r_free = 0.3398 target = 0.111182 restraints weight = 5229.283| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3438 r_free = 0.3438 target = 0.114249 restraints weight = 3688.749| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3463 r_free = 0.3463 target = 0.116139 restraints weight = 2933.601| |-----------------------------------------------------------------------------| r_work (final): 0.3451 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7830 moved from start: 0.2075 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.023 3316 Z= 0.102 Angle : 0.497 5.973 4506 Z= 0.247 Chirality : 0.044 0.126 468 Planarity : 0.003 0.023 579 Dihedral : 5.580 57.163 463 Min Nonbonded Distance : 2.520 Molprobity Statistics. All-atom Clashscore : 6.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.97 % Favored : 96.03 % Rotamer: Outliers : 2.34 % Allowed : 15.79 % Favored : 81.87 % 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 (0.42), residues: 403 helix: -3.75 (0.79), residues: 19 sheet: -0.01 (0.41), residues: 135 loop : 0.34 (0.42), residues: 249 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A 433 HIS 0.001 0.000 HIS L 41 PHE 0.020 0.001 PHE H 68 TYR 0.014 0.001 TYR H 109 ARG 0.002 0.000 ARG H 19 Details of bonding type rmsd hydrogen bonds : bond 0.02917 ( 102) hydrogen bonds : angle 5.18997 ( 237) SS BOND : bond 0.00170 ( 6) SS BOND : angle 0.57050 ( 12) covalent geometry : bond 0.00226 ( 3310) covalent geometry : angle 0.49631 ( 4494) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 806 Ramachandran restraints generated. 403 Oldfield, 0 Emsley, 403 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 806 Ramachandran restraints generated. 403 Oldfield, 0 Emsley, 403 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 66 residues out of total 345 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 58 time to evaluate : 0.332 Fit side-chains revert: symmetry clash REVERT: H 109 TYR cc_start: 0.7910 (t80) cc_final: 0.7610 (t80) REVERT: L 91 SER cc_start: 0.9274 (t) cc_final: 0.8939 (p) outliers start: 8 outliers final: 6 residues processed: 64 average time/residue: 0.1604 time to fit residues: 12.5623 Evaluate side-chains 61 residues out of total 345 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 55 time to evaluate : 0.337 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 329 VAL Chi-restraints excluded: chain A residue 465 ILE Chi-restraints excluded: chain A residue 514 LEU Chi-restraints excluded: chain H residue 68 PHE Chi-restraints excluded: chain H residue 104 TYR Chi-restraints excluded: chain L residue 98 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 40 random chunks: chunk 7 optimal weight: 3.9990 chunk 9 optimal weight: 0.0670 chunk 10 optimal weight: 0.6980 chunk 32 optimal weight: 8.9990 chunk 27 optimal weight: 9.9990 chunk 25 optimal weight: 8.9990 chunk 37 optimal weight: 5.9990 chunk 33 optimal weight: 1.9990 chunk 18 optimal weight: 2.9990 chunk 38 optimal weight: 8.9990 chunk 26 optimal weight: 5.9990 overall best weight: 1.9524 ------------------------------------------------------------------------------- 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 = 0.3754 r_free = 0.3754 target = 0.138041 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3371 r_free = 0.3371 target = 0.109007 restraints weight = 5243.248| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3411 r_free = 0.3411 target = 0.111967 restraints weight = 3675.438| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 42)----------------| | r_work = 0.3440 r_free = 0.3440 target = 0.114107 restraints weight = 2913.549| |-----------------------------------------------------------------------------| r_work (final): 0.3428 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7869 moved from start: 0.2283 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.051 3316 Z= 0.200 Angle : 0.562 8.027 4506 Z= 0.284 Chirality : 0.046 0.145 468 Planarity : 0.003 0.022 579 Dihedral : 5.569 53.490 463 Min Nonbonded Distance : 2.477 Molprobity Statistics. All-atom Clashscore : 8.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.21 % Favored : 94.79 % Rotamer: Outliers : 2.63 % Allowed : 17.25 % Favored : 80.12 % 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 (0.41), residues: 403 helix: -3.50 (0.70), residues: 27 sheet: -0.14 (0.41), residues: 141 loop : 0.26 (0.42), residues: 235 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 433 HIS 0.002 0.001 HIS H 113 PHE 0.025 0.002 PHE H 68 TYR 0.015 0.001 TYR H 95 ARG 0.002 0.000 ARG H 67 Details of bonding type rmsd hydrogen bonds : bond 0.03447 ( 102) hydrogen bonds : angle 5.37668 ( 237) SS BOND : bond 0.00138 ( 6) SS BOND : angle 0.54649 ( 12) covalent geometry : bond 0.00465 ( 3310) covalent geometry : angle 0.56192 ( 4494) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 806 Ramachandran restraints generated. 403 Oldfield, 0 Emsley, 403 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 806 Ramachandran restraints generated. 403 Oldfield, 0 Emsley, 403 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 65 residues out of total 345 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 56 time to evaluate : 0.338 Fit side-chains revert: symmetry clash REVERT: H 109 TYR cc_start: 0.7951 (t80) cc_final: 0.7675 (t80) REVERT: L 91 SER cc_start: 0.9296 (t) cc_final: 0.8949 (p) outliers start: 9 outliers final: 8 residues processed: 62 average time/residue: 0.1560 time to fit residues: 11.7363 Evaluate side-chains 63 residues out of total 345 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 55 time to evaluate : 0.371 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 329 VAL Chi-restraints excluded: chain A residue 465 ILE Chi-restraints excluded: chain A residue 496 THR Chi-restraints excluded: chain A residue 514 LEU Chi-restraints excluded: chain H residue 68 PHE Chi-restraints excluded: chain H residue 104 TYR Chi-restraints excluded: chain H residue 119 ASP Chi-restraints excluded: chain L residue 98 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 40 random chunks: chunk 29 optimal weight: 1.9990 chunk 11 optimal weight: 6.9990 chunk 6 optimal weight: 0.5980 chunk 37 optimal weight: 4.9990 chunk 27 optimal weight: 0.9980 chunk 15 optimal weight: 0.9990 chunk 0 optimal weight: 6.9990 chunk 8 optimal weight: 0.2980 chunk 19 optimal weight: 5.9990 chunk 21 optimal weight: 0.6980 chunk 7 optimal weight: 0.9980 overall best weight: 0.7180 ------------------------------------------------------------------------------- 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 = 0.3795 r_free = 0.3795 target = 0.141228 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3410 r_free = 0.3410 target = 0.111754 restraints weight = 5255.489| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3452 r_free = 0.3452 target = 0.114795 restraints weight = 3654.108| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3483 r_free = 0.3483 target = 0.117057 restraints weight = 2893.493| |-----------------------------------------------------------------------------| r_work (final): 0.3469 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7806 moved from start: 0.2280 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.029 3316 Z= 0.105 Angle : 0.507 6.468 4506 Z= 0.253 Chirality : 0.044 0.126 468 Planarity : 0.003 0.023 579 Dihedral : 5.594 55.611 463 Min Nonbonded Distance : 2.525 Molprobity Statistics. All-atom Clashscore : 7.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.72 % Favored : 96.28 % Rotamer: Outliers : 2.92 % Allowed : 17.84 % Favored : 79.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.21 (0.41), residues: 403 helix: -3.45 (0.71), residues: 27 sheet: -0.07 (0.41), residues: 139 loop : 0.39 (0.42), residues: 237 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 433 HIS 0.001 0.000 HIS L 41 PHE 0.021 0.001 PHE H 68 TYR 0.016 0.001 TYR H 114 ARG 0.002 0.000 ARG H 19 Details of bonding type rmsd hydrogen bonds : bond 0.02931 ( 102) hydrogen bonds : angle 5.16361 ( 237) SS BOND : bond 0.00155 ( 6) SS BOND : angle 0.53804 ( 12) covalent geometry : bond 0.00237 ( 3310) covalent geometry : angle 0.50647 ( 4494) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 806 Ramachandran restraints generated. 403 Oldfield, 0 Emsley, 403 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 806 Ramachandran restraints generated. 403 Oldfield, 0 Emsley, 403 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 73 residues out of total 345 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 63 time to evaluate : 0.356 Fit side-chains revert: symmetry clash REVERT: H 109 TYR cc_start: 0.7714 (t80) cc_final: 0.7476 (t80) REVERT: L 71 ASN cc_start: 0.6654 (m-40) cc_final: 0.5850 (t0) REVERT: L 91 SER cc_start: 0.9281 (t) cc_final: 0.8952 (p) outliers start: 10 outliers final: 7 residues processed: 71 average time/residue: 0.1643 time to fit residues: 14.1483 Evaluate side-chains 69 residues out of total 345 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 62 time to evaluate : 0.362 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 329 VAL Chi-restraints excluded: chain A residue 465 ILE Chi-restraints excluded: chain A residue 514 LEU Chi-restraints excluded: chain H residue 68 PHE Chi-restraints excluded: chain H residue 104 TYR Chi-restraints excluded: chain H residue 114 TYR Chi-restraints excluded: chain L residue 98 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 40 random chunks: chunk 24 optimal weight: 2.9990 chunk 34 optimal weight: 3.9990 chunk 39 optimal weight: 2.9990 chunk 23 optimal weight: 0.9990 chunk 5 optimal weight: 6.9990 chunk 31 optimal weight: 4.9990 chunk 14 optimal weight: 2.9990 chunk 4 optimal weight: 0.8980 chunk 21 optimal weight: 4.9990 chunk 30 optimal weight: 2.9990 chunk 13 optimal weight: 1.9990 overall best weight: 1.9788 ------------------------------------------------------------------------------- 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 = 0.3745 r_free = 0.3745 target = 0.137703 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3367 r_free = 0.3367 target = 0.108902 restraints weight = 5213.520| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3406 r_free = 0.3406 target = 0.111700 restraints weight = 3703.509| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3435 r_free = 0.3435 target = 0.113816 restraints weight = 2956.116| |-----------------------------------------------------------------------------| r_work (final): 0.3421 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7878 moved from start: 0.2479 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.043 3316 Z= 0.204 Angle : 0.579 10.826 4506 Z= 0.292 Chirality : 0.045 0.130 468 Planarity : 0.003 0.024 579 Dihedral : 5.633 53.421 463 Min Nonbonded Distance : 2.492 Molprobity Statistics. All-atom Clashscore : 8.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.71 % Favored : 94.29 % Rotamer: Outliers : 2.92 % Allowed : 17.25 % Favored : 79.82 % 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: -0.52 (0.41), residues: 403 helix: -4.03 (0.54), residues: 28 sheet: -0.17 (0.40), residues: 139 loop : 0.17 (0.41), residues: 236 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A 433 HIS 0.002 0.001 HIS H 113 PHE 0.027 0.002 PHE H 68 TYR 0.017 0.002 TYR H 114 ARG 0.002 0.000 ARG H 30 Details of bonding type rmsd hydrogen bonds : bond 0.03540 ( 102) hydrogen bonds : angle 5.46381 ( 237) SS BOND : bond 0.00143 ( 6) SS BOND : angle 0.52477 ( 12) covalent geometry : bond 0.00468 ( 3310) covalent geometry : angle 0.57961 ( 4494) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 806 Ramachandran restraints generated. 403 Oldfield, 0 Emsley, 403 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 806 Ramachandran restraints generated. 403 Oldfield, 0 Emsley, 403 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 68 residues out of total 345 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 58 time to evaluate : 0.367 Fit side-chains revert: symmetry clash REVERT: L 71 ASN cc_start: 0.6907 (m-40) cc_final: 0.6047 (t0) REVERT: L 91 SER cc_start: 0.9292 (t) cc_final: 0.8958 (p) outliers start: 10 outliers final: 10 residues processed: 64 average time/residue: 0.1710 time to fit residues: 13.4339 Evaluate side-chains 65 residues out of total 345 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 55 time to evaluate : 0.351 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 329 VAL Chi-restraints excluded: chain A residue 465 ILE Chi-restraints excluded: chain A residue 496 THR Chi-restraints excluded: chain A residue 514 LEU Chi-restraints excluded: chain H residue 68 PHE Chi-restraints excluded: chain H residue 104 TYR Chi-restraints excluded: chain H residue 114 TYR Chi-restraints excluded: chain H residue 119 ASP Chi-restraints excluded: chain L residue 98 THR Chi-restraints excluded: chain L residue 106 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 40 random chunks: chunk 25 optimal weight: 0.8980 chunk 36 optimal weight: 6.9990 chunk 14 optimal weight: 0.9990 chunk 20 optimal weight: 10.0000 chunk 28 optimal weight: 1.9990 chunk 9 optimal weight: 2.9990 chunk 38 optimal weight: 3.9990 chunk 5 optimal weight: 0.8980 chunk 24 optimal weight: 5.9990 chunk 37 optimal weight: 5.9990 chunk 19 optimal weight: 5.9990 overall best weight: 1.5586 ------------------------------------------------------------------------------- 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 = 0.3756 r_free = 0.3756 target = 0.138332 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3368 r_free = 0.3368 target = 0.108852 restraints weight = 5112.193| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3409 r_free = 0.3409 target = 0.111831 restraints weight = 3617.870| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3440 r_free = 0.3440 target = 0.114054 restraints weight = 2871.160| |-----------------------------------------------------------------------------| r_work (final): 0.3430 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7866 moved from start: 0.2559 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 3316 Z= 0.169 Angle : 0.561 10.040 4506 Z= 0.283 Chirality : 0.044 0.131 468 Planarity : 0.003 0.024 579 Dihedral : 5.641 52.935 463 Min Nonbonded Distance : 2.503 Molprobity Statistics. All-atom Clashscore : 7.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.71 % Favored : 95.29 % Rotamer: Outliers : 3.51 % Allowed : 16.37 % Favored : 80.12 % 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: -0.51 (0.40), residues: 403 helix: -3.85 (0.62), residues: 27 sheet: -0.10 (0.41), residues: 128 loop : 0.07 (0.40), residues: 248 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A 433 HIS 0.001 0.001 HIS A 442 PHE 0.026 0.002 PHE H 68 TYR 0.016 0.001 TYR H 114 ARG 0.002 0.000 ARG H 30 Details of bonding type rmsd hydrogen bonds : bond 0.03326 ( 102) hydrogen bonds : angle 5.41961 ( 237) SS BOND : bond 0.00115 ( 6) SS BOND : angle 0.53030 ( 12) covalent geometry : bond 0.00389 ( 3310) covalent geometry : angle 0.56141 ( 4494) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 806 Ramachandran restraints generated. 403 Oldfield, 0 Emsley, 403 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 806 Ramachandran restraints generated. 403 Oldfield, 0 Emsley, 403 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 70 residues out of total 345 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 58 time to evaluate : 0.371 Fit side-chains revert: symmetry clash REVERT: L 71 ASN cc_start: 0.6881 (m-40) cc_final: 0.6001 (t0) REVERT: L 84 ASP cc_start: 0.7703 (t0) cc_final: 0.7502 (t0) REVERT: L 91 SER cc_start: 0.9276 (t) cc_final: 0.8952 (p) outliers start: 12 outliers final: 9 residues processed: 67 average time/residue: 0.1553 time to fit residues: 12.7616 Evaluate side-chains 65 residues out of total 345 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 56 time to evaluate : 0.368 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 329 VAL Chi-restraints excluded: chain A residue 465 ILE Chi-restraints excluded: chain A residue 496 THR Chi-restraints excluded: chain A residue 514 LEU Chi-restraints excluded: chain H residue 68 PHE Chi-restraints excluded: chain H residue 104 TYR Chi-restraints excluded: chain H residue 114 TYR Chi-restraints excluded: chain H residue 119 ASP Chi-restraints excluded: chain L residue 98 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 40 random chunks: chunk 20 optimal weight: 0.0370 chunk 33 optimal weight: 10.0000 chunk 5 optimal weight: 3.9990 chunk 14 optimal weight: 0.8980 chunk 25 optimal weight: 0.9980 chunk 13 optimal weight: 0.5980 chunk 8 optimal weight: 0.9980 chunk 3 optimal weight: 4.9990 chunk 36 optimal weight: 4.9990 chunk 12 optimal weight: 0.9980 chunk 24 optimal weight: 0.9980 overall best weight: 0.7058 ------------------------------------------------------------------------------- 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 = 0.3787 r_free = 0.3787 target = 0.140777 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3405 r_free = 0.3405 target = 0.111410 restraints weight = 5215.811| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3446 r_free = 0.3446 target = 0.114494 restraints weight = 3605.214| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3478 r_free = 0.3478 target = 0.116786 restraints weight = 2830.969| |-----------------------------------------------------------------------------| r_work (final): 0.3468 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7810 moved from start: 0.2575 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.031 3316 Z= 0.108 Angle : 0.534 9.410 4506 Z= 0.268 Chirality : 0.043 0.138 468 Planarity : 0.003 0.024 579 Dihedral : 5.569 54.241 463 Min Nonbonded Distance : 2.530 Molprobity Statistics. All-atom Clashscore : 6.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.47 % Favored : 95.53 % Rotamer: Outliers : 2.63 % Allowed : 18.13 % Favored : 79.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.37 (0.40), residues: 403 helix: -3.80 (0.65), residues: 27 sheet: 0.18 (0.43), residues: 113 loop : 0.05 (0.39), residues: 263 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 433 HIS 0.001 0.000 HIS A 442 PHE 0.022 0.001 PHE H 68 TYR 0.021 0.001 TYR H 109 ARG 0.002 0.000 ARG H 30 Details of bonding type rmsd hydrogen bonds : bond 0.02959 ( 102) hydrogen bonds : angle 5.21301 ( 237) SS BOND : bond 0.00135 ( 6) SS BOND : angle 0.49736 ( 12) covalent geometry : bond 0.00244 ( 3310) covalent geometry : angle 0.53423 ( 4494) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 806 Ramachandran restraints generated. 403 Oldfield, 0 Emsley, 403 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 806 Ramachandran restraints generated. 403 Oldfield, 0 Emsley, 403 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 70 residues out of total 345 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 61 time to evaluate : 0.369 Fit side-chains revert: symmetry clash REVERT: L 71 ASN cc_start: 0.6641 (m-40) cc_final: 0.5861 (t0) REVERT: L 91 SER cc_start: 0.9272 (t) cc_final: 0.8949 (p) outliers start: 9 outliers final: 9 residues processed: 67 average time/residue: 0.1565 time to fit residues: 12.9035 Evaluate side-chains 67 residues out of total 345 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 58 time to evaluate : 0.330 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 329 VAL Chi-restraints excluded: chain A residue 368 PHE Chi-restraints excluded: chain A residue 465 ILE Chi-restraints excluded: chain A residue 514 LEU Chi-restraints excluded: chain H residue 68 PHE Chi-restraints excluded: chain H residue 104 TYR Chi-restraints excluded: chain H residue 114 TYR Chi-restraints excluded: chain L residue 98 THR Chi-restraints excluded: chain L residue 106 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 40 random chunks: chunk 17 optimal weight: 2.9990 chunk 34 optimal weight: 0.9990 chunk 9 optimal weight: 3.9990 chunk 18 optimal weight: 0.7980 chunk 19 optimal weight: 4.9990 chunk 28 optimal weight: 0.9980 chunk 32 optimal weight: 0.9990 chunk 4 optimal weight: 0.8980 chunk 39 optimal weight: 2.9990 chunk 27 optimal weight: 7.9990 chunk 30 optimal weight: 0.9990 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 = 0.3785 r_free = 0.3785 target = 0.140528 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3399 r_free = 0.3399 target = 0.111000 restraints weight = 5162.767| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3443 r_free = 0.3443 target = 0.114192 restraints weight = 3566.876| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.3475 r_free = 0.3475 target = 0.116474 restraints weight = 2794.507| |-----------------------------------------------------------------------------| r_work (final): 0.3464 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7814 moved from start: 0.2630 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 3316 Z= 0.124 Angle : 0.545 9.298 4506 Z= 0.275 Chirality : 0.044 0.136 468 Planarity : 0.003 0.026 579 Dihedral : 5.540 54.025 463 Min Nonbonded Distance : 2.449 Molprobity Statistics. All-atom Clashscore : 7.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.22 % Favored : 95.78 % Rotamer: Outliers : 2.92 % Allowed : 17.84 % Favored : 79.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.34 (0.41), residues: 403 helix: -3.88 (0.63), residues: 27 sheet: 0.08 (0.42), residues: 124 loop : 0.15 (0.40), residues: 252 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP H 47 HIS 0.001 0.000 HIS A 442 PHE 0.021 0.001 PHE H 68 TYR 0.021 0.001 TYR H 109 ARG 0.002 0.000 ARG H 30 Details of bonding type rmsd hydrogen bonds : bond 0.03083 ( 102) hydrogen bonds : angle 5.18898 ( 237) SS BOND : bond 0.00122 ( 6) SS BOND : angle 0.47714 ( 12) covalent geometry : bond 0.00283 ( 3310) covalent geometry : angle 0.54550 ( 4494) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 806 Ramachandran restraints generated. 403 Oldfield, 0 Emsley, 403 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 806 Ramachandran restraints generated. 403 Oldfield, 0 Emsley, 403 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 69 residues out of total 345 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 59 time to evaluate : 0.378 Fit side-chains revert: symmetry clash REVERT: L 71 ASN cc_start: 0.6601 (m-40) cc_final: 0.5828 (t0) REVERT: L 91 SER cc_start: 0.9281 (t) cc_final: 0.8957 (p) outliers start: 10 outliers final: 9 residues processed: 66 average time/residue: 0.1599 time to fit residues: 13.1292 Evaluate side-chains 68 residues out of total 345 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 59 time to evaluate : 0.386 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 329 VAL Chi-restraints excluded: chain A residue 368 PHE Chi-restraints excluded: chain A residue 465 ILE Chi-restraints excluded: chain A residue 514 LEU Chi-restraints excluded: chain H residue 68 PHE Chi-restraints excluded: chain H residue 104 TYR Chi-restraints excluded: chain H residue 114 TYR Chi-restraints excluded: chain L residue 98 THR Chi-restraints excluded: chain L residue 106 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 40 random chunks: chunk 12 optimal weight: 0.2980 chunk 25 optimal weight: 8.9990 chunk 35 optimal weight: 2.9990 chunk 23 optimal weight: 0.8980 chunk 36 optimal weight: 2.9990 chunk 39 optimal weight: 1.9990 chunk 1 optimal weight: 3.9990 chunk 13 optimal weight: 0.3980 chunk 29 optimal weight: 1.9990 chunk 10 optimal weight: 4.9990 chunk 27 optimal weight: 4.9990 overall best weight: 1.1184 ------------------------------------------------------------------------------- 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 = 0.3783 r_free = 0.3783 target = 0.140458 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3399 r_free = 0.3399 target = 0.110862 restraints weight = 5171.932| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3443 r_free = 0.3443 target = 0.114106 restraints weight = 3579.281| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3475 r_free = 0.3475 target = 0.116403 restraints weight = 2798.788| |-----------------------------------------------------------------------------| r_work (final): 0.3464 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7838 moved from start: 0.2693 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 3316 Z= 0.136 Angle : 0.548 9.229 4506 Z= 0.279 Chirality : 0.044 0.135 468 Planarity : 0.003 0.028 579 Dihedral : 5.589 55.568 463 Min Nonbonded Distance : 2.441 Molprobity Statistics. All-atom Clashscore : 7.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.22 % Favored : 95.78 % Rotamer: Outliers : 2.92 % Allowed : 17.54 % Favored : 79.53 % 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: -0.34 (0.40), residues: 403 helix: -3.96 (0.61), residues: 27 sheet: 0.12 (0.42), residues: 123 loop : 0.15 (0.40), residues: 253 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP H 47 HIS 0.002 0.000 HIS H 113 PHE 0.022 0.001 PHE H 68 TYR 0.021 0.001 TYR H 109 ARG 0.002 0.000 ARG H 30 Details of bonding type rmsd hydrogen bonds : bond 0.03160 ( 102) hydrogen bonds : angle 5.19929 ( 237) SS BOND : bond 0.00116 ( 6) SS BOND : angle 0.47841 ( 12) covalent geometry : bond 0.00310 ( 3310) covalent geometry : angle 0.54850 ( 4494) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1662.01 seconds wall clock time: 29 minutes 51.93 seconds (1791.93 seconds total)