Starting phenix.real_space_refine on Tue Jan 14 01:18:54 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9b57_44202/01_2025/9b57_44202.cif Found real_map, /net/cci-nas-00/data/ceres_data/9b57_44202/01_2025/9b57_44202.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.37 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9b57_44202/01_2025/9b57_44202.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9b57_44202/01_2025/9b57_44202.map" model { file = "/net/cci-nas-00/data/ceres_data/9b57_44202/01_2025/9b57_44202.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9b57_44202/01_2025/9b57_44202.cif" } resolution = 3.37 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= 0.039 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 14 5.16 5 C 3110 2.51 5 N 824 2.21 5 O 923 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/modules/chem_data/mon_lib" Total number of atoms: 4871 Number of models: 1 Model: "" Number of chains: 4 Chain: "A" Number of atoms: 1162 Number of conformers: 1 Conformer: "" Number of residues, atoms: 147, 1162 Classifications: {'peptide': 147} Link IDs: {'PCIS': 1, 'PTRANS': 14, 'TRANS': 131} Chain: "B" Number of atoms: 596 Number of conformers: 1 Conformer: "" Number of residues, atoms: 75, 596 Classifications: {'peptide': 75} Link IDs: {'PTRANS': 2, 'TRANS': 72} Chain: "C" Number of atoms: 3107 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 377, 3099 Classifications: {'peptide': 377} Link IDs: {'PTRANS': 14, 'TRANS': 362} Conformer: "B" Number of residues, atoms: 377, 3099 Classifications: {'peptide': 377} Link IDs: {'PTRANS': 14, 'TRANS': 362} bond proxies already assigned to first conformer: 3161 Chain: "B" Number of atoms: 6 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 6 Unusual residues: {'A1AIV': 1} Classifications: {'undetermined': 1} Time building chain proxies: 4.63, per 1000 atoms: 0.95 Number of scatterers: 4871 At special positions: 0 Unit cell: (63.84, 82.992, 103.208, 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 14 16.00 O 923 8.00 N 824 7.00 C 3110 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=2, symmetry=0 Number of additional bonds: simple=2, symmetry=0 Coordination: Other bonds: Time building additional restraints: 1.16 Conformation dependent library (CDL) restraints added in 838.3 milliseconds 1188 Ramachandran restraints generated. 594 Oldfield, 0 Emsley, 594 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1140 Finding SS restraints... Secondary structure from input PDB file: 28 helices and 6 sheets defined 48.4% alpha, 11.9% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.57 Creating SS restraints... Processing helix chain 'A' and resid 3 through 16 Processing helix chain 'A' and resid 98 through 110 removed outlier: 3.827A pdb=" N VAL A 102 " --> pdb=" O THR A 98 " (cutoff:3.500A) Processing helix chain 'A' and resid 120 through 130 Processing helix chain 'A' and resid 130 through 146 Processing helix chain 'B' and resid 22 through 35 Processing helix chain 'B' and resid 37 through 41 Processing helix chain 'B' and resid 56 through 60 Processing helix chain 'C' and resid 293 through 306 Processing helix chain 'C' and resid 325 through 335 Processing helix chain 'C' and resid 338 through 343 Processing helix chain 'C' and resid 357 through 374 Processing helix chain 'C' and resid 375 through 379 Processing helix chain 'C' and resid 395 through 400 removed outlier: 3.547A pdb=" N SER C 398 " --> pdb=" O PRO C 395 " (cutoff:3.500A) Processing helix chain 'C' and resid 402 through 420 removed outlier: 4.472A pdb=" N TYR C 406 " --> pdb=" O ASP C 402 " (cutoff:3.500A) Processing helix chain 'C' and resid 429 through 437 removed outlier: 3.610A pdb=" N TYR C 433 " --> pdb=" O VAL C 429 " (cutoff:3.500A) Processing helix chain 'C' and resid 442 through 444 No H-bonds generated for 'chain 'C' and resid 442 through 444' Processing helix chain 'C' and resid 445 through 450 removed outlier: 3.816A pdb=" N VAL C 449 " --> pdb=" O ASP C 445 " (cutoff:3.500A) Processing helix chain 'C' and resid 450 through 463 Processing helix chain 'C' and resid 491 through 495 removed outlier: 3.937A pdb=" N ASN C 494 " --> pdb=" O ASN C 491 " (cutoff:3.500A) Processing helix chain 'C' and resid 501 through 515 Processing helix chain 'C' and resid 518 through 533 removed outlier: 4.315A pdb=" N LEU C 532 " --> pdb=" O GLY C 528 " (cutoff:3.500A) Processing helix chain 'C' and resid 534 through 539 removed outlier: 3.585A pdb=" N LEU C 538 " --> pdb=" O PRO C 534 " (cutoff:3.500A) Processing helix chain 'C' and resid 544 through 552 Processing helix chain 'C' and resid 558 through 564 Processing helix chain 'C' and resid 574 through 586 removed outlier: 3.893A pdb=" N PHE C 580 " --> pdb=" O ILE C 576 " (cutoff:3.500A) Processing helix chain 'C' and resid 588 through 600 Processing helix chain 'C' and resid 638 through 640 No H-bonds generated for 'chain 'C' and resid 638 through 640' Processing helix chain 'C' and resid 650 through 662 removed outlier: 3.569A pdb=" N ILE C 662 " --> pdb=" O LEU C 658 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 22 through 25 Processing sheet with id=AA2, first strand: chain 'B' and resid 12 through 16 removed outlier: 3.963A pdb=" N SER B 65 " --> pdb=" O GLN B 2 " (cutoff:3.500A) removed outlier: 3.966A pdb=" N ARG B 42 " --> pdb=" O VAL B 70 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'C' and resid 313 through 321 removed outlier: 3.707A pdb=" N VAL C 321 " --> pdb=" O ARG C 349 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'C' and resid 381 through 383 Processing sheet with id=AA5, first strand: chain 'C' and resid 475 through 479 removed outlier: 3.675A pdb=" N GLU C 482 " --> pdb=" O ARG C 479 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'C' and resid 565 through 568 223 hydrogen bonds defined for protein. 623 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: 1.39 Time building geometry restraints manager: 1.34 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.13 - 1.27: 820 1.27 - 1.41: 1241 1.41 - 1.55: 2898 1.55 - 1.69: 0 1.69 - 1.83: 24 Bond restraints: 4983 Sorted by residual: bond pdb=" C04 A1AIV B 101 " pdb=" C05 A1AIV B 101 " ideal model delta sigma weight residual 1.453 1.526 -0.073 2.00e-02 2.50e+03 1.35e+01 bond pdb=" N MET B 1 " pdb=" CA MET B 1 " ideal model delta sigma weight residual 1.458 1.491 -0.033 1.90e-02 2.77e+03 2.93e+00 bond pdb=" N MET A 1 " pdb=" CA MET A 1 " ideal model delta sigma weight residual 1.458 1.490 -0.032 1.90e-02 2.77e+03 2.85e+00 bond pdb=" C05 A1AIV B 101 " pdb=" N06 A1AIV B 101 " ideal model delta sigma weight residual 1.151 1.133 0.018 2.00e-02 2.50e+03 8.36e-01 bond pdb=" CG LEU C 595 " pdb=" CD2 LEU C 595 " ideal model delta sigma weight residual 1.521 1.499 0.022 3.30e-02 9.18e+02 4.35e-01 ... (remaining 4978 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.05: 6513 1.05 - 2.10: 185 2.10 - 3.15: 24 3.15 - 4.20: 24 4.20 - 5.26: 1 Bond angle restraints: 6747 Sorted by residual: angle pdb=" C03 A1AIV B 101 " pdb=" C02 A1AIV B 101 " pdb=" N01 A1AIV B 101 " ideal model delta sigma weight residual 111.06 105.80 5.26 3.00e+00 1.11e-01 3.07e+00 angle pdb=" N LEU C 424 " pdb=" CA LEU C 424 " pdb=" C LEU C 424 " ideal model delta sigma weight residual 110.35 108.12 2.23 1.38e+00 5.25e-01 2.62e+00 angle pdb=" CA CYS C 639 " pdb=" CB CYS C 639 " pdb=" SG CYS C 639 " ideal model delta sigma weight residual 114.40 117.45 -3.05 2.30e+00 1.89e-01 1.76e+00 angle pdb=" N VAL C 515 " pdb=" CA VAL C 515 " pdb=" C VAL C 515 " ideal model delta sigma weight residual 109.34 112.04 -2.70 2.08e+00 2.31e-01 1.68e+00 angle pdb=" CA GLU C 586 " pdb=" CB GLU C 586 " pdb=" CG GLU C 586 " ideal model delta sigma weight residual 114.10 116.34 -2.24 2.00e+00 2.50e-01 1.25e+00 ... (remaining 6742 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 13.29: 2740 13.29 - 26.59: 223 26.59 - 39.88: 44 39.88 - 53.17: 9 53.17 - 66.46: 2 Dihedral angle restraints: 3018 sinusoidal: 1254 harmonic: 1764 Sorted by residual: dihedral pdb=" CA TYR C 423 " pdb=" C TYR C 423 " pdb=" N LEU C 424 " pdb=" CA LEU C 424 " ideal model delta harmonic sigma weight residual 180.00 162.48 17.52 0 5.00e+00 4.00e-02 1.23e+01 dihedral pdb=" CA VAL C 515 " pdb=" C VAL C 515 " pdb=" N THR C 516 " pdb=" CA THR C 516 " ideal model delta harmonic sigma weight residual -180.00 -163.88 -16.12 0 5.00e+00 4.00e-02 1.04e+01 dihedral pdb=" CA ASP C 357 " pdb=" CB ASP C 357 " pdb=" CG ASP C 357 " pdb=" OD1 ASP C 357 " ideal model delta sinusoidal sigma weight residual -30.00 -81.99 51.99 1 2.00e+01 2.50e-03 9.22e+00 ... (remaining 3015 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.027: 443 0.027 - 0.054: 192 0.054 - 0.081: 59 0.081 - 0.109: 25 0.109 - 0.136: 18 Chirality restraints: 737 Sorted by residual: chirality pdb=" CA ILE C 645 " pdb=" N ILE C 645 " pdb=" C ILE C 645 " pdb=" CB ILE C 645 " both_signs ideal model delta sigma weight residual False 2.43 2.57 -0.14 2.00e-01 2.50e+01 4.61e-01 chirality pdb=" CA ILE C 533 " pdb=" N ILE C 533 " pdb=" C ILE C 533 " pdb=" CB ILE C 533 " both_signs ideal model delta sigma weight residual False 2.43 2.57 -0.13 2.00e-01 2.50e+01 4.33e-01 chirality pdb=" CA VAL A 49 " pdb=" N VAL A 49 " pdb=" C VAL A 49 " pdb=" CB VAL A 49 " both_signs ideal model delta sigma weight residual False 2.44 2.57 -0.13 2.00e-01 2.50e+01 4.03e-01 ... (remaining 734 not shown) Planarity restraints: 873 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C LEU C 430 " 0.020 5.00e-02 4.00e+02 3.04e-02 1.48e+00 pdb=" N PRO C 431 " -0.053 5.00e-02 4.00e+02 pdb=" CA PRO C 431 " 0.015 5.00e-02 4.00e+02 pdb=" CD PRO C 431 " 0.017 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ASN A 114 " 0.018 5.00e-02 4.00e+02 2.78e-02 1.24e+00 pdb=" N PRO A 115 " -0.048 5.00e-02 4.00e+02 pdb=" CA PRO A 115 " 0.014 5.00e-02 4.00e+02 pdb=" CD PRO A 115 " 0.016 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C SER A 94 " -0.017 5.00e-02 4.00e+02 2.63e-02 1.10e+00 pdb=" N PRO A 95 " 0.045 5.00e-02 4.00e+02 pdb=" CA PRO A 95 " -0.013 5.00e-02 4.00e+02 pdb=" CD PRO A 95 " -0.015 5.00e-02 4.00e+02 ... (remaining 870 not shown) Histogram of nonbonded interaction distances: 1.83 - 2.44: 16 2.44 - 3.06: 3199 3.06 - 3.67: 6746 3.67 - 4.29: 10189 4.29 - 4.90: 17722 Nonbonded interactions: 37872 Sorted by model distance: nonbonded pdb=" SG CYS C 639 " pdb=" C03 A1AIV B 101 " model vdw 1.831 3.800 nonbonded pdb=" OE1 GLN B 2 " pdb=" OG1 THR B 14 " model vdw 2.288 3.040 nonbonded pdb=" OD1 ASN C 478 " pdb=" OG SER C 483 " model vdw 2.313 3.040 nonbonded pdb=" OG SER C 608 " pdb=" OD2 ASP C 612 " model vdw 2.324 3.040 nonbonded pdb=" OE2 GLU A 9 " pdb=" OH TYR A 60 " model vdw 2.344 3.040 ... (remaining 37867 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=0.37 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.720 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.000 Extract box with map and model: 0.200 Check model and map are aligned: 0.040 Set scattering table: 0.050 Process input model: 17.130 Find NCS groups from input model: 0.050 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.710 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 21.930 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7752 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 : 0.003 0.073 4983 Z= 0.176 Angle : 0.471 5.255 6747 Z= 0.232 Chirality : 0.039 0.136 737 Planarity : 0.003 0.030 873 Dihedral : 10.222 66.463 1878 Min Nonbonded Distance : 1.831 Molprobity Statistics. All-atom Clashscore : 2.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.38 % Favored : 95.62 % Rotamer: Outliers : 1.29 % Allowed : 6.08 % Favored : 92.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.23 % 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: 1.13 (0.37), residues: 594 helix: 1.70 (0.34), residues: 250 sheet: 0.68 (0.61), residues: 82 loop : -0.09 (0.42), residues: 262 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP C 581 HIS 0.001 0.000 HIS A 75 PHE 0.009 0.001 PHE C 522 TYR 0.007 0.001 TYR C 367 ARG 0.002 0.000 ARG C 422 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1188 Ramachandran restraints generated. 594 Oldfield, 0 Emsley, 594 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1188 Ramachandran restraints generated. 594 Oldfield, 0 Emsley, 594 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 101 residues out of total 541 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 94 time to evaluate : 0.564 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 9 GLU cc_start: 0.7849 (mt-10) cc_final: 0.7525 (mt-10) REVERT: A 83 SER cc_start: 0.8825 (m) cc_final: 0.8602 (t) REVERT: B 42 ARG cc_start: 0.6175 (ttt90) cc_final: 0.5960 (ttt90) REVERT: C 613 MET cc_start: 0.8614 (ttt) cc_final: 0.8319 (ttt) outliers start: 7 outliers final: 5 residues processed: 98 average time/residue: 0.2356 time to fit residues: 27.7281 Evaluate side-chains 61 residues out of total 541 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 56 time to evaluate : 0.590 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 73 ILE Chi-restraints excluded: chain C residue 387 ASP Chi-restraints excluded: chain C residue 463 ASN Chi-restraints excluded: chain C residue 487 ASP Chi-restraints excluded: chain C residue 570 TYR Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 58 random chunks: chunk 48 optimal weight: 0.9990 chunk 43 optimal weight: 1.9990 chunk 24 optimal weight: 0.8980 chunk 15 optimal weight: 3.9990 chunk 29 optimal weight: 0.8980 chunk 23 optimal weight: 1.9990 chunk 45 optimal weight: 0.6980 chunk 17 optimal weight: 1.9990 chunk 27 optimal weight: 0.8980 chunk 33 optimal weight: 0.5980 chunk 52 optimal weight: 0.8980 overall best weight: 0.7980 ------------------------------------------------------------------------------- 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 = 0.3843 r_free = 0.3843 target = 0.135526 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3201 r_free = 0.3201 target = 0.087623 restraints weight = 12760.791| |-----------------------------------------------------------------------------| r_work (start): 0.3175 rms_B_bonded: 4.81 r_work (final): 0.3175 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3173 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3173 r_free = 0.3173 target_work(ls_wunit_k1) = 0.088 | | occupancies: max = 1.00 min = 0.37 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3173 r_free = 0.3173 target_work(ls_wunit_k1) = 0.088 | | occupancies: max = 1.00 min = 0.41 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3173 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7698 moved from start: 0.1640 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.042 4983 Z= 0.310 Angle : 0.570 6.641 6747 Z= 0.291 Chirality : 0.043 0.164 737 Planarity : 0.004 0.034 873 Dihedral : 4.968 41.088 670 Min Nonbonded Distance : 2.583 Molprobity Statistics. All-atom Clashscore : 6.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.72 % Favored : 95.28 % Rotamer: Outliers : 2.39 % Allowed : 10.13 % Favored : 87.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.23 % 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: 0.92 (0.37), residues: 594 helix: 1.58 (0.34), residues: 259 sheet: 0.46 (0.61), residues: 83 loop : -0.30 (0.42), residues: 252 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP C 581 HIS 0.002 0.000 HIS A 55 PHE 0.019 0.002 PHE C 480 TYR 0.012 0.002 TYR C 419 ARG 0.007 0.001 ARG A 139 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1188 Ramachandran restraints generated. 594 Oldfield, 0 Emsley, 594 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1188 Ramachandran restraints generated. 594 Oldfield, 0 Emsley, 594 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 76 residues out of total 541 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 63 time to evaluate : 0.572 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 72 ARG cc_start: 0.7729 (mtp85) cc_final: 0.7396 (ttm-80) REVERT: A 83 SER cc_start: 0.8897 (m) cc_final: 0.8602 (t) REVERT: A 92 GLN cc_start: 0.7422 (mt0) cc_final: 0.6711 (mt0) REVERT: A 114 ASN cc_start: 0.6956 (t0) cc_final: 0.6635 (t0) REVERT: A 140 GLU cc_start: 0.9112 (mm-30) cc_final: 0.8886 (mm-30) REVERT: A 143 ARG cc_start: 0.8368 (tpm170) cc_final: 0.8072 (tpm170) REVERT: C 587 TRP cc_start: 0.8452 (OUTLIER) cc_final: 0.7995 (m-10) REVERT: C 613 MET cc_start: 0.8556 (ttt) cc_final: 0.8268 (ttt) outliers start: 13 outliers final: 10 residues processed: 73 average time/residue: 0.2327 time to fit residues: 20.8350 Evaluate side-chains 68 residues out of total 541 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 57 time to evaluate : 0.564 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 10 LEU Chi-restraints excluded: chain A residue 43 SER Chi-restraints excluded: chain A residue 73 ILE Chi-restraints excluded: chain A residue 98 THR Chi-restraints excluded: chain B residue 14 THR Chi-restraints excluded: chain C residue 317 LEU Chi-restraints excluded: chain C residue 389 TYR Chi-restraints excluded: chain C residue 516 THR Chi-restraints excluded: chain C residue 570 TYR Chi-restraints excluded: chain C residue 584 LEU Chi-restraints excluded: chain C residue 587 TRP Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 58 random chunks: chunk 44 optimal weight: 0.9980 chunk 38 optimal weight: 0.0270 chunk 0 optimal weight: 0.9980 chunk 53 optimal weight: 1.9990 chunk 21 optimal weight: 0.6980 chunk 5 optimal weight: 0.9990 chunk 49 optimal weight: 0.5980 chunk 24 optimal weight: 0.7980 chunk 34 optimal weight: 0.6980 chunk 57 optimal weight: 0.5980 chunk 54 optimal weight: 0.0570 overall best weight: 0.3956 ------------------------------------------------------------------------------- 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 = 0.3870 r_free = 0.3870 target = 0.137627 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3254 r_free = 0.3254 target = 0.091277 restraints weight = 10350.653| |-----------------------------------------------------------------------------| r_work (start): 0.3224 rms_B_bonded: 4.31 r_work: 0.3035 rms_B_bonded: 4.85 restraints_weight: 0.5000 r_work (final): 0.3035 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3042 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3042 r_free = 0.3042 target_work(ls_wunit_k1) = 0.078 | | occupancies: max = 1.00 min = 0.41 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3042 r_free = 0.3042 target_work(ls_wunit_k1) = 0.078 | | occupancies: max = 1.00 min = 0.42 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3042 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7865 moved from start: 0.1860 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 4983 Z= 0.188 Angle : 0.523 7.075 6747 Z= 0.266 Chirality : 0.042 0.248 737 Planarity : 0.004 0.064 873 Dihedral : 4.432 38.391 664 Min Nonbonded Distance : 2.607 Molprobity Statistics. All-atom Clashscore : 7.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.88 % Favored : 96.12 % Rotamer: Outliers : 2.03 % Allowed : 12.15 % Favored : 85.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.23 % 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: 1.06 (0.37), residues: 594 helix: 1.73 (0.34), residues: 259 sheet: 0.70 (0.61), residues: 81 loop : -0.32 (0.42), residues: 254 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP C 581 HIS 0.002 0.000 HIS C 293 PHE 0.011 0.001 PHE C 480 TYR 0.022 0.001 TYR A 145 ARG 0.004 0.000 ARG A 139 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1188 Ramachandran restraints generated. 594 Oldfield, 0 Emsley, 594 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1188 Ramachandran restraints generated. 594 Oldfield, 0 Emsley, 594 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 72 residues out of total 541 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 61 time to evaluate : 0.529 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 83 SER cc_start: 0.9066 (m) cc_final: 0.8708 (t) REVERT: A 92 GLN cc_start: 0.7389 (mt0) cc_final: 0.6866 (mt0) REVERT: A 114 ASN cc_start: 0.7103 (t0) cc_final: 0.6593 (t0) REVERT: B 43 LEU cc_start: 0.8129 (tt) cc_final: 0.7791 (mm) REVERT: C 613 MET cc_start: 0.8797 (ttt) cc_final: 0.8573 (ttt) outliers start: 11 outliers final: 8 residues processed: 69 average time/residue: 0.2366 time to fit residues: 20.2388 Evaluate side-chains 64 residues out of total 541 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 56 time to evaluate : 0.592 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 10 LEU Chi-restraints excluded: chain A residue 43 SER Chi-restraints excluded: chain A residue 73 ILE Chi-restraints excluded: chain B residue 14 THR Chi-restraints excluded: chain B residue 32 ASP Chi-restraints excluded: chain C residue 389 TYR Chi-restraints excluded: chain C residue 413 VAL Chi-restraints excluded: chain C residue 570 TYR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 58 random chunks: chunk 12 optimal weight: 0.9980 chunk 4 optimal weight: 0.6980 chunk 15 optimal weight: 8.9990 chunk 35 optimal weight: 0.6980 chunk 52 optimal weight: 0.9990 chunk 51 optimal weight: 0.3980 chunk 44 optimal weight: 0.9980 chunk 45 optimal weight: 0.2980 chunk 27 optimal weight: 0.0980 chunk 8 optimal weight: 0.0870 chunk 19 optimal weight: 4.9990 overall best weight: 0.3158 ------------------------------------------------------------------------------- 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 = 0.3953 r_free = 0.3953 target = 0.142920 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3401 r_free = 0.3401 target = 0.097343 restraints weight = 16138.965| |-----------------------------------------------------------------------------| r_work (start): 0.3417 rms_B_bonded: 4.85 r_work (final): 0.3417 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3415 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3415 r_free = 0.3415 target_work(ls_wunit_k1) = 0.100 | | occupancies: max = 1.00 min = 0.42 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3415 r_free = 0.3415 target_work(ls_wunit_k1) = 0.100 | | occupancies: max = 1.00 min = 0.43 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3415 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7832 moved from start: 0.2030 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.025 4983 Z= 0.161 Angle : 0.497 6.982 6747 Z= 0.251 Chirality : 0.040 0.129 737 Planarity : 0.004 0.047 873 Dihedral : 4.359 38.424 664 Min Nonbonded Distance : 2.606 Molprobity Statistics. All-atom Clashscore : 7.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.22 % Favored : 95.78 % Rotamer: Outliers : 1.84 % Allowed : 11.97 % Favored : 86.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.23 % 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: 1.15 (0.37), residues: 594 helix: 1.81 (0.34), residues: 259 sheet: 0.78 (0.62), residues: 81 loop : -0.29 (0.42), residues: 254 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 93 HIS 0.001 0.000 HIS A 55 PHE 0.008 0.001 PHE C 480 TYR 0.010 0.001 TYR A 145 ARG 0.007 0.001 ARG A 72 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1188 Ramachandran restraints generated. 594 Oldfield, 0 Emsley, 594 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1188 Ramachandran restraints generated. 594 Oldfield, 0 Emsley, 594 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 70 residues out of total 541 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 60 time to evaluate : 0.578 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 83 SER cc_start: 0.8886 (m) cc_final: 0.8569 (t) REVERT: A 92 GLN cc_start: 0.7535 (mt0) cc_final: 0.6927 (mt0) REVERT: A 99 ILE cc_start: 0.7730 (OUTLIER) cc_final: 0.7231 (tp) REVERT: A 114 ASN cc_start: 0.6746 (t0) cc_final: 0.6316 (t0) REVERT: A 140 GLU cc_start: 0.8938 (mm-30) cc_final: 0.8681 (mm-30) REVERT: C 613 MET cc_start: 0.8791 (ttt) cc_final: 0.8560 (ttt) outliers start: 10 outliers final: 8 residues processed: 68 average time/residue: 0.2394 time to fit residues: 19.9954 Evaluate side-chains 67 residues out of total 541 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 58 time to evaluate : 0.581 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 10 LEU Chi-restraints excluded: chain A residue 43 SER Chi-restraints excluded: chain A residue 67 VAL Chi-restraints excluded: chain A residue 73 ILE Chi-restraints excluded: chain A residue 99 ILE Chi-restraints excluded: chain A residue 120 VAL Chi-restraints excluded: chain B residue 32 ASP Chi-restraints excluded: chain C residue 389 TYR Chi-restraints excluded: chain C residue 570 TYR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 58 random chunks: chunk 24 optimal weight: 1.9990 chunk 12 optimal weight: 0.9990 chunk 56 optimal weight: 0.6980 chunk 40 optimal weight: 3.9990 chunk 20 optimal weight: 8.9990 chunk 32 optimal weight: 0.5980 chunk 15 optimal weight: 9.9990 chunk 13 optimal weight: 0.7980 chunk 10 optimal weight: 0.1980 chunk 17 optimal weight: 10.0000 chunk 1 optimal weight: 0.9980 overall best weight: 0.6580 ------------------------------------------------------------------------------- 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 = 0.3908 r_free = 0.3908 target = 0.139260 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3280 r_free = 0.3280 target = 0.091190 restraints weight = 21791.064| |-----------------------------------------------------------------------------| r_work (start): 0.3252 rms_B_bonded: 5.92 r_work (final): 0.3252 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3221 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3221 r_free = 0.3221 target_work(ls_wunit_k1) = 0.088 | | occupancies: max = 1.00 min = 0.43 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3221 r_free = 0.3221 target_work(ls_wunit_k1) = 0.088 | | occupancies: max = 1.00 min = 0.43 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3221 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7869 moved from start: 0.2136 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 4983 Z= 0.262 Angle : 0.552 8.895 6747 Z= 0.274 Chirality : 0.042 0.137 737 Planarity : 0.004 0.059 873 Dihedral : 4.458 38.470 664 Min Nonbonded Distance : 2.614 Molprobity Statistics. All-atom Clashscore : 6.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.55 % Favored : 95.45 % Rotamer: Outliers : 2.58 % Allowed : 12.52 % Favored : 84.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.23 % 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: 1.05 (0.37), residues: 594 helix: 1.69 (0.34), residues: 260 sheet: 0.79 (0.62), residues: 81 loop : -0.34 (0.42), residues: 253 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP C 581 HIS 0.001 0.001 HIS C 420 PHE 0.011 0.001 PHE C 522 TYR 0.028 0.001 TYR A 145 ARG 0.006 0.001 ARG A 133 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1188 Ramachandran restraints generated. 594 Oldfield, 0 Emsley, 594 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1188 Ramachandran restraints generated. 594 Oldfield, 0 Emsley, 594 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 68 residues out of total 541 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 54 time to evaluate : 0.557 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 83 SER cc_start: 0.9000 (m) cc_final: 0.8677 (t) REVERT: A 92 GLN cc_start: 0.7468 (mt0) cc_final: 0.6835 (mt0) REVERT: A 99 ILE cc_start: 0.7799 (OUTLIER) cc_final: 0.7275 (tp) REVERT: A 114 ASN cc_start: 0.6727 (t0) cc_final: 0.6257 (t0) REVERT: A 145 TYR cc_start: 0.7588 (m-10) cc_final: 0.7388 (m-10) REVERT: B 43 LEU cc_start: 0.8207 (tt) cc_final: 0.7876 (mm) REVERT: C 294 MET cc_start: 0.7283 (mmm) cc_final: 0.7038 (mmm) REVERT: C 613 MET cc_start: 0.8704 (ttt) cc_final: 0.8377 (ttp) outliers start: 14 outliers final: 10 residues processed: 66 average time/residue: 0.2396 time to fit residues: 19.4173 Evaluate side-chains 63 residues out of total 541 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 52 time to evaluate : 0.562 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 10 LEU Chi-restraints excluded: chain A residue 43 SER Chi-restraints excluded: chain A residue 67 VAL Chi-restraints excluded: chain A residue 73 ILE Chi-restraints excluded: chain A residue 98 THR Chi-restraints excluded: chain A residue 99 ILE Chi-restraints excluded: chain A residue 120 VAL Chi-restraints excluded: chain B residue 32 ASP Chi-restraints excluded: chain C residue 389 TYR Chi-restraints excluded: chain C residue 413 VAL Chi-restraints excluded: chain C residue 570 TYR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 58 random chunks: chunk 5 optimal weight: 0.9990 chunk 18 optimal weight: 2.9990 chunk 51 optimal weight: 0.9990 chunk 14 optimal weight: 0.6980 chunk 21 optimal weight: 0.5980 chunk 24 optimal weight: 2.9990 chunk 49 optimal weight: 0.8980 chunk 35 optimal weight: 0.5980 chunk 30 optimal weight: 0.9990 chunk 28 optimal weight: 0.1980 chunk 34 optimal weight: 0.6980 overall best weight: 0.5580 ------------------------------------------------------------------------------- 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 = 0.3985 r_free = 0.3985 target = 0.144467 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3436 r_free = 0.3436 target = 0.098801 restraints weight = 10368.242| |-----------------------------------------------------------------------------| r_work (start): 0.3391 rms_B_bonded: 3.83 r_work: 0.3211 rms_B_bonded: 4.51 restraints_weight: 0.5000 r_work (final): 0.3211 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3202 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3202 r_free = 0.3202 target_work(ls_wunit_k1) = 0.085 | | occupancies: max = 1.00 min = 0.43 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3202 r_free = 0.3202 target_work(ls_wunit_k1) = 0.085 | | occupancies: max = 1.00 min = 0.44 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3202 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8044 moved from start: 0.2169 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.032 4983 Z= 0.228 Angle : 0.541 8.528 6747 Z= 0.268 Chirality : 0.041 0.134 737 Planarity : 0.004 0.046 873 Dihedral : 4.464 38.310 664 Min Nonbonded Distance : 2.609 Molprobity Statistics. All-atom Clashscore : 6.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.38 % Favored : 95.62 % Rotamer: Outliers : 2.95 % Allowed : 12.71 % Favored : 84.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.23 % 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: 1.09 (0.37), residues: 594 helix: 1.77 (0.34), residues: 258 sheet: 0.82 (0.63), residues: 81 loop : -0.36 (0.42), residues: 255 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A 93 HIS 0.001 0.000 HIS A 55 PHE 0.009 0.001 PHE C 522 TYR 0.017 0.001 TYR A 145 ARG 0.011 0.001 ARG A 143 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1188 Ramachandran restraints generated. 594 Oldfield, 0 Emsley, 594 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1188 Ramachandran restraints generated. 594 Oldfield, 0 Emsley, 594 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 73 residues out of total 541 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 57 time to evaluate : 0.555 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 83 SER cc_start: 0.9077 (m) cc_final: 0.8740 (t) REVERT: A 92 GLN cc_start: 0.7448 (mt0) cc_final: 0.7045 (mt0) REVERT: A 99 ILE cc_start: 0.7959 (OUTLIER) cc_final: 0.7479 (tp) REVERT: B 54 ARG cc_start: 0.8695 (mtp180) cc_final: 0.8206 (mtp180) outliers start: 16 outliers final: 12 residues processed: 68 average time/residue: 0.2072 time to fit residues: 17.7816 Evaluate side-chains 70 residues out of total 541 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 57 time to evaluate : 0.521 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 10 LEU Chi-restraints excluded: chain A residue 43 SER Chi-restraints excluded: chain A residue 67 VAL Chi-restraints excluded: chain A residue 73 ILE Chi-restraints excluded: chain A residue 98 THR Chi-restraints excluded: chain A residue 99 ILE Chi-restraints excluded: chain A residue 120 VAL Chi-restraints excluded: chain B residue 14 THR Chi-restraints excluded: chain B residue 32 ASP Chi-restraints excluded: chain C residue 389 TYR Chi-restraints excluded: chain C residue 413 VAL Chi-restraints excluded: chain C residue 486 VAL Chi-restraints excluded: chain C residue 570 TYR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 58 random chunks: chunk 11 optimal weight: 0.0170 chunk 14 optimal weight: 0.7980 chunk 42 optimal weight: 0.5980 chunk 56 optimal weight: 0.3980 chunk 54 optimal weight: 0.7980 chunk 29 optimal weight: 1.9990 chunk 16 optimal weight: 7.9990 chunk 55 optimal weight: 0.9980 chunk 48 optimal weight: 0.5980 chunk 13 optimal weight: 1.9990 chunk 27 optimal weight: 1.9990 overall best weight: 0.4818 ------------------------------------------------------------------------------- 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 = 0.3874 r_free = 0.3874 target = 0.137614 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3212 r_free = 0.3212 target = 0.088230 restraints weight = 21681.209| |-----------------------------------------------------------------------------| r_work (start): 0.3160 rms_B_bonded: 6.49 r_work: 0.2885 rms_B_bonded: 6.46 restraints_weight: 2.0000 r_work (final): 0.2885 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2927 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2927 r_free = 0.2927 target_work(ls_wunit_k1) = 0.071 | | occupancies: max = 1.00 min = 0.44 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2927 r_free = 0.2927 target_work(ls_wunit_k1) = 0.071 | | occupancies: max = 1.00 min = 0.43 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2927 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7924 moved from start: 0.2263 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 4983 Z= 0.211 Angle : 0.554 9.440 6747 Z= 0.274 Chirality : 0.041 0.134 737 Planarity : 0.004 0.046 873 Dihedral : 4.507 38.206 664 Min Nonbonded Distance : 2.549 Molprobity Statistics. All-atom Clashscore : 7.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.55 % Favored : 95.45 % Rotamer: Outliers : 3.68 % Allowed : 12.34 % Favored : 83.98 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.23 % 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: 1.11 (0.37), residues: 594 helix: 1.79 (0.34), residues: 258 sheet: 0.93 (0.64), residues: 81 loop : -0.41 (0.42), residues: 255 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A 93 HIS 0.001 0.000 HIS A 55 PHE 0.009 0.001 PHE C 522 TYR 0.009 0.001 TYR A 127 ARG 0.008 0.001 ARG A 72 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1188 Ramachandran restraints generated. 594 Oldfield, 0 Emsley, 594 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1188 Ramachandran restraints generated. 594 Oldfield, 0 Emsley, 594 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 80 residues out of total 541 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 60 time to evaluate : 0.452 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 83 SER cc_start: 0.9196 (m) cc_final: 0.8859 (t) REVERT: A 92 GLN cc_start: 0.7306 (mt0) cc_final: 0.6828 (mt0) REVERT: A 99 ILE cc_start: 0.7850 (OUTLIER) cc_final: 0.7386 (tp) REVERT: A 104 LEU cc_start: 0.7313 (OUTLIER) cc_final: 0.7000 (tt) REVERT: B 43 LEU cc_start: 0.8300 (tt) cc_final: 0.7995 (mm) REVERT: B 54 ARG cc_start: 0.8789 (mtp180) cc_final: 0.8507 (mtp180) REVERT: B 67 LEU cc_start: 0.6110 (OUTLIER) cc_final: 0.5852 (tp) outliers start: 20 outliers final: 13 residues processed: 72 average time/residue: 0.2017 time to fit residues: 18.3329 Evaluate side-chains 73 residues out of total 541 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 57 time to evaluate : 0.530 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 10 LEU Chi-restraints excluded: chain A residue 43 SER Chi-restraints excluded: chain A residue 67 VAL Chi-restraints excluded: chain A residue 73 ILE Chi-restraints excluded: chain A residue 98 THR Chi-restraints excluded: chain A residue 99 ILE Chi-restraints excluded: chain A residue 104 LEU Chi-restraints excluded: chain A residue 120 VAL Chi-restraints excluded: chain A residue 144 LYS Chi-restraints excluded: chain B residue 14 THR Chi-restraints excluded: chain B residue 67 LEU Chi-restraints excluded: chain C residue 389 TYR Chi-restraints excluded: chain C residue 413 VAL Chi-restraints excluded: chain C residue 486 VAL Chi-restraints excluded: chain C residue 516 THR Chi-restraints excluded: chain C residue 570 TYR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 58 random chunks: chunk 40 optimal weight: 3.9990 chunk 56 optimal weight: 0.8980 chunk 55 optimal weight: 0.2980 chunk 26 optimal weight: 0.5980 chunk 15 optimal weight: 8.9990 chunk 44 optimal weight: 0.9990 chunk 45 optimal weight: 0.0270 chunk 24 optimal weight: 0.3980 chunk 57 optimal weight: 0.5980 chunk 33 optimal weight: 0.9980 chunk 49 optimal weight: 0.6980 overall best weight: 0.3838 ------------------------------------------------------------------------------- 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 = 0.4004 r_free = 0.4004 target = 0.146710 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3430 r_free = 0.3430 target = 0.098757 restraints weight = 12976.857| |-----------------------------------------------------------------------------| r_work (start): 0.3371 rms_B_bonded: 4.51 r_work: 0.3195 rms_B_bonded: 4.93 restraints_weight: 0.5000 r_work (final): 0.3195 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3179 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3179 r_free = 0.3179 target_work(ls_wunit_k1) = 0.084 | | occupancies: max = 1.00 min = 0.43 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3179 r_free = 0.3179 target_work(ls_wunit_k1) = 0.084 | | occupancies: max = 1.00 min = 0.43 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3179 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8057 moved from start: 0.2290 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 4983 Z= 0.181 Angle : 0.534 8.539 6747 Z= 0.266 Chirality : 0.040 0.128 737 Planarity : 0.004 0.050 873 Dihedral : 4.475 38.302 664 Min Nonbonded Distance : 2.607 Molprobity Statistics. All-atom Clashscore : 7.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.38 % Favored : 95.62 % Rotamer: Outliers : 2.39 % Allowed : 13.81 % Favored : 83.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.23 % 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: 1.17 (0.37), residues: 594 helix: 1.82 (0.34), residues: 258 sheet: 0.97 (0.64), residues: 81 loop : -0.34 (0.42), residues: 255 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 93 HIS 0.001 0.000 HIS A 55 PHE 0.008 0.001 PHE C 522 TYR 0.012 0.001 TYR A 145 ARG 0.010 0.001 ARG A 143 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1188 Ramachandran restraints generated. 594 Oldfield, 0 Emsley, 594 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1188 Ramachandran restraints generated. 594 Oldfield, 0 Emsley, 594 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 69 residues out of total 541 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 56 time to evaluate : 0.688 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 83 SER cc_start: 0.9088 (m) cc_final: 0.8743 (t) REVERT: A 92 GLN cc_start: 0.7426 (mt0) cc_final: 0.7069 (mt0) REVERT: A 99 ILE cc_start: 0.7957 (OUTLIER) cc_final: 0.7467 (tp) REVERT: A 114 ASN cc_start: 0.7961 (t0) cc_final: 0.7064 (t0) REVERT: A 144 LYS cc_start: 0.8472 (OUTLIER) cc_final: 0.7725 (tmmt) REVERT: B 43 LEU cc_start: 0.8572 (tt) cc_final: 0.8096 (mm) REVERT: B 67 LEU cc_start: 0.6177 (OUTLIER) cc_final: 0.5883 (tp) outliers start: 13 outliers final: 10 residues processed: 65 average time/residue: 0.2403 time to fit residues: 19.5612 Evaluate side-chains 69 residues out of total 541 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 56 time to evaluate : 0.579 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 10 LEU Chi-restraints excluded: chain A residue 43 SER Chi-restraints excluded: chain A residue 67 VAL Chi-restraints excluded: chain A residue 73 ILE Chi-restraints excluded: chain A residue 99 ILE Chi-restraints excluded: chain A residue 120 VAL Chi-restraints excluded: chain A residue 144 LYS Chi-restraints excluded: chain B residue 14 THR Chi-restraints excluded: chain B residue 67 LEU Chi-restraints excluded: chain C residue 389 TYR Chi-restraints excluded: chain C residue 413 VAL Chi-restraints excluded: chain C residue 486 VAL Chi-restraints excluded: chain C residue 570 TYR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 58 random chunks: chunk 7 optimal weight: 0.9980 chunk 45 optimal weight: 0.0980 chunk 18 optimal weight: 0.8980 chunk 52 optimal weight: 0.0370 chunk 16 optimal weight: 0.9980 chunk 14 optimal weight: 5.9990 chunk 25 optimal weight: 0.5980 chunk 9 optimal weight: 0.0020 chunk 13 optimal weight: 1.9990 chunk 30 optimal weight: 0.6980 chunk 21 optimal weight: 0.4980 overall best weight: 0.2466 ------------------------------------------------------------------------------- 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 = 0.4008 r_free = 0.4008 target = 0.146186 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3445 r_free = 0.3445 target = 0.100151 restraints weight = 12861.334| |-----------------------------------------------------------------------------| r_work (start): 0.3392 rms_B_bonded: 4.24 r_work: 0.3221 rms_B_bonded: 4.70 restraints_weight: 0.5000 r_work (final): 0.3221 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3227 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3227 r_free = 0.3227 target_work(ls_wunit_k1) = 0.089 | | occupancies: max = 1.00 min = 0.43 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3227 r_free = 0.3227 target_work(ls_wunit_k1) = 0.089 | | occupancies: max = 1.00 min = 0.42 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3227 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7968 moved from start: 0.2342 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.025 4983 Z= 0.146 Angle : 0.536 8.445 6747 Z= 0.263 Chirality : 0.040 0.133 737 Planarity : 0.004 0.052 873 Dihedral : 4.450 38.283 664 Min Nonbonded Distance : 2.607 Molprobity Statistics. All-atom Clashscore : 7.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.88 % Favored : 96.12 % Rotamer: Outliers : 2.03 % Allowed : 14.73 % Favored : 83.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.23 % 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: 1.24 (0.37), residues: 594 helix: 1.90 (0.34), residues: 257 sheet: 1.02 (0.64), residues: 81 loop : -0.32 (0.42), residues: 256 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 93 HIS 0.001 0.000 HIS C 512 PHE 0.006 0.001 PHE C 428 TYR 0.009 0.001 TYR A 127 ARG 0.009 0.000 ARG A 72 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1188 Ramachandran restraints generated. 594 Oldfield, 0 Emsley, 594 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1188 Ramachandran restraints generated. 594 Oldfield, 0 Emsley, 594 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 68 residues out of total 541 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 57 time to evaluate : 0.582 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 83 SER cc_start: 0.9049 (m) cc_final: 0.8706 (t) REVERT: A 92 GLN cc_start: 0.7284 (mt0) cc_final: 0.6912 (mt0) REVERT: A 99 ILE cc_start: 0.7868 (OUTLIER) cc_final: 0.7399 (tp) REVERT: A 114 ASN cc_start: 0.7905 (t0) cc_final: 0.6918 (t0) REVERT: B 43 LEU cc_start: 0.8566 (tt) cc_final: 0.8104 (mm) REVERT: B 67 LEU cc_start: 0.6082 (OUTLIER) cc_final: 0.5815 (tp) REVERT: C 294 MET cc_start: 0.6842 (mmm) cc_final: 0.6494 (mmm) outliers start: 11 outliers final: 8 residues processed: 65 average time/residue: 0.2176 time to fit residues: 17.8962 Evaluate side-chains 64 residues out of total 541 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 54 time to evaluate : 0.536 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 10 LEU Chi-restraints excluded: chain A residue 43 SER Chi-restraints excluded: chain A residue 67 VAL Chi-restraints excluded: chain A residue 73 ILE Chi-restraints excluded: chain A residue 99 ILE Chi-restraints excluded: chain A residue 120 VAL Chi-restraints excluded: chain B residue 67 LEU Chi-restraints excluded: chain C residue 389 TYR Chi-restraints excluded: chain C residue 486 VAL Chi-restraints excluded: chain C residue 570 TYR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 58 random chunks: chunk 14 optimal weight: 3.9990 chunk 57 optimal weight: 0.7980 chunk 33 optimal weight: 0.9990 chunk 43 optimal weight: 0.1980 chunk 44 optimal weight: 0.5980 chunk 18 optimal weight: 0.3980 chunk 17 optimal weight: 0.9990 chunk 53 optimal weight: 0.8980 chunk 54 optimal weight: 1.9990 chunk 13 optimal weight: 0.9990 chunk 42 optimal weight: 0.7980 overall best weight: 0.5580 ------------------------------------------------------------------------------- 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 = 0.3994 r_free = 0.3994 target = 0.145179 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3430 r_free = 0.3430 target = 0.098891 restraints weight = 11027.049| |-----------------------------------------------------------------------------| r_work (start): 0.3321 rms_B_bonded: 4.13 r_work (final): 0.3321 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3375 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3375 r_free = 0.3375 target_work(ls_wunit_k1) = 0.098 | | occupancies: max = 1.00 min = 0.42 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3375 r_free = 0.3375 target_work(ls_wunit_k1) = 0.098 | | occupancies: max = 1.00 min = 0.41 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3375 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7893 moved from start: 0.2365 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.033 4983 Z= 0.228 Angle : 0.550 8.420 6747 Z= 0.272 Chirality : 0.041 0.125 737 Planarity : 0.004 0.053 873 Dihedral : 4.531 38.421 664 Min Nonbonded Distance : 2.618 Molprobity Statistics. All-atom Clashscore : 7.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.38 % Favored : 95.62 % Rotamer: Outliers : 2.21 % Allowed : 14.18 % Favored : 83.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.23 % 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: 1.17 (0.37), residues: 594 helix: 1.83 (0.34), residues: 255 sheet: 1.03 (0.65), residues: 81 loop : -0.35 (0.41), residues: 258 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP C 581 HIS 0.001 0.000 HIS A 55 PHE 0.011 0.001 PHE C 522 TYR 0.009 0.001 TYR C 419 ARG 0.011 0.001 ARG A 143 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1188 Ramachandran restraints generated. 594 Oldfield, 0 Emsley, 594 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1188 Ramachandran restraints generated. 594 Oldfield, 0 Emsley, 594 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 69 residues out of total 541 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 57 time to evaluate : 0.734 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 83 SER cc_start: 0.8959 (m) cc_final: 0.8602 (t) REVERT: A 92 GLN cc_start: 0.7350 (mt0) cc_final: 0.6927 (mt0) REVERT: A 99 ILE cc_start: 0.7655 (OUTLIER) cc_final: 0.7201 (tp) REVERT: A 114 ASN cc_start: 0.7883 (t0) cc_final: 0.6916 (t0) REVERT: A 116 ASP cc_start: 0.8582 (m-30) cc_final: 0.8305 (m-30) REVERT: A 144 LYS cc_start: 0.8420 (tmmt) cc_final: 0.8112 (tmmt) REVERT: C 294 MET cc_start: 0.7138 (mmm) cc_final: 0.6782 (mmm) outliers start: 12 outliers final: 9 residues processed: 66 average time/residue: 0.2097 time to fit residues: 18.0118 Evaluate side-chains 66 residues out of total 541 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 56 time to evaluate : 0.636 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 10 LEU Chi-restraints excluded: chain A residue 43 SER Chi-restraints excluded: chain A residue 67 VAL Chi-restraints excluded: chain A residue 73 ILE Chi-restraints excluded: chain A residue 99 ILE Chi-restraints excluded: chain A residue 120 VAL Chi-restraints excluded: chain C residue 389 TYR Chi-restraints excluded: chain C residue 413 VAL Chi-restraints excluded: chain C residue 486 VAL Chi-restraints excluded: chain C residue 570 TYR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 58 random chunks: chunk 21 optimal weight: 0.9980 chunk 53 optimal weight: 0.9990 chunk 41 optimal weight: 0.3980 chunk 29 optimal weight: 0.6980 chunk 2 optimal weight: 3.9990 chunk 22 optimal weight: 0.3980 chunk 11 optimal weight: 1.9990 chunk 23 optimal weight: 0.0170 chunk 32 optimal weight: 0.3980 chunk 25 optimal weight: 0.5980 chunk 36 optimal weight: 0.9990 overall best weight: 0.3618 ------------------------------------------------------------------------------- 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 = 0.3923 r_free = 0.3923 target = 0.140702 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3279 r_free = 0.3279 target = 0.091363 restraints weight = 18028.176| |-----------------------------------------------------------------------------| r_work (start): 0.3215 rms_B_bonded: 5.37 r_work (final): 0.3215 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3219 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3219 r_free = 0.3219 target_work(ls_wunit_k1) = 0.088 | | occupancies: max = 1.00 min = 0.41 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3219 r_free = 0.3219 target_work(ls_wunit_k1) = 0.088 | | occupancies: max = 1.00 min = 0.42 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3219 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7804 moved from start: 0.2420 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 4983 Z= 0.178 Angle : 0.557 10.061 6747 Z= 0.273 Chirality : 0.041 0.127 737 Planarity : 0.005 0.062 873 Dihedral : 4.565 38.297 664 Min Nonbonded Distance : 2.543 Molprobity Statistics. All-atom Clashscore : 7.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.38 % Favored : 95.62 % Rotamer: Outliers : 2.21 % Allowed : 14.18 % Favored : 83.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.23 % 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: 1.22 (0.37), residues: 594 helix: 1.88 (0.34), residues: 255 sheet: 0.98 (0.64), residues: 81 loop : -0.31 (0.42), residues: 258 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP C 581 HIS 0.001 0.000 HIS A 55 PHE 0.009 0.001 PHE C 522 TYR 0.019 0.001 TYR A 145 ARG 0.013 0.001 ARG C 349 Origin is already at (0, 0, 0), no shifts will be applied Model does not fit in PDB format. =============================================================================== Job complete usr+sys time: 2691.69 seconds wall clock time: 48 minutes 23.98 seconds (2903.98 seconds total)