Starting phenix.real_space_refine on Thu Mar 6 04:35:52 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9b58_44203/03_2025/9b58_44203.cif Found real_map, /net/cci-nas-00/data/ceres_data/9b58_44203/03_2025/9b58_44203.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.39 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9b58_44203/03_2025/9b58_44203.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9b58_44203/03_2025/9b58_44203.map" model { file = "/net/cci-nas-00/data/ceres_data/9b58_44203/03_2025/9b58_44203.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9b58_44203/03_2025/9b58_44203.cif" } resolution = 3.39 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= 0.041 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 Symmetric amino acids flipped. Time to flip 1 residue(s): 0.01s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5624/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: 5.05, per 1000 atoms: 1.04 Number of scatterers: 4871 At special positions: 0 Unit cell: (69.16, 82.992, 101.08, 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: 1.35 Conformation dependent library (CDL) restraints added in 966.8 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: 30 helices and 6 sheets defined 50.3% alpha, 12.2% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.61 Creating SS restraints... Processing helix chain 'A' and resid 3 through 16 Processing helix chain 'A' and resid 86 through 91 Processing helix chain 'A' and resid 98 through 110 removed outlier: 4.094A 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 307 through 311 removed outlier: 4.057A pdb=" N ALA C 311 " --> pdb=" O PRO C 308 " (cutoff:3.500A) Processing helix chain 'C' and resid 325 through 335 removed outlier: 3.518A pdb=" N SER C 335 " --> pdb=" O TYR C 331 " (cutoff:3.500A) Processing helix chain 'C' and resid 338 through 343 Processing helix chain 'C' and resid 357 through 374 removed outlier: 3.518A pdb=" N PHE C 374 " --> pdb=" O SER C 370 " (cutoff:3.500A) Processing helix chain 'C' and resid 375 through 379 Processing helix chain 'C' and resid 395 through 400 removed outlier: 3.582A pdb=" N SER C 398 " --> pdb=" O PRO C 395 " (cutoff:3.500A) Processing helix chain 'C' and resid 402 through 420 removed outlier: 4.395A pdb=" N TYR C 406 " --> pdb=" O ASP C 402 " (cutoff:3.500A) Processing helix chain 'C' and resid 429 through 437 removed outlier: 3.567A 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: 3.857A 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: 3.820A pdb=" N ASN C 494 " --> pdb=" O ASN C 491 " (cutoff:3.500A) removed outlier: 3.671A pdb=" N ILE C 495 " --> pdb=" O GLY C 492 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 491 through 495' Processing helix chain 'C' and resid 501 through 515 Processing helix chain 'C' and resid 518 through 533 removed outlier: 4.284A pdb=" N LEU C 532 " --> pdb=" O GLY C 528 " (cutoff:3.500A) Processing helix chain 'C' and resid 534 through 539 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: 3.937A 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: 3.591A 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: 3.885A pdb=" N SER B 65 " --> pdb=" O GLN B 2 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'C' and resid 316 through 321 removed outlier: 3.703A 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 385 removed outlier: 6.764A pdb=" N GLY C 390 " --> pdb=" O ALA C 384 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'C' and resid 474 through 479 Processing sheet with id=AA6, first strand: chain 'C' and resid 565 through 568 224 hydrogen bonds defined for protein. 626 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 1.28 Time building geometry restraints manager: 1.58 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: 1234 1.41 - 1.54: 2889 1.54 - 1.68: 16 1.68 - 1.81: 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 1.527 -0.074 2.00e-02 2.50e+03 1.36e+01 bond pdb=" N MET B 1 " pdb=" CA MET B 1 " ideal model delta sigma weight residual 1.458 1.489 -0.031 1.90e-02 2.77e+03 2.75e+00 bond pdb=" N MET A 1 " pdb=" CA MET A 1 " ideal model delta sigma weight residual 1.458 1.489 -0.031 1.90e-02 2.77e+03 2.69e+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 8.00e-01 bond pdb=" CG LEU C 595 " pdb=" CD2 LEU C 595 " ideal model delta sigma weight residual 1.521 1.500 0.021 3.30e-02 9.18e+02 4.21e-01 ... (remaining 4978 not shown) Histogram of bond angle deviations from ideal: 0.00 - 0.78: 6321 0.78 - 1.56: 350 1.56 - 2.34: 36 2.34 - 3.12: 13 3.12 - 3.90: 27 Bond angle restraints: 6747 Sorted by residual: angle pdb=" N LEU C 424 " pdb=" CA LEU C 424 " pdb=" C LEU C 424 " ideal model delta sigma weight residual 110.35 108.22 2.13 1.38e+00 5.25e-01 2.39e+00 angle pdb=" N VAL C 515 " pdb=" CA VAL C 515 " pdb=" C VAL C 515 " ideal model delta sigma weight residual 109.34 111.91 -2.57 2.08e+00 2.31e-01 1.52e+00 angle pdb=" CA TRP C 561 " pdb=" CB TRP C 561 " pdb=" CG TRP C 561 " ideal model delta sigma weight residual 113.60 115.65 -2.05 1.90e+00 2.77e-01 1.16e+00 angle pdb=" C LEU A 89 " pdb=" N ARG A 90 " pdb=" CA ARG A 90 " ideal model delta sigma weight residual 121.54 119.51 2.03 1.91e+00 2.74e-01 1.13e+00 angle pdb=" N SER C 569 " pdb=" CA SER C 569 " pdb=" CB SER C 569 " ideal model delta sigma weight residual 112.78 111.20 1.58 1.53e+00 4.27e-01 1.06e+00 ... (remaining 6742 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 15.54: 2802 15.54 - 31.07: 186 31.07 - 46.61: 24 46.61 - 62.15: 4 62.15 - 77.68: 2 Dihedral angle restraints: 3018 sinusoidal: 1254 harmonic: 1764 Sorted by residual: dihedral pdb=" CA TYR A 145 " pdb=" C TYR A 145 " pdb=" N ALA A 146 " pdb=" CA ALA A 146 " ideal model delta harmonic sigma weight residual 180.00 -161.78 -18.22 0 5.00e+00 4.00e-02 1.33e+01 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 180.00 163.25 16.75 0 5.00e+00 4.00e-02 1.12e+01 dihedral pdb=" CA LEU A 119 " pdb=" C LEU A 119 " pdb=" N VAL A 120 " pdb=" CA VAL A 120 " ideal model delta harmonic sigma weight residual 180.00 164.00 16.00 0 5.00e+00 4.00e-02 1.02e+01 ... (remaining 3015 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.028: 441 0.028 - 0.055: 197 0.055 - 0.082: 57 0.082 - 0.110: 27 0.110 - 0.137: 15 Chirality restraints: 737 Sorted by residual: chirality pdb=" CA ILE A 54 " pdb=" N ILE A 54 " pdb=" C ILE A 54 " pdb=" CB ILE A 54 " both_signs ideal model delta sigma weight residual False 2.43 2.57 -0.14 2.00e-01 2.50e+01 4.72e-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 -0.14 2.00e-01 2.50e+01 4.62e-01 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 2.56 -0.13 2.00e-01 2.50e+01 4.14e-01 ... (remaining 734 not shown) Planarity restraints: 873 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ASP A 117 " -0.022 5.00e-02 4.00e+02 3.32e-02 1.76e+00 pdb=" N PRO A 118 " 0.057 5.00e-02 4.00e+02 pdb=" CA PRO A 118 " -0.017 5.00e-02 4.00e+02 pdb=" CD PRO A 118 " -0.018 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C LEU C 430 " 0.020 5.00e-02 4.00e+02 2.98e-02 1.42e+00 pdb=" N PRO C 431 " -0.052 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 PRO C 646 " -0.018 5.00e-02 4.00e+02 2.80e-02 1.26e+00 pdb=" N PRO C 647 " 0.048 5.00e-02 4.00e+02 pdb=" CA PRO C 647 " -0.014 5.00e-02 4.00e+02 pdb=" CD PRO C 647 " -0.016 5.00e-02 4.00e+02 ... (remaining 870 not shown) Histogram of nonbonded interaction distances: 1.81 - 2.43: 16 2.43 - 3.05: 3104 3.05 - 3.66: 6734 3.66 - 4.28: 10344 4.28 - 4.90: 17704 Nonbonded interactions: 37902 Sorted by model distance: nonbonded pdb=" SG CYS C 639 " pdb=" C03 A1AIV B 101 " model vdw 1.812 3.800 nonbonded pdb=" OD1 ASN B 25 " pdb=" NZ LYS B 29 " model vdw 2.221 3.120 nonbonded pdb=" OG SER C 608 " pdb=" OD2 ASP C 612 " model vdw 2.303 3.040 nonbonded pdb=" OG SER C 397 " pdb=" OE1 GLN C 521 " model vdw 2.304 3.040 nonbonded pdb=" OD1 ASN C 478 " pdb=" OG SER C 483 " model vdw 2.316 3.040 ... (remaining 37897 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=0.39 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: 1.930 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: 0.220 Check model and map are aligned: 0.050 Set scattering table: 0.060 Process input model: 18.440 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:2.850 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 23.640 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7794 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 0.074 4983 Z= 0.158 Angle : 0.453 3.898 6747 Z= 0.226 Chirality : 0.039 0.137 737 Planarity : 0.003 0.033 873 Dihedral : 10.328 77.683 1878 Min Nonbonded Distance : 1.812 Molprobity Statistics. All-atom Clashscore : 3.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.22 % Favored : 95.78 % Rotamer: Outliers : 1.10 % Allowed : 6.08 % Favored : 92.82 % 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: 0.81 (0.37), residues: 594 helix: 1.28 (0.33), residues: 257 sheet: 0.66 (0.61), residues: 85 loop : -0.19 (0.43), residues: 252 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP C 581 HIS 0.001 0.000 HIS A 125 PHE 0.009 0.001 PHE C 407 TYR 0.010 0.001 TYR C 367 ARG 0.002 0.000 ARG C 404 *********************** 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 75 residues out of total 541 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 69 time to evaluate : 0.571 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 131 ARG cc_start: 0.7889 (tpp80) cc_final: 0.7679 (ttt90) REVERT: C 318 GLN cc_start: 0.8449 (pt0) cc_final: 0.8232 (pm20) REVERT: C 347 LEU cc_start: 0.8076 (tp) cc_final: 0.7834 (mt) outliers start: 6 outliers final: 2 residues processed: 73 average time/residue: 0.2800 time to fit residues: 24.3810 Evaluate side-chains 50 residues out of total 541 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 48 time to evaluate : 0.570 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 73 ILE Chi-restraints excluded: chain C residue 385 THR 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: 0.8980 chunk 24 optimal weight: 1.9990 chunk 15 optimal weight: 0.9990 chunk 29 optimal weight: 0.9980 chunk 23 optimal weight: 1.9990 chunk 45 optimal weight: 0.9980 chunk 17 optimal weight: 0.4980 chunk 27 optimal weight: 8.9990 chunk 33 optimal weight: 0.5980 chunk 52 optimal weight: 0.6980 overall best weight: 0.7380 ------------------------------------------------------------------------------- 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 = 0.147210 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3550 r_free = 0.3550 target = 0.113146 restraints weight = 12014.348| |-----------------------------------------------------------------------------| r_work (start): 0.3554 rms_B_bonded: 3.58 r_work: 0.3299 rms_B_bonded: 3.68 restraints_weight: 0.5000 r_work (final): 0.3299 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3314 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3314 r_free = 0.3314 target_work(ls_wunit_k1) = 0.098 | | occupancies: max = 1.00 min = 0.39 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3314 r_free = 0.3314 target_work(ls_wunit_k1) = 0.098 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3314 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8163 moved from start: 0.1437 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 4983 Z= 0.286 Angle : 0.566 8.507 6747 Z= 0.290 Chirality : 0.042 0.155 737 Planarity : 0.004 0.044 873 Dihedral : 4.535 41.366 663 Min Nonbonded Distance : 2.480 Molprobity Statistics. All-atom Clashscore : 7.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.06 % Favored : 94.94 % Rotamer: Outliers : 1.66 % Allowed : 10.68 % Favored : 87.66 % 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: 0.66 (0.36), residues: 594 helix: 1.10 (0.33), residues: 262 sheet: 0.76 (0.61), residues: 82 loop : -0.30 (0.43), residues: 250 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP C 581 HIS 0.002 0.001 HIS C 420 PHE 0.016 0.001 PHE C 564 TYR 0.010 0.001 TYR C 419 ARG 0.009 0.001 ARG C 568 *********************** 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 65 residues out of total 541 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 56 time to evaluate : 0.719 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 347 LEU cc_start: 0.8205 (tp) cc_final: 0.8003 (mt) REVERT: C 572 GLU cc_start: 0.7659 (tp30) cc_final: 0.7354 (tp30) outliers start: 9 outliers final: 7 residues processed: 61 average time/residue: 0.2608 time to fit residues: 19.6103 Evaluate side-chains 55 residues out of total 541 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 48 time to evaluate : 0.622 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 73 ILE Chi-restraints excluded: chain A residue 109 LEU Chi-restraints excluded: chain B residue 4 PHE Chi-restraints excluded: chain C residue 310 MET Chi-restraints excluded: chain C residue 385 THR Chi-restraints excluded: chain C residue 389 TYR Chi-restraints excluded: chain C residue 627 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 58 random chunks: chunk 44 optimal weight: 0.9990 chunk 38 optimal weight: 0.0770 chunk 0 optimal weight: 1.9990 chunk 53 optimal weight: 0.9990 chunk 21 optimal weight: 0.7980 chunk 5 optimal weight: 0.9990 chunk 49 optimal weight: 0.5980 chunk 24 optimal weight: 0.9980 chunk 34 optimal weight: 0.5980 chunk 57 optimal weight: 0.5980 chunk 54 optimal weight: 1.9990 overall best weight: 0.5338 ------------------------------------------------------------------------------- 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 = 0.147536 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3543 r_free = 0.3543 target = 0.112180 restraints weight = 9858.334| |-----------------------------------------------------------------------------| r_work (start): 0.3534 rms_B_bonded: 2.91 r_work: 0.3321 rms_B_bonded: 3.47 restraints_weight: 0.5000 r_work (final): 0.3321 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3352 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3352 r_free = 0.3352 target_work(ls_wunit_k1) = 0.100 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3352 r_free = 0.3352 target_work(ls_wunit_k1) = 0.100 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3352 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8145 moved from start: 0.1599 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= 0.224 Angle : 0.516 6.593 6747 Z= 0.265 Chirality : 0.041 0.129 737 Planarity : 0.004 0.035 873 Dihedral : 4.411 37.379 663 Min Nonbonded Distance : 2.488 Molprobity Statistics. All-atom Clashscore : 7.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.71 % Favored : 96.29 % Rotamer: Outliers : 2.21 % Allowed : 11.05 % Favored : 86.74 % 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: 0.79 (0.36), residues: 594 helix: 1.25 (0.33), residues: 260 sheet: 0.83 (0.61), residues: 82 loop : -0.26 (0.43), residues: 252 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP C 581 HIS 0.002 0.001 HIS C 420 PHE 0.011 0.001 PHE C 564 TYR 0.009 0.001 TYR A 127 ARG 0.006 0.000 ARG C 568 *********************** 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 61 residues out of total 541 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 49 time to evaluate : 0.527 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 1 MET cc_start: 0.5344 (tmm) cc_final: 0.4853 (tmm) outliers start: 12 outliers final: 8 residues processed: 55 average time/residue: 0.2577 time to fit residues: 18.2064 Evaluate side-chains 52 residues out of total 541 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 44 time to evaluate : 0.597 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 73 ILE Chi-restraints excluded: chain B residue 4 PHE Chi-restraints excluded: chain B residue 14 THR Chi-restraints excluded: chain C residue 310 MET Chi-restraints excluded: chain C residue 385 THR Chi-restraints excluded: chain C residue 389 TYR Chi-restraints excluded: chain C residue 587 TRP Chi-restraints excluded: chain C residue 627 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 58 random chunks: chunk 12 optimal weight: 0.4980 chunk 4 optimal weight: 2.9990 chunk 15 optimal weight: 4.9990 chunk 35 optimal weight: 0.8980 chunk 52 optimal weight: 0.9990 chunk 51 optimal weight: 0.8980 chunk 44 optimal weight: 0.5980 chunk 45 optimal weight: 0.0980 chunk 27 optimal weight: 1.9990 chunk 8 optimal weight: 0.0870 chunk 19 optimal weight: 4.9990 overall best weight: 0.4358 ------------------------------------------------------------------------------- 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 = 0.3960 r_free = 0.3960 target = 0.146147 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3542 r_free = 0.3542 target = 0.111775 restraints weight = 15425.116| |-----------------------------------------------------------------------------| r_work (start): 0.3568 rms_B_bonded: 5.26 r_work: 0.3201 rms_B_bonded: 5.21 restraints_weight: 2.0000 r_work (final): 0.3201 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3212 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3212 r_free = 0.3212 target_work(ls_wunit_k1) = 0.091 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3212 r_free = 0.3212 target_work(ls_wunit_k1) = 0.091 | | occupancies: max = 1.00 min = 0.49 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3212 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8257 moved from start: 0.1785 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 4983 Z= 0.194 Angle : 0.513 6.907 6747 Z= 0.266 Chirality : 0.041 0.147 737 Planarity : 0.004 0.035 873 Dihedral : 4.275 33.212 663 Min Nonbonded Distance : 2.469 Molprobity Statistics. All-atom Clashscore : 7.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.38 % Favored : 95.62 % Rotamer: Outliers : 2.21 % Allowed : 11.23 % Favored : 86.56 % 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: 0.86 (0.36), residues: 594 helix: 1.25 (0.33), residues: 261 sheet: 0.96 (0.60), residues: 82 loop : -0.20 (0.43), residues: 251 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 141 HIS 0.002 0.000 HIS C 420 PHE 0.010 0.001 PHE C 428 TYR 0.007 0.001 TYR C 419 ARG 0.004 0.000 ARG C 568 *********************** 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 57 residues out of total 541 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 45 time to evaluate : 0.670 Fit side-chains revert: symmetry clash REVERT: B 1 MET cc_start: 0.6221 (tmm) cc_final: 0.5848 (tmm) REVERT: B 74 ARG cc_start: 0.7278 (mtp85) cc_final: 0.6605 (ttm110) outliers start: 12 outliers final: 8 residues processed: 53 average time/residue: 0.2571 time to fit residues: 17.3192 Evaluate side-chains 50 residues out of total 541 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 42 time to evaluate : 0.681 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 109 LEU Chi-restraints excluded: chain B residue 4 PHE Chi-restraints excluded: chain B residue 14 THR Chi-restraints excluded: chain C residue 310 MET Chi-restraints excluded: chain C residue 385 THR Chi-restraints excluded: chain C residue 389 TYR Chi-restraints excluded: chain C residue 587 TRP Chi-restraints excluded: chain C residue 627 VAL 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: 0.5980 chunk 56 optimal weight: 0.9990 chunk 40 optimal weight: 0.9990 chunk 20 optimal weight: 9.9990 chunk 32 optimal weight: 0.8980 chunk 15 optimal weight: 8.9990 chunk 13 optimal weight: 0.5980 chunk 10 optimal weight: 0.5980 chunk 17 optimal weight: 0.9980 chunk 1 optimal weight: 0.4980 overall best weight: 0.6380 ------------------------------------------------------------------------------- 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 = 0.3978 r_free = 0.3978 target = 0.146913 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 27)----------------| | r_work = 0.3575 r_free = 0.3575 target = 0.113475 restraints weight = 20508.013| |-----------------------------------------------------------------------------| r_work (start): 0.3579 rms_B_bonded: 7.43 r_work: 0.3087 rms_B_bonded: 7.26 restraints_weight: 2.0000 r_work (final): 0.3087 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3088 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3088 r_free = 0.3088 target_work(ls_wunit_k1) = 0.084 | | occupancies: max = 1.00 min = 0.49 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3088 r_free = 0.3088 target_work(ls_wunit_k1) = 0.084 | | occupancies: max = 1.00 min = 0.48 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3088 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8384 moved from start: 0.1903 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.027 4983 Z= 0.244 Angle : 0.528 7.122 6747 Z= 0.272 Chirality : 0.041 0.165 737 Planarity : 0.004 0.035 873 Dihedral : 4.279 33.533 661 Min Nonbonded Distance : 2.477 Molprobity Statistics. All-atom Clashscore : 7.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.22 % Favored : 95.78 % Rotamer: Outliers : 2.95 % Allowed : 11.23 % 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: 0.74 (0.36), residues: 594 helix: 1.18 (0.33), residues: 264 sheet: 0.92 (0.59), residues: 82 loop : -0.32 (0.42), residues: 248 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP C 581 HIS 0.002 0.000 HIS C 420 PHE 0.016 0.001 PHE C 640 TYR 0.016 0.001 TYR A 74 ARG 0.004 0.000 ARG C 568 *********************** 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 58 residues out of total 541 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 42 time to evaluate : 0.543 Fit side-chains revert: symmetry clash REVERT: A 99 ILE cc_start: 0.8735 (OUTLIER) cc_final: 0.8001 (tp) REVERT: B 1 MET cc_start: 0.6552 (tmm) cc_final: 0.5763 (tmm) REVERT: B 74 ARG cc_start: 0.7393 (mtp85) cc_final: 0.6817 (ttm110) outliers start: 16 outliers final: 11 residues processed: 52 average time/residue: 0.2272 time to fit residues: 14.7503 Evaluate side-chains 53 residues out of total 541 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 41 time to evaluate : 0.582 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 73 ILE Chi-restraints excluded: chain A residue 99 ILE Chi-restraints excluded: chain A residue 109 LEU Chi-restraints excluded: chain A residue 123 ILE Chi-restraints excluded: chain B residue 4 PHE Chi-restraints excluded: chain B residue 14 THR Chi-restraints excluded: chain C residue 310 MET Chi-restraints excluded: chain C residue 385 THR Chi-restraints excluded: chain C residue 389 TYR Chi-restraints excluded: chain C residue 584 LEU Chi-restraints excluded: chain C residue 587 TRP Chi-restraints excluded: chain C residue 627 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 58 random chunks: chunk 5 optimal weight: 0.3980 chunk 18 optimal weight: 4.9990 chunk 51 optimal weight: 0.3980 chunk 14 optimal weight: 2.9990 chunk 21 optimal weight: 0.4980 chunk 24 optimal weight: 0.9980 chunk 49 optimal weight: 0.9980 chunk 35 optimal weight: 0.2980 chunk 30 optimal weight: 0.6980 chunk 28 optimal weight: 0.5980 chunk 34 optimal weight: 0.7980 overall best weight: 0.4380 ------------------------------------------------------------------------------- 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 = 0.145670 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3530 r_free = 0.3530 target = 0.111029 restraints weight = 9895.246| |-----------------------------------------------------------------------------| r_work (start): 0.3556 rms_B_bonded: 2.74 r_work: 0.3333 rms_B_bonded: 3.32 restraints_weight: 0.5000 r_work (final): 0.3333 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3354 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3354 r_free = 0.3354 target_work(ls_wunit_k1) = 0.100 | | occupancies: max = 1.00 min = 0.48 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3354 r_free = 0.3354 target_work(ls_wunit_k1) = 0.100 | | occupancies: max = 1.00 min = 0.48 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3354 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8118 moved from start: 0.1953 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 4983 Z= 0.186 Angle : 0.504 7.451 6747 Z= 0.261 Chirality : 0.040 0.159 737 Planarity : 0.004 0.035 873 Dihedral : 4.239 32.040 661 Min Nonbonded Distance : 2.485 Molprobity Statistics. All-atom Clashscore : 6.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.22 % Favored : 95.78 % Rotamer: Outliers : 2.58 % Allowed : 11.97 % Favored : 85.45 % 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: 0.84 (0.36), residues: 594 helix: 1.28 (0.33), residues: 265 sheet: 0.99 (0.59), residues: 82 loop : -0.32 (0.43), residues: 247 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP C 581 HIS 0.001 0.000 HIS C 420 PHE 0.017 0.001 PHE C 564 TYR 0.011 0.001 TYR A 145 ARG 0.006 0.000 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 58 residues out of total 541 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 44 time to evaluate : 0.620 Fit side-chains revert: symmetry clash REVERT: A 99 ILE cc_start: 0.8430 (OUTLIER) cc_final: 0.7758 (tp) REVERT: B 1 MET cc_start: 0.6385 (tmm) cc_final: 0.5483 (tmm) REVERT: B 74 ARG cc_start: 0.7324 (mtp85) cc_final: 0.6807 (ttm110) outliers start: 14 outliers final: 8 residues processed: 53 average time/residue: 0.2221 time to fit residues: 14.8454 Evaluate side-chains 51 residues out of total 541 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 42 time to evaluate : 0.606 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 73 ILE Chi-restraints excluded: chain A residue 99 ILE Chi-restraints excluded: chain A residue 109 LEU Chi-restraints excluded: chain B residue 4 PHE Chi-restraints excluded: chain B residue 14 THR Chi-restraints excluded: chain C residue 385 THR Chi-restraints excluded: chain C residue 389 TYR Chi-restraints excluded: chain C residue 587 TRP Chi-restraints excluded: chain C residue 627 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 58 random chunks: chunk 11 optimal weight: 0.0670 chunk 14 optimal weight: 2.9990 chunk 42 optimal weight: 0.7980 chunk 56 optimal weight: 0.9990 chunk 54 optimal weight: 0.9990 chunk 29 optimal weight: 0.9990 chunk 16 optimal weight: 6.9990 chunk 55 optimal weight: 0.7980 chunk 48 optimal weight: 0.3980 chunk 13 optimal weight: 0.8980 chunk 27 optimal weight: 1.9990 overall best weight: 0.5918 ------------------------------------------------------------------------------- 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 = 0.3947 r_free = 0.3947 target = 0.144926 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3552 r_free = 0.3552 target = 0.112058 restraints weight = 20435.868| |-----------------------------------------------------------------------------| r_work (start): 0.3578 rms_B_bonded: 6.90 r_work (final): 0.3578 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3579 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3579 r_free = 0.3579 target_work(ls_wunit_k1) = 0.114 | | occupancies: max = 1.00 min = 0.48 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3579 r_free = 0.3579 target_work(ls_wunit_k1) = 0.114 | | occupancies: max = 1.00 min = 0.49 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3579 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7891 moved from start: 0.2039 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.034 4983 Z= 0.235 Angle : 0.559 14.479 6747 Z= 0.281 Chirality : 0.041 0.170 737 Planarity : 0.004 0.037 873 Dihedral : 4.245 31.622 661 Min Nonbonded Distance : 2.442 Molprobity Statistics. All-atom Clashscore : 7.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.22 % Favored : 95.78 % Rotamer: Outliers : 2.39 % Allowed : 11.97 % Favored : 85.64 % 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: 0.78 (0.36), residues: 594 helix: 1.23 (0.33), residues: 265 sheet: 1.00 (0.59), residues: 82 loop : -0.37 (0.42), residues: 247 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP C 581 HIS 0.001 0.000 HIS C 420 PHE 0.015 0.001 PHE C 564 TYR 0.017 0.001 TYR A 74 ARG 0.003 0.000 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 57 residues out of total 541 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 44 time to evaluate : 0.944 Fit side-chains REVERT: A 99 ILE cc_start: 0.8309 (OUTLIER) cc_final: 0.7595 (tp) REVERT: B 1 MET cc_start: 0.5294 (tmm) cc_final: 0.4182 (tmm) REVERT: B 74 ARG cc_start: 0.7507 (mtp85) cc_final: 0.7136 (ttm110) outliers start: 13 outliers final: 10 residues processed: 51 average time/residue: 0.2581 time to fit residues: 16.7722 Evaluate side-chains 53 residues out of total 541 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 42 time to evaluate : 0.798 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 73 ILE Chi-restraints excluded: chain A residue 99 ILE Chi-restraints excluded: chain A residue 109 LEU Chi-restraints excluded: chain A residue 123 ILE Chi-restraints excluded: chain B residue 4 PHE Chi-restraints excluded: chain B residue 14 THR Chi-restraints excluded: chain C residue 385 THR Chi-restraints excluded: chain C residue 389 TYR Chi-restraints excluded: chain C residue 442 CYS Chi-restraints excluded: chain C residue 584 LEU Chi-restraints excluded: chain C residue 627 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 58 random chunks: chunk 40 optimal weight: 1.9990 chunk 56 optimal weight: 0.0070 chunk 55 optimal weight: 0.7980 chunk 26 optimal weight: 1.9990 chunk 15 optimal weight: 10.0000 chunk 44 optimal weight: 0.9980 chunk 45 optimal weight: 0.2980 chunk 24 optimal weight: 0.8980 chunk 57 optimal weight: 0.6980 chunk 33 optimal weight: 0.8980 chunk 49 optimal weight: 0.4980 overall best weight: 0.4598 ------------------------------------------------------------------------------- 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 = 0.3955 r_free = 0.3955 target = 0.145488 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3530 r_free = 0.3530 target = 0.111924 restraints weight = 12205.912| |-----------------------------------------------------------------------------| r_work (start): 0.3585 rms_B_bonded: 3.45 r_work: 0.3331 rms_B_bonded: 3.66 restraints_weight: 0.5000 r_work (final): 0.3331 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3331 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3331 r_free = 0.3331 target_work(ls_wunit_k1) = 0.099 | | occupancies: max = 1.00 min = 0.49 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3331 r_free = 0.3331 target_work(ls_wunit_k1) = 0.099 | | occupancies: max = 1.00 min = 0.49 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3331 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8145 moved from start: 0.2180 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 4983 Z= 0.198 Angle : 0.545 12.676 6747 Z= 0.277 Chirality : 0.041 0.172 737 Planarity : 0.004 0.035 873 Dihedral : 4.212 29.841 661 Min Nonbonded Distance : 2.429 Molprobity Statistics. All-atom Clashscore : 6.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.22 % Favored : 95.78 % Rotamer: Outliers : 2.39 % Allowed : 11.97 % Favored : 85.64 % 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: 0.72 (0.36), residues: 594 helix: 1.16 (0.33), residues: 265 sheet: 1.00 (0.58), residues: 82 loop : -0.38 (0.42), residues: 247 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.036 0.002 TRP A 141 HIS 0.003 0.001 HIS A 125 PHE 0.010 0.001 PHE C 564 TYR 0.011 0.001 TYR A 145 ARG 0.008 0.001 ARG A 133 *********************** 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 59 residues out of total 541 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 46 time to evaluate : 0.540 Fit side-chains REVERT: A 74 TYR cc_start: 0.6843 (t80) cc_final: 0.6609 (t80) REVERT: A 99 ILE cc_start: 0.8467 (OUTLIER) cc_final: 0.7785 (tp) REVERT: A 144 LYS cc_start: 0.6651 (pttm) cc_final: 0.6348 (pttt) REVERT: B 1 MET cc_start: 0.6545 (tmm) cc_final: 0.5529 (tmm) REVERT: B 74 ARG cc_start: 0.7305 (mtp85) cc_final: 0.6480 (mtt180) outliers start: 13 outliers final: 11 residues processed: 53 average time/residue: 0.2619 time to fit residues: 17.0476 Evaluate side-chains 56 residues out of total 541 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 44 time to evaluate : 0.592 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 73 ILE Chi-restraints excluded: chain A residue 99 ILE Chi-restraints excluded: chain A residue 109 LEU Chi-restraints excluded: chain A residue 123 ILE Chi-restraints excluded: chain B residue 4 PHE Chi-restraints excluded: chain B residue 14 THR Chi-restraints excluded: chain C residue 385 THR Chi-restraints excluded: chain C residue 389 TYR Chi-restraints excluded: chain C residue 442 CYS Chi-restraints excluded: chain C residue 584 LEU Chi-restraints excluded: chain C residue 587 TRP Chi-restraints excluded: chain C residue 627 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 58 random chunks: chunk 7 optimal weight: 0.6980 chunk 45 optimal weight: 0.7980 chunk 18 optimal weight: 8.9990 chunk 52 optimal weight: 0.9990 chunk 16 optimal weight: 7.9990 chunk 14 optimal weight: 0.9980 chunk 25 optimal weight: 0.8980 chunk 9 optimal weight: 0.9980 chunk 13 optimal weight: 1.9990 chunk 30 optimal weight: 0.0370 chunk 21 optimal weight: 0.8980 overall best weight: 0.6658 ------------------------------------------------------------------------------- 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 = 0.3943 r_free = 0.3943 target = 0.144452 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3518 r_free = 0.3518 target = 0.110819 restraints weight = 12130.824| |-----------------------------------------------------------------------------| r_work (start): 0.3555 rms_B_bonded: 3.75 r_work: 0.3293 rms_B_bonded: 3.79 restraints_weight: 0.5000 r_work (final): 0.3293 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3295 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3295 r_free = 0.3295 target_work(ls_wunit_k1) = 0.096 | | occupancies: max = 1.00 min = 0.49 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3295 r_free = 0.3295 target_work(ls_wunit_k1) = 0.096 | | occupancies: max = 1.00 min = 0.47 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3295 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8179 moved from start: 0.2228 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.028 4983 Z= 0.255 Angle : 0.557 11.777 6747 Z= 0.284 Chirality : 0.042 0.168 737 Planarity : 0.004 0.034 873 Dihedral : 4.340 30.417 661 Min Nonbonded Distance : 2.443 Molprobity Statistics. All-atom Clashscore : 6.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.38 % Favored : 95.62 % Rotamer: Outliers : 2.58 % Allowed : 11.97 % Favored : 85.45 % 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: 0.58 (0.35), residues: 594 helix: 1.02 (0.32), residues: 265 sheet: 0.96 (0.58), residues: 82 loop : -0.43 (0.42), residues: 247 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.063 0.003 TRP A 141 HIS 0.004 0.001 HIS A 75 PHE 0.011 0.001 PHE C 564 TYR 0.010 0.001 TYR A 74 ARG 0.007 0.001 ARG A 143 *********************** 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 59 residues out of total 541 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 45 time to evaluate : 0.814 Fit side-chains REVERT: A 99 ILE cc_start: 0.8514 (OUTLIER) cc_final: 0.7841 (tp) REVERT: B 1 MET cc_start: 0.6453 (tmm) cc_final: 0.5444 (tmm) REVERT: B 74 ARG cc_start: 0.7272 (mtp85) cc_final: 0.6506 (mtt180) outliers start: 14 outliers final: 10 residues processed: 54 average time/residue: 0.2656 time to fit residues: 17.7234 Evaluate side-chains 53 residues out of total 541 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 42 time to evaluate : 0.659 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 73 ILE Chi-restraints excluded: chain A residue 99 ILE Chi-restraints excluded: chain A residue 109 LEU Chi-restraints excluded: chain A residue 123 ILE Chi-restraints excluded: chain B residue 4 PHE Chi-restraints excluded: chain B residue 14 THR Chi-restraints excluded: chain C residue 385 THR Chi-restraints excluded: chain C residue 389 TYR Chi-restraints excluded: chain C residue 442 CYS Chi-restraints excluded: chain C residue 584 LEU Chi-restraints excluded: chain C residue 627 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 58 random chunks: chunk 14 optimal weight: 0.7980 chunk 57 optimal weight: 0.9990 chunk 33 optimal weight: 0.6980 chunk 43 optimal weight: 0.0170 chunk 44 optimal weight: 0.9990 chunk 18 optimal weight: 8.9990 chunk 17 optimal weight: 4.9990 chunk 53 optimal weight: 0.0070 chunk 54 optimal weight: 0.6980 chunk 13 optimal weight: 0.0870 chunk 42 optimal weight: 0.5980 overall best weight: 0.2814 ------------------------------------------------------------------------------- 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 = 0.3975 r_free = 0.3975 target = 0.147017 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3562 r_free = 0.3562 target = 0.112950 restraints weight = 10287.196| |-----------------------------------------------------------------------------| r_work (start): 0.3590 rms_B_bonded: 2.76 r_work: 0.3381 rms_B_bonded: 3.32 restraints_weight: 0.5000 r_work (final): 0.3381 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3383 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3383 r_free = 0.3383 target_work(ls_wunit_k1) = 0.102 | | occupancies: max = 1.00 min = 0.47 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3383 r_free = 0.3383 target_work(ls_wunit_k1) = 0.102 | | occupancies: max = 1.00 min = 0.48 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3383 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8091 moved from start: 0.2293 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.026 4983 Z= 0.150 Angle : 0.539 12.295 6747 Z= 0.274 Chirality : 0.041 0.187 737 Planarity : 0.004 0.036 873 Dihedral : 4.118 26.610 661 Min Nonbonded Distance : 2.448 Molprobity Statistics. All-atom Clashscore : 6.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.54 % Favored : 96.46 % Rotamer: Outliers : 1.84 % Allowed : 12.89 % Favored : 85.27 % 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: 0.70 (0.36), residues: 594 helix: 1.16 (0.33), residues: 265 sheet: 0.92 (0.61), residues: 75 loop : -0.33 (0.42), residues: 254 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.080 0.003 TRP A 141 HIS 0.005 0.001 HIS A 75 PHE 0.008 0.001 PHE C 428 TYR 0.013 0.001 TYR A 74 ARG 0.008 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 54 residues out of total 541 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 44 time to evaluate : 0.661 Fit side-chains REVERT: A 99 ILE cc_start: 0.8413 (OUTLIER) cc_final: 0.7721 (tp) REVERT: A 133 ARG cc_start: 0.7750 (ptt-90) cc_final: 0.7450 (ptt90) REVERT: B 1 MET cc_start: 0.6370 (tmm) cc_final: 0.5331 (tmm) REVERT: B 74 ARG cc_start: 0.7263 (mtp85) cc_final: 0.6919 (ttm110) outliers start: 10 outliers final: 8 residues processed: 49 average time/residue: 0.2871 time to fit residues: 17.2663 Evaluate side-chains 52 residues out of total 541 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 43 time to evaluate : 0.674 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 73 ILE Chi-restraints excluded: chain A residue 99 ILE Chi-restraints excluded: chain A residue 123 ILE Chi-restraints excluded: chain B residue 4 PHE Chi-restraints excluded: chain B residue 14 THR Chi-restraints excluded: chain C residue 385 THR Chi-restraints excluded: chain C residue 389 TYR Chi-restraints excluded: chain C residue 442 CYS Chi-restraints excluded: chain C residue 627 VAL 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: 1.9990 chunk 41 optimal weight: 0.7980 chunk 29 optimal weight: 0.5980 chunk 2 optimal weight: 2.9990 chunk 22 optimal weight: 0.3980 chunk 11 optimal weight: 0.8980 chunk 23 optimal weight: 0.0000 chunk 32 optimal weight: 0.5980 chunk 25 optimal weight: 0.6980 chunk 36 optimal weight: 0.9980 overall best weight: 0.4584 ------------------------------------------------------------------------------- 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 = 0.3966 r_free = 0.3966 target = 0.146129 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3555 r_free = 0.3555 target = 0.112724 restraints weight = 16936.208| |-----------------------------------------------------------------------------| r_work (start): 0.3576 rms_B_bonded: 5.73 r_work: 0.3187 rms_B_bonded: 5.59 restraints_weight: 2.0000 r_work (final): 0.3187 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3190 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3190 r_free = 0.3190 target_work(ls_wunit_k1) = 0.089 | | occupancies: max = 1.00 min = 0.48 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3190 r_free = 0.3190 target_work(ls_wunit_k1) = 0.089 | | occupancies: max = 1.00 min = 0.47 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3190 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8279 moved from start: 0.2334 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.023 4983 Z= 0.193 Angle : 0.552 11.878 6747 Z= 0.281 Chirality : 0.042 0.185 737 Planarity : 0.004 0.041 873 Dihedral : 4.109 26.779 661 Min Nonbonded Distance : 2.453 Molprobity Statistics. All-atom Clashscore : 5.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.22 % Favored : 95.78 % Rotamer: Outliers : 2.03 % Allowed : 13.08 % 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: 0.67 (0.36), residues: 594 helix: 1.08 (0.33), residues: 265 sheet: 1.00 (0.58), residues: 82 loop : -0.36 (0.42), residues: 247 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.108 0.004 TRP A 141 HIS 0.003 0.001 HIS A 75 PHE 0.018 0.001 PHE C 327 TYR 0.023 0.001 TYR A 74 ARG 0.008 0.000 ARG A 143 Origin is already at (0, 0, 0), no shifts will be applied Model does not fit in PDB format. =============================================================================== Job complete usr+sys time: 3044.93 seconds wall clock time: 54 minutes 57.07 seconds (3297.07 seconds total)