Starting phenix.real_space_refine on Thu Mar 6 04:34:07 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9b5b_44206/03_2025/9b5b_44206.cif Found real_map, /net/cci-nas-00/data/ceres_data/9b5b_44206/03_2025/9b5b_44206.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.31 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9b5b_44206/03_2025/9b5b_44206.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9b5b_44206/03_2025/9b5b_44206.map" model { file = "/net/cci-nas-00/data/ceres_data/9b5b_44206/03_2025/9b5b_44206.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9b5b_44206/03_2025/9b5b_44206.cif" } resolution = 3.31 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= 0.044 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-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: 5.49, per 1000 atoms: 1.13 Number of scatterers: 4871 At special positions: 0 Unit cell: (74.48, 82.992, 98.952, 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: 1.40 Conformation dependent library (CDL) restraints added in 879.2 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: 27 helices and 6 sheets defined 48.2% alpha, 11.5% 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: 3.690A 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 56 through 60 Processing helix chain 'C' and resid 293 through 306 Processing helix chain 'C' and resid 307 through 311 removed outlier: 4.119A pdb=" N ALA C 311 " --> pdb=" O PRO C 308 " (cutoff:3.500A) 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 Processing helix chain 'C' and resid 402 through 420 removed outlier: 4.489A pdb=" N TYR C 406 " --> pdb=" O ASP C 402 " (cutoff:3.500A) Processing helix chain 'C' and resid 429 through 437 removed outlier: 3.516A pdb=" N TYR C 433 " --> pdb=" O VAL C 429 " (cutoff:3.500A) Processing helix chain 'C' and resid 442 through 449 Processing helix chain 'C' and resid 450 through 463 Processing helix chain 'C' and resid 491 through 495 removed outlier: 3.807A pdb=" N ASN C 494 " --> pdb=" O ASN C 491 " (cutoff:3.500A) removed outlier: 3.552A 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 531 Processing helix chain 'C' and resid 534 through 539 removed outlier: 3.579A 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 Processing helix chain 'C' and resid 588 through 601 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 663 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 Processing sheet with id=AA3, first strand: chain 'C' and resid 316 through 321 removed outlier: 3.764A 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: 3.699A 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 568 228 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: 1.40 Time building geometry restraints manager: 1.66 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 - 1.40: 1233 1.40 - 1.54: 2853 1.54 - 1.67: 53 1.67 - 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 1.525 -0.072 2.00e-02 2.50e+03 1.30e+01 bond pdb=" N MET A 1 " pdb=" CA MET A 1 " ideal model delta sigma weight residual 1.458 1.491 -0.033 1.90e-02 2.77e+03 2.96e+00 bond pdb=" N MET B 1 " pdb=" CA MET B 1 " ideal model delta sigma weight residual 1.458 1.490 -0.032 1.90e-02 2.77e+03 2.81e+00 bond pdb=" C05 A1AIV B 101 " pdb=" N06 A1AIV B 101 " ideal model delta sigma weight residual 1.151 1.132 0.019 2.00e-02 2.50e+03 9.21e-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 4.11e-01 ... (remaining 4978 not shown) Histogram of bond angle deviations from ideal: 0.00 - 0.77: 6352 0.77 - 1.54: 331 1.54 - 2.31: 29 2.31 - 3.08: 9 3.08 - 3.85: 26 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 109.79 107.61 2.18 1.56e+00 4.11e-01 1.96e+00 angle pdb=" N VAL C 515 " pdb=" CA VAL C 515 " pdb=" C VAL C 515 " ideal model delta sigma weight residual 109.34 111.99 -2.65 2.08e+00 2.31e-01 1.63e+00 angle pdb=" N GLY B 75 " pdb=" CA GLY B 75 " pdb=" C GLY B 75 " ideal model delta sigma weight residual 113.30 109.74 3.56 2.90e+00 1.19e-01 1.51e+00 angle pdb=" C SER A 19 " pdb=" CA SER A 19 " pdb=" CB SER A 19 " ideal model delta sigma weight residual 110.65 108.56 2.09 1.95e+00 2.63e-01 1.15e+00 angle pdb=" N GLY A 82 " pdb=" CA GLY A 82 " pdb=" C GLY A 82 " ideal model delta sigma weight residual 114.95 113.49 1.46 1.41e+00 5.03e-01 1.08e+00 ... (remaining 6742 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 14.30: 2818 14.30 - 28.59: 166 28.59 - 42.89: 30 42.89 - 57.19: 2 57.19 - 71.48: 2 Dihedral angle restraints: 3018 sinusoidal: 1254 harmonic: 1764 Sorted by residual: 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 -163.59 -16.41 0 5.00e+00 4.00e-02 1.08e+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 -81.35 51.35 1 2.00e+01 2.50e-03 9.01e+00 dihedral pdb=" N LEU C 509 " pdb=" CA LEU C 509 " pdb=" CB LEU C 509 " pdb=" CG LEU C 509 " ideal model delta sinusoidal sigma weight residual -60.00 -103.44 43.44 3 1.50e+01 4.44e-03 7.81e+00 ... (remaining 3015 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.028: 450 0.028 - 0.056: 192 0.056 - 0.084: 51 0.084 - 0.112: 30 0.112 - 0.140: 14 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 4.90e-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 4.54e-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 4.06e-01 ... (remaining 734 not shown) Planarity restraints: 873 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C HIS A 75 " 0.023 5.00e-02 4.00e+02 3.43e-02 1.88e+00 pdb=" N PRO A 76 " -0.059 5.00e-02 4.00e+02 pdb=" CA PRO A 76 " 0.018 5.00e-02 4.00e+02 pdb=" CD PRO A 76 " 0.019 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C LEU C 430 " 0.019 5.00e-02 4.00e+02 2.94e-02 1.38e+00 pdb=" N PRO C 431 " -0.051 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 SER A 94 " -0.016 5.00e-02 4.00e+02 2.39e-02 9.18e-01 pdb=" N PRO A 95 " 0.041 5.00e-02 4.00e+02 pdb=" CA PRO A 95 " -0.012 5.00e-02 4.00e+02 pdb=" CD PRO A 95 " -0.013 5.00e-02 4.00e+02 ... (remaining 870 not shown) Histogram of nonbonded interaction distances: 1.78 - 2.41: 6 2.41 - 3.03: 2955 3.03 - 3.65: 6690 3.65 - 4.28: 10351 4.28 - 4.90: 17782 Nonbonded interactions: 37784 Sorted by model distance: nonbonded pdb=" SG CYS C 639 " pdb=" C03 A1AIV B 101 " model vdw 1.782 3.800 nonbonded pdb=" OG SER C 397 " pdb=" OE1 GLN C 521 " model vdw 2.333 3.040 nonbonded pdb=" OG SER C 608 " pdb=" OD2 ASP C 612 " model vdw 2.341 3.040 nonbonded pdb=" OE2 GLU A 9 " pdb=" OH TYR A 60 " model vdw 2.380 3.040 nonbonded pdb=" ND2 ASN C 478 " pdb=" O GLY C 481 " model vdw 2.392 3.120 ... (remaining 37779 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=0.34 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: 2.800 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: 0.190 Check model and map are aligned: 0.030 Set scattering table: 0.050 Process input model: 18.650 Find NCS groups from input model: 0.050 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.950 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 24.760 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7896 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 0.072 4983 Z= 0.203 Angle : 0.435 3.846 6747 Z= 0.217 Chirality : 0.039 0.140 737 Planarity : 0.003 0.034 873 Dihedral : 9.362 71.483 1878 Min Nonbonded Distance : 1.782 Molprobity Statistics. All-atom Clashscore : 2.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.88 % Favored : 96.12 % Rotamer: Outliers : 1.29 % Allowed : 3.87 % Favored : 94.84 % 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: 1.85 (0.37), residues: 594 helix: 2.12 (0.34), residues: 252 sheet: 1.04 (0.56), residues: 97 loop : 0.47 (0.45), residues: 245 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 0.009 0.001 PHE C 580 TYR 0.009 0.001 TYR C 367 ARG 0.002 0.000 ARG C 412 *********************** 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 100 residues out of total 541 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 93 time to evaluate : 0.592 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 34 GLN cc_start: 0.7737 (pt0) cc_final: 0.7533 (tt0) REVERT: A 66 LYS cc_start: 0.8680 (mtpp) cc_final: 0.8160 (tttm) REVERT: A 87 ASP cc_start: 0.8764 (p0) cc_final: 0.8335 (p0) REVERT: A 91 ASP cc_start: 0.8054 (t0) cc_final: 0.7420 (t0) REVERT: A 114 ASN cc_start: 0.7940 (t0) cc_final: 0.6212 (t0) REVERT: A 130 ASP cc_start: 0.7058 (t0) cc_final: 0.6337 (t0) REVERT: A 140 GLU cc_start: 0.8771 (mm-30) cc_final: 0.7906 (mm-30) REVERT: B 1 MET cc_start: 0.1932 (ptt) cc_final: 0.1383 (ptt) REVERT: C 554 ARG cc_start: 0.8647 (ttm110) cc_final: 0.8234 (ttm-80) REVERT: C 640 PHE cc_start: 0.8417 (t80) cc_final: 0.8206 (t80) outliers start: 7 outliers final: 2 residues processed: 99 average time/residue: 0.2603 time to fit residues: 30.7114 Evaluate side-chains 58 residues out of total 541 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 56 time to evaluate : 0.608 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 71 LEU Chi-restraints excluded: chain C residue 587 TRP Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 58 random chunks: chunk 48 optimal weight: 0.5980 chunk 43 optimal weight: 1.9990 chunk 24 optimal weight: 0.0070 chunk 15 optimal weight: 20.0000 chunk 29 optimal weight: 0.9980 chunk 23 optimal weight: 3.9990 chunk 45 optimal weight: 0.6980 chunk 17 optimal weight: 10.0000 chunk 27 optimal weight: 1.9990 chunk 33 optimal weight: 0.5980 chunk 52 optimal weight: 1.9990 overall best weight: 0.5798 ------------------------------------------------------------------------------- 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 = 0.3846 r_free = 0.3846 target = 0.134755 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 65)----------------| | r_work = 0.3189 r_free = 0.3189 target = 0.084760 restraints weight = 13016.768| |-----------------------------------------------------------------------------| r_work (start): 0.3229 rms_B_bonded: 4.45 r_work (final): 0.3229 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3227 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3227 r_free = 0.3227 target_work(ls_wunit_k1) = 0.086 | | occupancies: max = 1.00 min = 0.34 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3227 r_free = 0.3227 target_work(ls_wunit_k1) = 0.086 | | occupancies: max = 1.00 min = 0.38 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3227 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8136 moved from start: 0.1564 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.029 4983 Z= 0.236 Angle : 0.540 6.566 6747 Z= 0.274 Chirality : 0.041 0.133 737 Planarity : 0.004 0.034 873 Dihedral : 4.719 47.745 664 Min Nonbonded Distance : 2.352 Molprobity Statistics. All-atom Clashscore : 5.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.71 % Favored : 96.29 % Rotamer: Outliers : 1.29 % Allowed : 9.21 % Favored : 89.50 % 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: 1.79 (0.37), residues: 594 helix: 2.03 (0.34), residues: 254 sheet: 1.11 (0.56), residues: 95 loop : 0.43 (0.45), residues: 245 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP C 581 HIS 0.002 0.000 HIS C 420 PHE 0.011 0.001 PHE C 522 TYR 0.011 0.001 TYR A 145 ARG 0.006 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 71 residues out of total 541 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 64 time to evaluate : 0.507 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 66 LYS cc_start: 0.8539 (mtpp) cc_final: 0.8319 (tttm) REVERT: A 140 GLU cc_start: 0.8512 (mm-30) cc_final: 0.8042 (mm-30) REVERT: C 554 ARG cc_start: 0.8628 (ttm110) cc_final: 0.8227 (ttm-80) outliers start: 7 outliers final: 7 residues processed: 68 average time/residue: 0.2886 time to fit residues: 24.7936 Evaluate side-chains 54 residues out of total 541 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 47 time to evaluate : 0.623 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 43 SER Chi-restraints excluded: chain A residue 73 ILE Chi-restraints excluded: chain A residue 85 CYS Chi-restraints excluded: chain A residue 142 THR Chi-restraints excluded: chain B residue 71 LEU Chi-restraints excluded: chain C residue 399 VAL 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: 0.5980 chunk 38 optimal weight: 1.9990 chunk 0 optimal weight: 1.9990 chunk 53 optimal weight: 0.0870 chunk 21 optimal weight: 0.9990 chunk 5 optimal weight: 0.8980 chunk 49 optimal weight: 0.5980 chunk 24 optimal weight: 1.9990 chunk 34 optimal weight: 0.9990 chunk 57 optimal weight: 0.8980 chunk 54 optimal weight: 0.9990 overall best weight: 0.6158 ------------------------------------------------------------------------------- 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 = 0.3833 r_free = 0.3833 target = 0.133721 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3190 r_free = 0.3190 target = 0.084831 restraints weight = 10600.039| |-----------------------------------------------------------------------------| r_work (start): 0.3236 rms_B_bonded: 3.97 r_work: 0.3015 rms_B_bonded: 4.76 restraints_weight: 0.5000 r_work (final): 0.3015 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3032 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3032 r_free = 0.3032 target_work(ls_wunit_k1) = 0.075 | | occupancies: max = 1.00 min = 0.38 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3032 r_free = 0.3032 target_work(ls_wunit_k1) = 0.075 | | occupancies: max = 1.00 min = 0.35 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3032 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8229 moved from start: 0.1806 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.031 4983 Z= 0.247 Angle : 0.525 7.213 6747 Z= 0.265 Chirality : 0.041 0.134 737 Planarity : 0.004 0.037 873 Dihedral : 4.760 49.582 664 Min Nonbonded Distance : 2.377 Molprobity Statistics. All-atom Clashscore : 5.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.54 % Favored : 96.46 % Rotamer: Outliers : 1.84 % Allowed : 10.13 % Favored : 88.03 % 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: 1.82 (0.37), residues: 594 helix: 2.07 (0.34), residues: 254 sheet: 1.11 (0.57), residues: 95 loop : 0.42 (0.45), residues: 245 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP C 581 HIS 0.002 0.000 HIS C 420 PHE 0.012 0.001 PHE C 522 TYR 0.010 0.001 TYR A 145 ARG 0.005 0.000 ARG C 349 *********************** 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 59 residues out of total 541 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 49 time to evaluate : 0.803 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 66 LYS cc_start: 0.8849 (mtpp) cc_final: 0.8374 (tttm) REVERT: A 81 ASN cc_start: 0.8718 (m110) cc_final: 0.8425 (m110) REVERT: A 140 GLU cc_start: 0.8877 (mm-30) cc_final: 0.8434 (mm-30) REVERT: C 554 ARG cc_start: 0.8734 (ttm110) cc_final: 0.8367 (ttm-80) outliers start: 10 outliers final: 9 residues processed: 56 average time/residue: 0.3342 time to fit residues: 23.6100 Evaluate side-chains 56 residues out of total 541 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 47 time to evaluate : 0.653 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 43 SER Chi-restraints excluded: chain A residue 85 CYS Chi-restraints excluded: chain A residue 98 THR Chi-restraints excluded: chain B residue 71 LEU Chi-restraints excluded: chain C residue 310 MET Chi-restraints excluded: chain C residue 317 LEU Chi-restraints excluded: chain C residue 399 VAL Chi-restraints excluded: chain C residue 587 TRP Chi-restraints excluded: chain C residue 640 PHE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 58 random chunks: chunk 12 optimal weight: 0.7980 chunk 4 optimal weight: 2.9990 chunk 15 optimal weight: 20.0000 chunk 35 optimal weight: 0.6980 chunk 52 optimal weight: 0.8980 chunk 51 optimal weight: 0.4980 chunk 44 optimal weight: 0.9990 chunk 45 optimal weight: 0.2980 chunk 27 optimal weight: 0.5980 chunk 8 optimal weight: 0.3980 chunk 19 optimal weight: 1.9990 overall best weight: 0.4980 ------------------------------------------------------------------------------- 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 = 0.3834 r_free = 0.3834 target = 0.134013 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3156 r_free = 0.3156 target = 0.082698 restraints weight = 16570.173| |-----------------------------------------------------------------------------| r_work (start): 0.3202 rms_B_bonded: 4.94 r_work (final): 0.3202 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3206 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3206 r_free = 0.3206 target_work(ls_wunit_k1) = 0.084 | | occupancies: max = 1.00 min = 0.35 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3206 r_free = 0.3206 target_work(ls_wunit_k1) = 0.084 | | occupancies: max = 1.00 min = 0.35 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3206 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8168 moved from start: 0.1907 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= 0.206 Angle : 0.503 6.859 6747 Z= 0.255 Chirality : 0.040 0.133 737 Planarity : 0.004 0.051 873 Dihedral : 4.727 50.603 664 Min Nonbonded Distance : 2.420 Molprobity Statistics. All-atom Clashscore : 5.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.20 % Favored : 96.80 % Rotamer: Outliers : 2.21 % Allowed : 10.50 % Favored : 87.29 % 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: 1.90 (0.37), residues: 594 helix: 2.16 (0.34), residues: 254 sheet: 1.13 (0.56), residues: 95 loop : 0.44 (0.45), residues: 245 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 0.010 0.001 PHE C 522 TYR 0.012 0.001 TYR A 145 ARG 0.006 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 61 residues out of total 541 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 49 time to evaluate : 0.591 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 66 LYS cc_start: 0.8526 (mtpp) cc_final: 0.8323 (tttm) REVERT: A 81 ASN cc_start: 0.8679 (m110) cc_final: 0.8413 (m110) REVERT: A 140 GLU cc_start: 0.8534 (mm-30) cc_final: 0.8027 (mm-30) outliers start: 12 outliers final: 10 residues processed: 57 average time/residue: 0.2350 time to fit residues: 16.6975 Evaluate side-chains 53 residues out of total 541 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 43 time to evaluate : 0.543 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 43 SER Chi-restraints excluded: chain A residue 85 CYS Chi-restraints excluded: chain A residue 98 THR Chi-restraints excluded: chain B residue 71 LEU Chi-restraints excluded: chain C residue 310 MET Chi-restraints excluded: chain C residue 317 LEU Chi-restraints excluded: chain C residue 389 TYR Chi-restraints excluded: chain C residue 399 VAL Chi-restraints excluded: chain C residue 587 TRP Chi-restraints excluded: chain C residue 640 PHE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 58 random chunks: chunk 24 optimal weight: 0.5980 chunk 12 optimal weight: 0.5980 chunk 56 optimal weight: 0.9990 chunk 40 optimal weight: 0.0270 chunk 20 optimal weight: 8.9990 chunk 32 optimal weight: 0.6980 chunk 15 optimal weight: 20.0000 chunk 13 optimal weight: 0.9990 chunk 10 optimal weight: 0.0870 chunk 17 optimal weight: 1.9990 chunk 1 optimal weight: 0.1980 overall best weight: 0.3016 ------------------------------------------------------------------------------- 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 = 0.3844 r_free = 0.3844 target = 0.134996 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3190 r_free = 0.3190 target = 0.084692 restraints weight = 21928.198| |-----------------------------------------------------------------------------| r_work (start): 0.3142 rms_B_bonded: 6.17 r_work: 0.2842 rms_B_bonded: 6.11 restraints_weight: 2.0000 r_work (final): 0.2842 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2946 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2946 r_free = 0.2946 target_work(ls_wunit_k1) = 0.070 | | occupancies: max = 1.00 min = 0.35 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2946 r_free = 0.2946 target_work(ls_wunit_k1) = 0.070 | | occupancies: max = 1.00 min = 0.34 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2946 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8193 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 : 0.002 0.031 4983 Z= 0.160 Angle : 0.485 7.126 6747 Z= 0.246 Chirality : 0.039 0.132 737 Planarity : 0.004 0.037 873 Dihedral : 4.676 50.169 664 Min Nonbonded Distance : 2.502 Molprobity Statistics. All-atom Clashscore : 5.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.37 % Favored : 96.63 % Rotamer: Outliers : 2.03 % Allowed : 10.87 % Favored : 87.11 % 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: 1.99 (0.37), residues: 594 helix: 2.20 (0.34), residues: 255 sheet: 1.20 (0.57), residues: 95 loop : 0.51 (0.45), residues: 244 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP C 581 HIS 0.002 0.000 HIS C 420 PHE 0.008 0.001 PHE C 522 TYR 0.007 0.001 TYR C 419 ARG 0.006 0.000 ARG A 72 *********************** 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 60 residues out of total 541 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 49 time to evaluate : 0.531 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 66 LYS cc_start: 0.8914 (mtpp) cc_final: 0.8339 (tttm) REVERT: A 81 ASN cc_start: 0.8720 (m110) cc_final: 0.8469 (m110) REVERT: A 92 GLN cc_start: 0.8886 (mp10) cc_final: 0.8509 (mp10) REVERT: A 140 GLU cc_start: 0.8973 (mm-30) cc_final: 0.8552 (mm-30) REVERT: C 640 PHE cc_start: 0.8632 (OUTLIER) cc_final: 0.7951 (m-80) outliers start: 11 outliers final: 9 residues processed: 55 average time/residue: 0.2238 time to fit residues: 15.2401 Evaluate side-chains 57 residues out of total 541 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 47 time to evaluate : 0.703 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 43 SER Chi-restraints excluded: chain A residue 85 CYS Chi-restraints excluded: chain A residue 98 THR Chi-restraints excluded: chain B residue 71 LEU Chi-restraints excluded: chain C residue 310 MET Chi-restraints excluded: chain C residue 317 LEU Chi-restraints excluded: chain C residue 389 TYR Chi-restraints excluded: chain C residue 399 VAL Chi-restraints excluded: chain C residue 587 TRP Chi-restraints excluded: chain C residue 640 PHE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 58 random chunks: chunk 5 optimal weight: 0.9980 chunk 18 optimal weight: 9.9990 chunk 51 optimal weight: 0.5980 chunk 14 optimal weight: 10.0000 chunk 21 optimal weight: 0.3980 chunk 24 optimal weight: 0.4980 chunk 49 optimal weight: 0.7980 chunk 35 optimal weight: 0.8980 chunk 30 optimal weight: 0.9990 chunk 28 optimal weight: 0.5980 chunk 34 optimal weight: 0.7980 overall best weight: 0.5780 ------------------------------------------------------------------------------- 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 = 0.3831 r_free = 0.3831 target = 0.133821 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3194 r_free = 0.3194 target = 0.085062 restraints weight = 10640.060| |-----------------------------------------------------------------------------| r_work (start): 0.3239 rms_B_bonded: 3.97 r_work: 0.3014 rms_B_bonded: 4.71 restraints_weight: 0.5000 r_work (final): 0.3014 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3029 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3029 r_free = 0.3029 target_work(ls_wunit_k1) = 0.075 | | occupancies: max = 1.00 min = 0.34 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3029 r_free = 0.3029 target_work(ls_wunit_k1) = 0.075 | | occupancies: max = 1.00 min = 0.34 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3029 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8233 moved from start: 0.2035 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= 0.229 Angle : 0.508 7.282 6747 Z= 0.259 Chirality : 0.041 0.169 737 Planarity : 0.004 0.038 873 Dihedral : 4.753 50.805 664 Min Nonbonded Distance : 2.436 Molprobity Statistics. All-atom Clashscore : 5.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.88 % Favored : 96.12 % 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: 1.99 (0.37), residues: 594 helix: 2.26 (0.34), residues: 253 sheet: 1.14 (0.57), residues: 95 loop : 0.49 (0.45), residues: 246 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 0.012 0.001 PHE C 522 TYR 0.008 0.001 TYR C 419 ARG 0.007 0.001 ARG A 139 *********************** 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 60 residues out of total 541 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 48 time to evaluate : 0.583 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 66 LYS cc_start: 0.8883 (mtpp) cc_final: 0.8395 (tttm) REVERT: A 81 ASN cc_start: 0.8666 (m110) cc_final: 0.8412 (m110) REVERT: A 92 GLN cc_start: 0.8945 (mp10) cc_final: 0.8352 (mp10) REVERT: A 140 GLU cc_start: 0.8828 (mm-30) cc_final: 0.8318 (mm-30) REVERT: C 640 PHE cc_start: 0.8583 (OUTLIER) cc_final: 0.7895 (m-80) outliers start: 12 outliers final: 10 residues processed: 54 average time/residue: 0.2255 time to fit residues: 15.6619 Evaluate side-chains 54 residues out of total 541 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 43 time to evaluate : 0.492 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 43 SER Chi-restraints excluded: chain A residue 85 CYS Chi-restraints excluded: chain A residue 98 THR Chi-restraints excluded: chain B residue 7 THR Chi-restraints excluded: chain B residue 71 LEU Chi-restraints excluded: chain C residue 310 MET Chi-restraints excluded: chain C residue 317 LEU Chi-restraints excluded: chain C residue 389 TYR Chi-restraints excluded: chain C residue 399 VAL Chi-restraints excluded: chain C residue 587 TRP Chi-restraints excluded: chain C residue 640 PHE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 58 random chunks: chunk 11 optimal weight: 0.9990 chunk 14 optimal weight: 7.9990 chunk 42 optimal weight: 0.1980 chunk 56 optimal weight: 0.7980 chunk 54 optimal weight: 0.8980 chunk 29 optimal weight: 0.9990 chunk 16 optimal weight: 5.9990 chunk 55 optimal weight: 0.8980 chunk 48 optimal weight: 0.9990 chunk 13 optimal weight: 0.9990 chunk 27 optimal weight: 0.2980 overall best weight: 0.6180 ------------------------------------------------------------------------------- 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 = 0.3829 r_free = 0.3829 target = 0.133637 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3171 r_free = 0.3171 target = 0.083252 restraints weight = 22000.617| |-----------------------------------------------------------------------------| r_work (start): 0.3119 rms_B_bonded: 6.06 r_work (final): 0.3119 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3118 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3118 r_free = 0.3118 target_work(ls_wunit_k1) = 0.081 | | occupancies: max = 1.00 min = 0.34 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3118 r_free = 0.3118 target_work(ls_wunit_k1) = 0.081 | | occupancies: max = 1.00 min = 0.36 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3118 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8081 moved from start: 0.2091 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= 0.241 Angle : 0.511 7.528 6747 Z= 0.260 Chirality : 0.041 0.160 737 Planarity : 0.004 0.038 873 Dihedral : 4.800 51.412 664 Min Nonbonded Distance : 2.439 Molprobity Statistics. All-atom Clashscore : 5.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.55 % Favored : 95.45 % Rotamer: Outliers : 2.39 % Allowed : 10.87 % 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: 1.92 (0.37), residues: 594 helix: 2.22 (0.34), residues: 253 sheet: 1.11 (0.57), residues: 95 loop : 0.44 (0.45), residues: 246 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 0.011 0.001 PHE C 522 TYR 0.009 0.001 TYR C 419 ARG 0.005 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 59 residues out of total 541 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 46 time to evaluate : 0.621 Fit side-chains revert: symmetry clash REVERT: A 66 LYS cc_start: 0.8606 (mtpp) cc_final: 0.8315 (tttm) REVERT: A 81 ASN cc_start: 0.8696 (m110) cc_final: 0.8448 (m110) REVERT: A 92 GLN cc_start: 0.8747 (mp10) cc_final: 0.8165 (mp10) REVERT: A 140 GLU cc_start: 0.8611 (mm-30) cc_final: 0.8113 (mm-30) REVERT: A 143 ARG cc_start: 0.8658 (tmm-80) cc_final: 0.7981 (tmm-80) REVERT: C 640 PHE cc_start: 0.8314 (OUTLIER) cc_final: 0.7569 (m-80) outliers start: 13 outliers final: 10 residues processed: 53 average time/residue: 0.2421 time to fit residues: 16.0085 Evaluate side-chains 54 residues out of total 541 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 43 time to evaluate : 0.586 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 43 SER Chi-restraints excluded: chain A residue 85 CYS Chi-restraints excluded: chain A residue 98 THR Chi-restraints excluded: chain B residue 7 THR Chi-restraints excluded: chain B residue 71 LEU Chi-restraints excluded: chain C residue 310 MET Chi-restraints excluded: chain C residue 317 LEU Chi-restraints excluded: chain C residue 389 TYR Chi-restraints excluded: chain C residue 399 VAL Chi-restraints excluded: chain C residue 587 TRP Chi-restraints excluded: chain C residue 640 PHE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 58 random chunks: chunk 40 optimal weight: 0.6980 chunk 56 optimal weight: 1.9990 chunk 55 optimal weight: 0.4980 chunk 26 optimal weight: 0.9980 chunk 15 optimal weight: 0.9980 chunk 44 optimal weight: 0.9990 chunk 45 optimal weight: 0.0070 chunk 24 optimal weight: 0.7980 chunk 57 optimal weight: 0.8980 chunk 33 optimal weight: 0.6980 chunk 49 optimal weight: 0.6980 overall best weight: 0.5198 ------------------------------------------------------------------------------- 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 = 0.3830 r_free = 0.3830 target = 0.133713 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3170 r_free = 0.3170 target = 0.083653 restraints weight = 13076.826| |-----------------------------------------------------------------------------| r_work (start): 0.3207 rms_B_bonded: 4.40 r_work (final): 0.3207 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3206 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3206 r_free = 0.3206 target_work(ls_wunit_k1) = 0.084 | | occupancies: max = 1.00 min = 0.36 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3206 r_free = 0.3206 target_work(ls_wunit_k1) = 0.084 | | occupancies: max = 1.00 min = 0.34 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3206 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8148 moved from start: 0.2112 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 4983 Z= 0.219 Angle : 0.509 8.058 6747 Z= 0.258 Chirality : 0.040 0.160 737 Planarity : 0.004 0.038 873 Dihedral : 4.808 51.374 664 Min Nonbonded Distance : 2.425 Molprobity Statistics. All-atom Clashscore : 5.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.20 % Favored : 96.80 % 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: 1.95 (0.37), residues: 594 helix: 2.23 (0.34), residues: 253 sheet: 1.13 (0.57), residues: 95 loop : 0.46 (0.45), residues: 246 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 0.011 0.001 PHE C 522 TYR 0.008 0.001 TYR C 419 ARG 0.005 0.000 ARG A 139 *********************** 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 57 residues out of total 541 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 45 time to evaluate : 0.536 Fit side-chains revert: symmetry clash REVERT: A 66 LYS cc_start: 0.8543 (mtpp) cc_final: 0.8322 (tttm) REVERT: A 81 ASN cc_start: 0.8572 (m110) cc_final: 0.8293 (m110) REVERT: A 92 GLN cc_start: 0.8715 (mp10) cc_final: 0.8210 (mp10) REVERT: A 140 GLU cc_start: 0.8477 (mm-30) cc_final: 0.7913 (mm-30) REVERT: A 143 ARG cc_start: 0.8609 (tmm-80) cc_final: 0.7964 (tmm-80) REVERT: C 640 PHE cc_start: 0.8295 (OUTLIER) cc_final: 0.7562 (m-80) outliers start: 12 outliers final: 10 residues processed: 53 average time/residue: 0.1894 time to fit residues: 13.0997 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 : 0.588 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 43 SER Chi-restraints excluded: chain A residue 85 CYS Chi-restraints excluded: chain A residue 98 THR Chi-restraints excluded: chain B residue 7 THR Chi-restraints excluded: chain B residue 71 LEU Chi-restraints excluded: chain C residue 310 MET Chi-restraints excluded: chain C residue 317 LEU Chi-restraints excluded: chain C residue 389 TYR Chi-restraints excluded: chain C residue 399 VAL Chi-restraints excluded: chain C residue 587 TRP Chi-restraints excluded: chain C residue 640 PHE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 58 random chunks: chunk 7 optimal weight: 0.0010 chunk 45 optimal weight: 0.0270 chunk 18 optimal weight: 3.9990 chunk 52 optimal weight: 0.9980 chunk 16 optimal weight: 0.9990 chunk 14 optimal weight: 4.9990 chunk 25 optimal weight: 0.5980 chunk 9 optimal weight: 0.7980 chunk 13 optimal weight: 0.9980 chunk 30 optimal weight: 0.9990 chunk 21 optimal weight: 0.2980 overall best weight: 0.3444 ------------------------------------------------------------------------------- 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 = 0.3837 r_free = 0.3837 target = 0.134318 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3181 r_free = 0.3181 target = 0.084305 restraints weight = 12990.122| |-----------------------------------------------------------------------------| r_work (start): 0.3216 rms_B_bonded: 4.42 r_work (final): 0.3216 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3216 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3216 r_free = 0.3216 target_work(ls_wunit_k1) = 0.085 | | occupancies: max = 1.00 min = 0.34 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3216 r_free = 0.3216 target_work(ls_wunit_k1) = 0.085 | | occupancies: max = 1.00 min = 0.34 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3216 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8134 moved from start: 0.2130 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 4983 Z= 0.173 Angle : 0.499 8.357 6747 Z= 0.253 Chirality : 0.040 0.156 737 Planarity : 0.004 0.037 873 Dihedral : 4.765 51.362 664 Min Nonbonded Distance : 2.480 Molprobity Statistics. All-atom Clashscore : 5.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.20 % Favored : 96.80 % Rotamer: Outliers : 1.84 % Allowed : 11.42 % 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: 1.98 (0.37), residues: 594 helix: 2.24 (0.34), residues: 253 sheet: 1.16 (0.57), residues: 95 loop : 0.49 (0.45), residues: 246 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP C 581 HIS 0.002 0.000 HIS C 420 PHE 0.009 0.001 PHE C 522 TYR 0.007 0.001 TYR C 419 ARG 0.003 0.000 ARG A 139 *********************** 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 52 residues out of total 541 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 42 time to evaluate : 0.625 Fit side-chains revert: symmetry clash REVERT: A 66 LYS cc_start: 0.8548 (mtpp) cc_final: 0.8287 (tttm) REVERT: A 81 ASN cc_start: 0.8541 (m110) cc_final: 0.8259 (m110) REVERT: A 92 GLN cc_start: 0.8708 (mp10) cc_final: 0.8189 (mp10) REVERT: A 140 GLU cc_start: 0.8582 (mm-30) cc_final: 0.8043 (mm-30) REVERT: A 143 ARG cc_start: 0.8638 (tmm-80) cc_final: 0.7997 (tmm-80) REVERT: C 640 PHE cc_start: 0.8276 (OUTLIER) cc_final: 0.7593 (m-80) outliers start: 10 outliers final: 9 residues processed: 48 average time/residue: 0.2261 time to fit residues: 14.5186 Evaluate side-chains 52 residues out of total 541 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 42 time to evaluate : 0.683 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 43 SER Chi-restraints excluded: chain A residue 85 CYS Chi-restraints excluded: chain A residue 98 THR Chi-restraints excluded: chain B residue 7 THR Chi-restraints excluded: chain B residue 71 LEU Chi-restraints excluded: chain C residue 310 MET Chi-restraints excluded: chain C residue 317 LEU Chi-restraints excluded: chain C residue 389 TYR Chi-restraints excluded: chain C residue 587 TRP Chi-restraints excluded: chain C residue 640 PHE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 58 random chunks: chunk 14 optimal weight: 0.9980 chunk 57 optimal weight: 0.7980 chunk 33 optimal weight: 0.3980 chunk 43 optimal weight: 0.8980 chunk 44 optimal weight: 0.6980 chunk 18 optimal weight: 6.9990 chunk 17 optimal weight: 0.0670 chunk 53 optimal weight: 0.2980 chunk 54 optimal weight: 0.7980 chunk 13 optimal weight: 0.5980 chunk 42 optimal weight: 0.7980 overall best weight: 0.4118 ------------------------------------------------------------------------------- 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 = 0.3837 r_free = 0.3837 target = 0.134333 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 65)----------------| | r_work = 0.3194 r_free = 0.3194 target = 0.085117 restraints weight = 11127.655| |-----------------------------------------------------------------------------| r_work (start): 0.3229 rms_B_bonded: 4.12 r_work: 0.3001 rms_B_bonded: 4.85 restraints_weight: 0.5000 r_work (final): 0.3001 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3036 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3036 r_free = 0.3036 target_work(ls_wunit_k1) = 0.075 | | occupancies: max = 1.00 min = 0.34 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3036 r_free = 0.3036 target_work(ls_wunit_k1) = 0.075 | | occupancies: max = 1.00 min = 0.34 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3036 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8227 moved from start: 0.2142 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.050 4983 Z= 0.191 Angle : 0.506 8.538 6747 Z= 0.256 Chirality : 0.040 0.155 737 Planarity : 0.004 0.037 873 Dihedral : 4.750 51.711 664 Min Nonbonded Distance : 2.447 Molprobity Statistics. All-atom Clashscore : 5.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.04 % Favored : 96.96 % Rotamer: Outliers : 1.84 % Allowed : 11.42 % 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: 1.99 (0.37), residues: 594 helix: 2.25 (0.34), residues: 253 sheet: 1.17 (0.57), residues: 95 loop : 0.49 (0.45), residues: 246 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP C 581 HIS 0.002 0.000 HIS C 420 PHE 0.009 0.001 PHE C 522 TYR 0.008 0.001 TYR C 419 ARG 0.004 0.000 ARG A 139 ********************** 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 52 residues out of total 541 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 42 time to evaluate : 0.787 Fit side-chains revert: symmetry clash REVERT: A 66 LYS cc_start: 0.8907 (mtpp) cc_final: 0.8356 (tttm) REVERT: A 81 ASN cc_start: 0.8557 (m110) cc_final: 0.8261 (m110) REVERT: A 92 GLN cc_start: 0.8925 (mp10) cc_final: 0.8419 (mp10) REVERT: A 140 GLU cc_start: 0.8905 (mm-30) cc_final: 0.8373 (mm-30) REVERT: A 143 ARG cc_start: 0.8751 (tmm-80) cc_final: 0.8120 (tmm-80) REVERT: C 640 PHE cc_start: 0.8542 (OUTLIER) cc_final: 0.7929 (m-80) outliers start: 10 outliers final: 9 residues processed: 48 average time/residue: 0.2435 time to fit residues: 15.1057 Evaluate side-chains 52 residues out of total 541 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 42 time to evaluate : 0.555 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 43 SER Chi-restraints excluded: chain A residue 85 CYS Chi-restraints excluded: chain A residue 98 THR Chi-restraints excluded: chain B residue 7 THR Chi-restraints excluded: chain B residue 71 LEU Chi-restraints excluded: chain C residue 310 MET Chi-restraints excluded: chain C residue 317 LEU Chi-restraints excluded: chain C residue 389 TYR Chi-restraints excluded: chain C residue 587 TRP Chi-restraints excluded: chain C residue 640 PHE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 58 random chunks: chunk 21 optimal weight: 0.3980 chunk 53 optimal weight: 0.6980 chunk 41 optimal weight: 0.0980 chunk 29 optimal weight: 0.9990 chunk 2 optimal weight: 2.9990 chunk 22 optimal weight: 0.1980 chunk 11 optimal weight: 0.9980 chunk 23 optimal weight: 1.9990 chunk 32 optimal weight: 0.4980 chunk 25 optimal weight: 0.7980 chunk 36 optimal weight: 0.0060 overall best weight: 0.2396 ------------------------------------------------------------------------------- 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 = 0.3853 r_free = 0.3853 target = 0.135531 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 60)----------------| | r_work = 0.3182 r_free = 0.3182 target = 0.084051 restraints weight = 18148.194| |-----------------------------------------------------------------------------| r_work (start): 0.3210 rms_B_bonded: 5.18 r_work (final): 0.3210 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3208 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3208 r_free = 0.3208 target_work(ls_wunit_k1) = 0.085 | | occupancies: max = 1.00 min = 0.34 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3208 r_free = 0.3208 target_work(ls_wunit_k1) = 0.085 | | occupancies: max = 1.00 min = 0.35 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3208 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8123 moved from start: 0.2176 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.041 4983 Z= 0.150 Angle : 0.488 9.166 6747 Z= 0.247 Chirality : 0.039 0.152 737 Planarity : 0.004 0.036 873 Dihedral : 4.624 51.722 664 Min Nonbonded Distance : 2.483 Molprobity Statistics. All-atom Clashscore : 5.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.20 % Favored : 96.80 % Rotamer: Outliers : 1.84 % Allowed : 11.42 % 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: 2.13 (0.38), residues: 594 helix: 2.37 (0.34), residues: 254 sheet: 1.27 (0.57), residues: 95 loop : 0.55 (0.45), residues: 245 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 0.006 0.001 PHE C 428 TYR 0.007 0.001 TYR C 419 ARG 0.004 0.000 ARG A 139 Origin is already at (0, 0, 0), no shifts will be applied Model does not fit in PDB format. =============================================================================== Job complete usr+sys time: 3206.99 seconds wall clock time: 57 minutes 25.02 seconds (3445.02 seconds total)