Starting phenix.real_space_refine on Fri Aug 22 15:23:41 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9b55_44200/08_2025/9b55_44200.cif Found real_map, /net/cci-nas-00/data/ceres_data/9b55_44200/08_2025/9b55_44200.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.23 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/9b55_44200/08_2025/9b55_44200.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9b55_44200/08_2025/9b55_44200.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9b55_44200/08_2025/9b55_44200.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9b55_44200/08_2025/9b55_44200.map" } resolution = 3.23 write_initial_geo_file = False refinement { macro_cycles = 10 } 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= 0.053 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 3 residue(s): 0.00s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/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: 1.33, per 1000 atoms: 0.27 Number of scatterers: 4871 At special positions: 0 Unit cell: (59.584, 81.928, 105.336, 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: 0.41 Conformation dependent library (CDL) restraints added in 217.1 milliseconds Enol-peptide restraints added in 238.4 nanoseconds 1188 Ramachandran restraints generated. 594 Oldfield, 0 Emsley, 594 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1140 Finding SS restraints... Secondary structure from input PDB file: 28 helices and 6 sheets defined 48.2% alpha, 11.9% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.23 Creating SS restraints... Processing helix chain 'A' and resid 3 through 16 Processing helix chain 'A' and resid 98 through 111 removed outlier: 3.999A 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 145 Processing helix chain 'B' and resid 22 through 35 Processing helix chain 'B' and resid 37 through 41 Processing helix chain 'B' and resid 56 through 60 Processing helix chain 'C' and resid 293 through 306 Processing helix chain 'C' and resid 325 through 335 Processing helix chain 'C' and resid 338 through 343 Processing helix chain 'C' and resid 357 through 374 Processing helix chain 'C' and resid 375 through 379 Processing helix chain 'C' and resid 395 through 400 removed outlier: 3.585A pdb=" N SER C 398 " --> pdb=" O PRO C 395 " (cutoff:3.500A) Processing helix chain 'C' and resid 402 through 420 removed outlier: 4.332A pdb=" N TYR C 406 " --> pdb=" O ASP C 402 " (cutoff:3.500A) Processing helix chain 'C' and resid 429 through 437 removed outlier: 3.753A 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: 3.840A 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: 3.713A pdb=" N ASN C 494 " --> pdb=" O ASN C 491 " (cutoff:3.500A) Processing helix chain 'C' and resid 501 through 515 Processing helix chain 'C' and resid 518 through 531 Processing helix chain 'C' and resid 534 through 539 removed outlier: 3.649A pdb=" N LEU C 538 " --> pdb=" O PRO C 534 " (cutoff:3.500A) removed outlier: 3.535A pdb=" N GLN C 539 " --> pdb=" O ASP C 535 " (cutoff:3.500A) No H-bonds generated for '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: 3.948A pdb=" N PHE C 580 " --> pdb=" O ILE C 576 " (cutoff:3.500A) 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 662 removed outlier: 3.706A 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: 4.145A pdb=" N SER B 65 " --> pdb=" O GLN B 2 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'C' and resid 313 through 321 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 474 through 479 removed outlier: 3.734A 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 568 222 hydrogen bonds defined for protein. 623 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 0.56 Time building geometry restraints manager: 0.54 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.13 - 1.27: 820 1.27 - 1.41: 1241 1.41 - 1.54: 2896 1.54 - 1.68: 2 1.68 - 1.82: 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 3.08e+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 2.79e+00 bond pdb=" C05 A1AIV B 101 " pdb=" N06 A1AIV B 101 " ideal model delta sigma weight residual 1.151 1.131 0.020 2.00e-02 2.50e+03 1.04e+00 bond pdb=" CA VAL A 120 " pdb=" CB VAL A 120 " ideal model delta sigma weight residual 1.540 1.534 0.006 9.00e-03 1.23e+04 4.25e-01 ... (remaining 4978 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.00: 6451 1.00 - 2.00: 228 2.00 - 3.00: 34 3.00 - 4.00: 33 4.00 - 5.00: 1 Bond angle restraints: 6747 Sorted by residual: angle pdb=" N LEU A 89 " pdb=" CA LEU A 89 " pdb=" C LEU A 89 " ideal model delta sigma weight residual 108.24 105.14 3.10 1.32e+00 5.74e-01 5.51e+00 angle pdb=" C ILE A 88 " pdb=" N LEU A 89 " pdb=" CA LEU A 89 " ideal model delta sigma weight residual 122.32 125.55 -3.23 1.76e+00 3.23e-01 3.36e+00 angle pdb=" N ILE A 88 " pdb=" CA ILE A 88 " pdb=" C ILE A 88 " ideal model delta sigma weight residual 111.58 109.70 1.88 1.06e+00 8.90e-01 3.16e+00 angle pdb=" CA VAL A 120 " pdb=" C VAL A 120 " pdb=" O VAL A 120 " ideal model delta sigma weight residual 120.88 119.68 1.20 6.80e-01 2.16e+00 3.12e+00 angle pdb=" N HIS B 68 " pdb=" CA HIS B 68 " pdb=" C HIS B 68 " ideal model delta sigma weight residual 108.90 111.76 -2.86 1.63e+00 3.76e-01 3.07e+00 ... (remaining 6742 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 13.01: 2769 13.01 - 26.02: 199 26.02 - 39.03: 38 39.03 - 52.04: 11 52.04 - 65.05: 1 Dihedral angle restraints: 3018 sinusoidal: 1254 harmonic: 1764 Sorted by residual: dihedral pdb=" CA ASP A 87 " pdb=" C ASP A 87 " pdb=" N ILE A 88 " pdb=" CA ILE A 88 " ideal model delta harmonic sigma weight residual 180.00 152.32 27.68 0 5.00e+00 4.00e-02 3.07e+01 dihedral pdb=" CA LEU B 69 " pdb=" C LEU B 69 " pdb=" N VAL B 70 " pdb=" CA VAL B 70 " ideal model delta harmonic sigma weight residual -180.00 -158.37 -21.63 0 5.00e+00 4.00e-02 1.87e+01 dihedral pdb=" CA VAL C 515 " pdb=" C VAL C 515 " pdb=" N THR C 516 " pdb=" CA THR C 516 " ideal model delta harmonic sigma weight residual -180.00 -161.33 -18.67 0 5.00e+00 4.00e-02 1.39e+01 ... (remaining 3015 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.028: 438 0.028 - 0.056: 205 0.056 - 0.084: 49 0.084 - 0.112: 30 0.112 - 0.140: 15 Chirality restraints: 737 Sorted by residual: chirality pdb=" CA ILE B 36 " pdb=" N ILE B 36 " pdb=" C ILE B 36 " pdb=" CB ILE B 36 " both_signs ideal model delta sigma weight residual False 2.43 2.57 -0.14 2.00e-01 2.50e+01 4.88e-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 4.67e-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 2.57 -0.13 2.00e-01 2.50e+01 4.39e-01 ... (remaining 734 not shown) Planarity restraints: 873 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA LEU B 67 " 0.006 2.00e-02 2.50e+03 1.29e-02 1.67e+00 pdb=" C LEU B 67 " -0.022 2.00e-02 2.50e+03 pdb=" O LEU B 67 " 0.009 2.00e-02 2.50e+03 pdb=" N HIS B 68 " 0.007 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C HIS A 75 " 0.016 5.00e-02 4.00e+02 2.38e-02 9.08e-01 pdb=" N PRO A 76 " -0.041 5.00e-02 4.00e+02 pdb=" CA PRO A 76 " 0.012 5.00e-02 4.00e+02 pdb=" CD PRO A 76 " 0.013 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA VAL B 5 " -0.005 2.00e-02 2.50e+03 9.50e-03 9.02e-01 pdb=" C VAL B 5 " 0.016 2.00e-02 2.50e+03 pdb=" O VAL B 5 " -0.006 2.00e-02 2.50e+03 pdb=" N LYS B 6 " -0.006 2.00e-02 2.50e+03 ... (remaining 870 not shown) Histogram of nonbonded interaction distances: 1.83 - 2.45: 11 2.45 - 3.06: 3323 3.06 - 3.67: 6653 3.67 - 4.29: 10184 4.29 - 4.90: 17785 Nonbonded interactions: 37956 Sorted by model distance: nonbonded pdb=" SG CYS A 85 " pdb=" C03 A1AIV B 101 " model vdw 1.834 3.800 nonbonded pdb=" OD1 ASN B 25 " pdb=" NZ LYS B 29 " model vdw 2.222 3.120 nonbonded pdb=" OD1 ASP C 555 " pdb=" N ILE C 556 " model vdw 2.240 3.120 nonbonded pdb=" N GLU C 664 " pdb=" OE1 GLU C 664 " model vdw 2.300 3.120 nonbonded pdb=" OG SER C 608 " pdb=" OD2 ASP C 612 " model vdw 2.304 3.040 ... (remaining 37951 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=0.45 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: 1.890 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.000 Extract box with map and model: 0.060 Check model and map are aligned: 0.010 Set scattering table: 0.010 Process input model: 5.570 Find NCS groups from input model: 0.020 Set up NCS constraints: 0.010 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.230 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 8.800 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8081 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.118 4985 Z= 0.251 Angle : 0.505 5.004 6747 Z= 0.274 Chirality : 0.040 0.140 737 Planarity : 0.003 0.024 873 Dihedral : 9.785 65.045 1878 Min Nonbonded Distance : 1.834 Molprobity Statistics. All-atom Clashscore : 2.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.55 % Favored : 95.45 % Rotamer: Outliers : 0.18 % Allowed : 3.50 % Favored : 96.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.23 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.82 (0.35), residues: 594 helix: 1.85 (0.35), residues: 242 sheet: 0.58 (0.57), residues: 80 loop : -0.66 (0.38), residues: 272 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG B 42 TYR 0.008 0.001 TYR C 453 PHE 0.009 0.001 PHE C 407 TRP 0.008 0.001 TRP C 581 HIS 0.003 0.001 HIS A 75 Details of bonding type rmsd covalent geometry : bond 0.00414 ( 4983) covalent geometry : angle 0.50493 ( 6747) hydrogen bonds : bond 0.12925 ( 222) hydrogen bonds : angle 6.29748 ( 623) Misc. bond : bond 0.08718 ( 2) *********************** 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 61 residues out of total 541 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 60 time to evaluate : 0.127 Fit side-chains revert: symmetry clash REVERT: A 112 ASP cc_start: 0.8718 (m-30) cc_final: 0.8390 (m-30) REVERT: A 114 ASN cc_start: 0.8851 (t0) cc_final: 0.8519 (t0) REVERT: C 347 LEU cc_start: 0.8753 (tp) cc_final: 0.8488 (tt) outliers start: 1 outliers final: 0 residues processed: 61 average time/residue: 0.0848 time to fit residues: 6.3096 Evaluate side-chains 43 residues out of total 541 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 43 time to evaluate : 0.178 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 58 random chunks: chunk 54 optimal weight: 0.5980 chunk 24 optimal weight: 0.0970 chunk 48 optimal weight: 0.5980 chunk 56 optimal weight: 0.7980 chunk 26 optimal weight: 0.5980 chunk 2 optimal weight: 3.9990 chunk 16 optimal weight: 1.9990 chunk 32 optimal weight: 0.8980 chunk 31 optimal weight: 0.8980 chunk 25 optimal weight: 0.3980 chunk 50 optimal weight: 0.5980 overall best weight: 0.4578 ------------------------------------------------------------------------------- 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 = 0.3671 r_free = 0.3671 target = 0.128977 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3154 r_free = 0.3154 target = 0.089613 restraints weight = 14991.646| |-----------------------------------------------------------------------------| r_work (start): 0.3137 rms_B_bonded: 4.69 r_work (final): 0.3137 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3139 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3139 r_free = 0.3139 target_work(ls_wunit_k1) = 0.088 | | occupancies: max = 1.00 min = 0.45 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3139 r_free = 0.3139 target_work(ls_wunit_k1) = 0.088 | | occupancies: max = 1.00 min = 0.46 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3139 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7888 moved from start: 0.0971 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 4985 Z= 0.143 Angle : 0.533 7.323 6747 Z= 0.275 Chirality : 0.042 0.143 737 Planarity : 0.004 0.032 873 Dihedral : 5.462 86.224 660 Min Nonbonded Distance : 2.411 Molprobity Statistics. All-atom Clashscore : 2.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.22 % Favored : 95.78 % Rotamer: Outliers : 1.10 % Allowed : 7.18 % Favored : 91.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.23 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.20 (0.35), residues: 594 helix: 1.93 (0.34), residues: 245 sheet: 1.03 (0.58), residues: 78 loop : -0.31 (0.39), residues: 271 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG C 351 TYR 0.013 0.001 TYR A 145 PHE 0.010 0.001 PHE C 428 TRP 0.010 0.001 TRP A 93 HIS 0.002 0.001 HIS A 32 Details of bonding type rmsd covalent geometry : bond 0.00349 ( 4983) covalent geometry : angle 0.53269 ( 6747) hydrogen bonds : bond 0.03968 ( 222) hydrogen bonds : angle 4.92139 ( 623) Misc. bond : bond 0.00060 ( 2) *********************** 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 54 residues out of total 541 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 48 time to evaluate : 0.176 Fit side-chains REVERT: A 112 ASP cc_start: 0.8643 (m-30) cc_final: 0.8251 (m-30) REVERT: A 114 ASN cc_start: 0.8964 (t0) cc_final: 0.8626 (t0) REVERT: A 140 GLU cc_start: 0.7934 (mm-30) cc_final: 0.7540 (mm-30) outliers start: 6 outliers final: 3 residues processed: 52 average time/residue: 0.0875 time to fit residues: 5.7138 Evaluate side-chains 48 residues out of total 541 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 45 time to evaluate : 0.169 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 88 ILE Chi-restraints excluded: chain A residue 98 THR Chi-restraints excluded: chain B residue 8 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 58 random chunks: chunk 53 optimal weight: 0.9990 chunk 3 optimal weight: 0.4980 chunk 33 optimal weight: 0.9980 chunk 2 optimal weight: 1.9990 chunk 44 optimal weight: 0.9990 chunk 47 optimal weight: 1.9990 chunk 5 optimal weight: 0.7980 chunk 50 optimal weight: 0.4980 chunk 46 optimal weight: 0.9990 chunk 6 optimal weight: 0.8980 chunk 56 optimal weight: 0.6980 overall best weight: 0.6780 ------------------------------------------------------------------------------- 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 = 0.3658 r_free = 0.3658 target = 0.128247 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3148 r_free = 0.3148 target = 0.089413 restraints weight = 13815.373| |-----------------------------------------------------------------------------| r_work (start): 0.3126 rms_B_bonded: 4.49 r_work: 0.2899 rms_B_bonded: 4.96 restraints_weight: 0.5000 r_work (final): 0.2899 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2924 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2924 r_free = 0.2924 target_work(ls_wunit_k1) = 0.076 | | occupancies: max = 1.00 min = 0.46 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2924 r_free = 0.2924 target_work(ls_wunit_k1) = 0.076 | | occupancies: max = 1.00 min = 0.45 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2924 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7976 moved from start: 0.1141 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 4985 Z= 0.179 Angle : 0.527 6.522 6747 Z= 0.274 Chirality : 0.042 0.144 737 Planarity : 0.004 0.034 873 Dihedral : 5.459 84.613 660 Min Nonbonded Distance : 2.396 Molprobity Statistics. All-atom Clashscore : 3.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.55 % Favored : 95.45 % Rotamer: Outliers : 1.66 % Allowed : 7.00 % Favored : 91.34 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.23 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.02 (0.35), residues: 594 helix: 1.70 (0.33), residues: 254 sheet: 1.07 (0.59), residues: 78 loop : -0.45 (0.40), residues: 262 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG C 351 TYR 0.010 0.001 TYR C 367 PHE 0.009 0.001 PHE C 407 TRP 0.011 0.001 TRP A 93 HIS 0.002 0.001 HIS C 420 Details of bonding type rmsd covalent geometry : bond 0.00443 ( 4983) covalent geometry : angle 0.52715 ( 6747) hydrogen bonds : bond 0.03954 ( 222) hydrogen bonds : angle 4.72055 ( 623) Misc. bond : bond 0.00046 ( 2) *********************** 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 54 residues out of total 541 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 45 time to evaluate : 0.169 Fit side-chains REVERT: A 112 ASP cc_start: 0.8864 (m-30) cc_final: 0.8470 (m-30) REVERT: A 140 GLU cc_start: 0.8333 (mm-30) cc_final: 0.7880 (mm-30) REVERT: C 347 LEU cc_start: 0.8456 (tp) cc_final: 0.8170 (tt) outliers start: 9 outliers final: 5 residues processed: 50 average time/residue: 0.0786 time to fit residues: 4.8817 Evaluate side-chains 45 residues out of total 541 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 40 time to evaluate : 0.199 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 88 ILE Chi-restraints excluded: chain A residue 98 THR Chi-restraints excluded: chain A residue 142 THR Chi-restraints excluded: chain B residue 8 LEU Chi-restraints excluded: chain C residue 389 TYR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 58 random chunks: chunk 44 optimal weight: 0.9990 chunk 50 optimal weight: 0.5980 chunk 29 optimal weight: 0.9990 chunk 49 optimal weight: 0.6980 chunk 47 optimal weight: 1.9990 chunk 45 optimal weight: 0.1980 chunk 39 optimal weight: 0.4980 chunk 40 optimal weight: 3.9990 chunk 33 optimal weight: 0.2980 chunk 22 optimal weight: 0.5980 chunk 52 optimal weight: 0.9990 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 = 0.3566 r_free = 0.3566 target = 0.126692 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3001 r_free = 0.3001 target = 0.083656 restraints weight = 14716.376| |-----------------------------------------------------------------------------| r_work (start): 0.3007 rms_B_bonded: 5.09 r_work (final): 0.3007 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2970 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2970 r_free = 0.2970 target_work(ls_wunit_k1) = 0.082 | | occupancies: max = 1.00 min = 0.45 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2970 r_free = 0.2970 target_work(ls_wunit_k1) = 0.082 | | occupancies: max = 1.00 min = 0.47 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2970 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7750 moved from start: 0.1244 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 4985 Z= 0.133 Angle : 0.488 6.485 6747 Z= 0.255 Chirality : 0.041 0.142 737 Planarity : 0.004 0.035 873 Dihedral : 5.228 76.571 660 Min Nonbonded Distance : 2.428 Molprobity Statistics. All-atom Clashscore : 4.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.88 % Favored : 96.12 % Rotamer: Outliers : 1.29 % Allowed : 8.10 % Favored : 90.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.23 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.18 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.11 (0.36), residues: 594 helix: 1.76 (0.33), residues: 254 sheet: 1.13 (0.59), residues: 78 loop : -0.39 (0.40), residues: 262 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG C 351 TYR 0.013 0.001 TYR A 145 PHE 0.009 0.001 PHE C 522 TRP 0.010 0.001 TRP A 93 HIS 0.002 0.001 HIS C 420 Details of bonding type rmsd covalent geometry : bond 0.00320 ( 4983) covalent geometry : angle 0.48799 ( 6747) hydrogen bonds : bond 0.03549 ( 222) hydrogen bonds : angle 4.54818 ( 623) Misc. bond : bond 0.00072 ( 2) *********************** 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 52 residues out of total 541 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 45 time to evaluate : 0.188 Fit side-chains REVERT: A 112 ASP cc_start: 0.8722 (m-30) cc_final: 0.8265 (m-30) REVERT: A 140 GLU cc_start: 0.7966 (mm-30) cc_final: 0.7709 (mm-30) REVERT: C 347 LEU cc_start: 0.8303 (tp) cc_final: 0.8014 (tt) outliers start: 7 outliers final: 3 residues processed: 50 average time/residue: 0.0747 time to fit residues: 4.7239 Evaluate side-chains 44 residues out of total 541 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 41 time to evaluate : 0.184 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 88 ILE Chi-restraints excluded: chain A residue 98 THR Chi-restraints excluded: chain B residue 8 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 58 random chunks: chunk 30 optimal weight: 0.1980 chunk 26 optimal weight: 1.9990 chunk 41 optimal weight: 0.9990 chunk 18 optimal weight: 0.7980 chunk 15 optimal weight: 2.9990 chunk 10 optimal weight: 0.0980 chunk 9 optimal weight: 0.9980 chunk 42 optimal weight: 0.7980 chunk 47 optimal weight: 0.0050 chunk 52 optimal weight: 0.6980 chunk 2 optimal weight: 3.9990 overall best weight: 0.3594 ------------------------------------------------------------------------------- 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 = 0.3572 r_free = 0.3572 target = 0.127041 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3033 r_free = 0.3033 target = 0.086007 restraints weight = 10401.657| |-----------------------------------------------------------------------------| r_work (start): 0.3043 rms_B_bonded: 4.35 r_work: 0.2819 rms_B_bonded: 4.86 restraints_weight: 0.5000 r_work (final): 0.2819 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2841 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2841 r_free = 0.2841 target_work(ls_wunit_k1) = 0.074 | | occupancies: max = 1.00 min = 0.47 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2841 r_free = 0.2841 target_work(ls_wunit_k1) = 0.074 | | occupancies: max = 1.00 min = 0.46 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2841 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7768 moved from start: 0.1377 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 4985 Z= 0.114 Angle : 0.467 6.870 6747 Z= 0.244 Chirality : 0.041 0.136 737 Planarity : 0.003 0.035 873 Dihedral : 5.010 66.517 660 Min Nonbonded Distance : 2.451 Molprobity Statistics. All-atom Clashscore : 3.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.54 % Favored : 96.46 % Rotamer: Outliers : 1.47 % Allowed : 8.29 % Favored : 90.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.23 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.18 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.20 (0.36), residues: 594 helix: 1.85 (0.33), residues: 253 sheet: 1.20 (0.58), residues: 83 loop : -0.37 (0.41), residues: 258 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG C 351 TYR 0.012 0.001 TYR A 145 PHE 0.009 0.001 PHE C 522 TRP 0.010 0.001 TRP A 93 HIS 0.002 0.000 HIS C 420 Details of bonding type rmsd covalent geometry : bond 0.00274 ( 4983) covalent geometry : angle 0.46736 ( 6747) hydrogen bonds : bond 0.03311 ( 222) hydrogen bonds : angle 4.40863 ( 623) Misc. bond : bond 0.00077 ( 2) *********************** 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 52 residues out of total 541 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 44 time to evaluate : 0.197 Fit side-chains revert: symmetry clash REVERT: A 112 ASP cc_start: 0.8746 (m-30) cc_final: 0.8280 (m-30) REVERT: A 140 GLU cc_start: 0.8309 (mm-30) cc_final: 0.7905 (mm-30) REVERT: B 40 GLN cc_start: 0.8180 (pm20) cc_final: 0.7862 (pm20) outliers start: 8 outliers final: 6 residues processed: 48 average time/residue: 0.0824 time to fit residues: 5.0901 Evaluate side-chains 48 residues out of total 541 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 42 time to evaluate : 0.186 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 88 ILE Chi-restraints excluded: chain A residue 98 THR Chi-restraints excluded: chain A residue 142 THR Chi-restraints excluded: chain B residue 8 LEU Chi-restraints excluded: chain C residue 317 LEU Chi-restraints excluded: chain C residue 389 TYR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 58 random chunks: chunk 35 optimal weight: 0.5980 chunk 34 optimal weight: 0.7980 chunk 21 optimal weight: 1.9990 chunk 24 optimal weight: 1.9990 chunk 26 optimal weight: 0.5980 chunk 37 optimal weight: 0.7980 chunk 29 optimal weight: 0.9990 chunk 23 optimal weight: 0.0370 chunk 1 optimal weight: 0.9980 chunk 5 optimal weight: 0.9980 chunk 4 optimal weight: 0.8980 overall best weight: 0.5658 ------------------------------------------------------------------------------- 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 = 0.3559 r_free = 0.3559 target = 0.125959 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.2996 r_free = 0.2996 target = 0.083503 restraints weight = 13703.740| |-----------------------------------------------------------------------------| r_work (start): 0.3007 rms_B_bonded: 4.89 r_work (final): 0.3007 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3004 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3004 r_free = 0.3004 target_work(ls_wunit_k1) = 0.084 | | occupancies: max = 1.00 min = 0.46 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3004 r_free = 0.3004 target_work(ls_wunit_k1) = 0.084 | | occupancies: max = 1.00 min = 0.46 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3004 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7757 moved from start: 0.1399 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.032 4985 Z= 0.153 Angle : 0.486 6.977 6747 Z= 0.253 Chirality : 0.041 0.136 737 Planarity : 0.004 0.035 873 Dihedral : 4.504 41.516 660 Min Nonbonded Distance : 2.442 Molprobity Statistics. All-atom Clashscore : 3.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.71 % Favored : 96.29 % Rotamer: Outliers : 1.84 % Allowed : 8.66 % Favored : 89.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.23 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.18 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.16 (0.36), residues: 594 helix: 1.80 (0.33), residues: 253 sheet: 1.18 (0.59), residues: 83 loop : -0.39 (0.41), residues: 258 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG C 351 TYR 0.010 0.001 TYR C 367 PHE 0.009 0.001 PHE C 407 TRP 0.009 0.001 TRP A 93 HIS 0.002 0.000 HIS C 420 Details of bonding type rmsd covalent geometry : bond 0.00380 ( 4983) covalent geometry : angle 0.48572 ( 6747) hydrogen bonds : bond 0.03563 ( 222) hydrogen bonds : angle 4.40220 ( 623) Misc. bond : bond 0.00074 ( 2) *********************** 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 51 residues out of total 541 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 41 time to evaluate : 0.183 Fit side-chains revert: symmetry clash REVERT: A 72 ARG cc_start: 0.8173 (mtp-110) cc_final: 0.7806 (mtp85) REVERT: A 112 ASP cc_start: 0.8746 (m-30) cc_final: 0.8248 (m-30) outliers start: 10 outliers final: 6 residues processed: 47 average time/residue: 0.0787 time to fit residues: 4.6563 Evaluate side-chains 47 residues out of total 541 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 41 time to evaluate : 0.183 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 88 ILE Chi-restraints excluded: chain A residue 98 THR Chi-restraints excluded: chain A residue 142 THR Chi-restraints excluded: chain B residue 8 LEU Chi-restraints excluded: chain B residue 70 VAL Chi-restraints excluded: chain C residue 317 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 58 random chunks: chunk 7 optimal weight: 1.9990 chunk 50 optimal weight: 0.5980 chunk 42 optimal weight: 0.9990 chunk 48 optimal weight: 0.9980 chunk 11 optimal weight: 0.7980 chunk 2 optimal weight: 0.0980 chunk 12 optimal weight: 0.5980 chunk 16 optimal weight: 0.3980 chunk 45 optimal weight: 0.0020 chunk 6 optimal weight: 0.8980 chunk 23 optimal weight: 1.9990 overall best weight: 0.3388 ------------------------------------------------------------------------------- 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 = 0.3579 r_free = 0.3579 target = 0.127651 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3019 r_free = 0.3019 target = 0.084966 restraints weight = 13637.814| |-----------------------------------------------------------------------------| r_work (start): 0.3022 rms_B_bonded: 4.92 r_work (final): 0.3022 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3021 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3021 r_free = 0.3021 target_work(ls_wunit_k1) = 0.085 | | occupancies: max = 1.00 min = 0.46 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3021 r_free = 0.3021 target_work(ls_wunit_k1) = 0.085 | | occupancies: max = 1.00 min = 0.46 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3021 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7722 moved from start: 0.1509 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 4985 Z= 0.108 Angle : 0.454 7.090 6747 Z= 0.237 Chirality : 0.040 0.132 737 Planarity : 0.003 0.035 873 Dihedral : 4.282 30.562 660 Min Nonbonded Distance : 2.499 Molprobity Statistics. All-atom Clashscore : 3.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.37 % Favored : 96.63 % Rotamer: Outliers : 1.47 % Allowed : 8.84 % Favored : 89.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.23 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.18 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.28 (0.36), residues: 594 helix: 1.90 (0.34), residues: 253 sheet: 1.23 (0.58), residues: 83 loop : -0.33 (0.41), residues: 258 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG C 351 TYR 0.010 0.001 TYR C 367 PHE 0.009 0.001 PHE C 428 TRP 0.010 0.001 TRP A 93 HIS 0.002 0.000 HIS C 420 Details of bonding type rmsd covalent geometry : bond 0.00257 ( 4983) covalent geometry : angle 0.45377 ( 6747) hydrogen bonds : bond 0.03174 ( 222) hydrogen bonds : angle 4.28053 ( 623) Misc. bond : bond 0.00024 ( 2) *********************** 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 53 residues out of total 541 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 45 time to evaluate : 0.188 Fit side-chains REVERT: A 72 ARG cc_start: 0.8107 (mtp-110) cc_final: 0.7706 (mtp85) REVERT: A 112 ASP cc_start: 0.8631 (m-30) cc_final: 0.8102 (m-30) REVERT: A 140 GLU cc_start: 0.7953 (mm-30) cc_final: 0.7551 (mm-30) REVERT: C 294 MET cc_start: 0.4421 (tpp) cc_final: 0.4001 (tpp) REVERT: C 347 LEU cc_start: 0.8212 (tp) cc_final: 0.8004 (tt) outliers start: 8 outliers final: 6 residues processed: 50 average time/residue: 0.0645 time to fit residues: 4.2692 Evaluate side-chains 49 residues out of total 541 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 43 time to evaluate : 0.187 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 88 ILE Chi-restraints excluded: chain A residue 98 THR Chi-restraints excluded: chain B residue 8 LEU Chi-restraints excluded: chain B residue 36 ILE Chi-restraints excluded: chain B residue 70 VAL Chi-restraints excluded: chain C residue 317 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 58 random chunks: chunk 23 optimal weight: 1.9990 chunk 38 optimal weight: 0.7980 chunk 5 optimal weight: 0.9990 chunk 41 optimal weight: 0.5980 chunk 26 optimal weight: 0.9980 chunk 54 optimal weight: 0.0370 chunk 33 optimal weight: 0.5980 chunk 21 optimal weight: 1.9990 chunk 31 optimal weight: 0.0060 chunk 55 optimal weight: 0.6980 chunk 43 optimal weight: 0.5980 overall best weight: 0.3674 ------------------------------------------------------------------------------- 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 = 0.3580 r_free = 0.3580 target = 0.127438 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3072 r_free = 0.3072 target = 0.089098 restraints weight = 6673.624| |-----------------------------------------------------------------------------| r_work (start): 0.3084 rms_B_bonded: 3.51 r_work: 0.2884 rms_B_bonded: 4.20 restraints_weight: 0.5000 r_work (final): 0.2884 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2901 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2901 r_free = 0.2901 target_work(ls_wunit_k1) = 0.078 | | occupancies: max = 1.00 min = 0.46 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2901 r_free = 0.2901 target_work(ls_wunit_k1) = 0.078 | | occupancies: max = 1.00 min = 0.47 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2901 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7722 moved from start: 0.1549 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 4985 Z= 0.113 Angle : 0.456 6.728 6747 Z= 0.238 Chirality : 0.040 0.142 737 Planarity : 0.003 0.035 873 Dihedral : 4.237 30.986 660 Min Nonbonded Distance : 2.474 Molprobity Statistics. All-atom Clashscore : 3.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.37 % Favored : 96.63 % Rotamer: Outliers : 1.47 % Allowed : 8.84 % Favored : 89.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.23 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.18 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.30 (0.36), residues: 594 helix: 1.93 (0.33), residues: 253 sheet: 1.37 (0.59), residues: 82 loop : -0.37 (0.41), residues: 259 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG C 351 TYR 0.010 0.001 TYR C 367 PHE 0.009 0.001 PHE C 522 TRP 0.009 0.001 TRP A 93 HIS 0.002 0.000 HIS C 420 Details of bonding type rmsd covalent geometry : bond 0.00274 ( 4983) covalent geometry : angle 0.45614 ( 6747) hydrogen bonds : bond 0.03197 ( 222) hydrogen bonds : angle 4.25402 ( 623) Misc. bond : bond 0.00030 ( 2) *********************** 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 49 residues out of total 541 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 41 time to evaluate : 0.153 Fit side-chains revert: symmetry clash REVERT: A 72 ARG cc_start: 0.8489 (mtp-110) cc_final: 0.8121 (mtp85) REVERT: A 112 ASP cc_start: 0.8670 (m-30) cc_final: 0.8154 (m-30) REVERT: A 140 GLU cc_start: 0.8190 (mm-30) cc_final: 0.7755 (mm-30) REVERT: C 347 LEU cc_start: 0.8190 (tp) cc_final: 0.7983 (tt) outliers start: 8 outliers final: 4 residues processed: 45 average time/residue: 0.0784 time to fit residues: 4.4913 Evaluate side-chains 45 residues out of total 541 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 41 time to evaluate : 0.128 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 98 THR Chi-restraints excluded: chain B residue 8 LEU Chi-restraints excluded: chain B residue 36 ILE Chi-restraints excluded: chain B residue 70 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 58 random chunks: chunk 54 optimal weight: 0.5980 chunk 45 optimal weight: 0.6980 chunk 37 optimal weight: 0.7980 chunk 41 optimal weight: 0.8980 chunk 38 optimal weight: 0.5980 chunk 2 optimal weight: 0.5980 chunk 56 optimal weight: 0.2980 chunk 51 optimal weight: 0.2980 chunk 48 optimal weight: 0.9980 chunk 19 optimal weight: 1.9990 chunk 53 optimal weight: 0.0980 overall best weight: 0.3780 ------------------------------------------------------------------------------- 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 = 0.3554 r_free = 0.3554 target = 0.125597 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3031 r_free = 0.3031 target = 0.085805 restraints weight = 10761.447| |-----------------------------------------------------------------------------| r_work (start): 0.3047 rms_B_bonded: 4.26 r_work: 0.2826 rms_B_bonded: 4.84 restraints_weight: 0.5000 r_work (final): 0.2826 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2846 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2846 r_free = 0.2846 target_work(ls_wunit_k1) = 0.074 | | occupancies: max = 1.00 min = 0.47 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2846 r_free = 0.2846 target_work(ls_wunit_k1) = 0.074 | | occupancies: max = 1.00 min = 0.46 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2846 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7750 moved from start: 0.1562 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 4985 Z= 0.113 Angle : 0.456 6.728 6747 Z= 0.238 Chirality : 0.040 0.142 737 Planarity : 0.003 0.035 873 Dihedral : 4.236 30.986 660 Min Nonbonded Distance : 2.474 Molprobity Statistics. All-atom Clashscore : 4.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.37 % Favored : 96.63 % Rotamer: Outliers : 0.92 % Allowed : 9.76 % Favored : 89.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.23 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.18 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.30 (0.36), residues: 594 helix: 1.93 (0.33), residues: 253 sheet: 1.37 (0.59), residues: 82 loop : -0.37 (0.41), residues: 259 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG C 351 TYR 0.010 0.001 TYR C 367 PHE 0.009 0.001 PHE C 522 TRP 0.009 0.001 TRP A 93 HIS 0.002 0.000 HIS C 420 Details of bonding type rmsd covalent geometry : bond 0.00274 ( 4983) covalent geometry : angle 0.45612 ( 6747) hydrogen bonds : bond 0.03197 ( 222) hydrogen bonds : angle 4.25402 ( 623) Misc. bond : bond 0.00031 ( 2) *********************** 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 46 residues out of total 541 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 41 time to evaluate : 0.209 Fit side-chains revert: symmetry clash REVERT: A 72 ARG cc_start: 0.8516 (mtp-110) cc_final: 0.8153 (mtp85) REVERT: A 112 ASP cc_start: 0.8696 (m-30) cc_final: 0.8187 (m-30) REVERT: A 140 GLU cc_start: 0.8220 (mm-30) cc_final: 0.7779 (mm-30) REVERT: C 347 LEU cc_start: 0.8183 (tp) cc_final: 0.7978 (tt) outliers start: 5 outliers final: 5 residues processed: 44 average time/residue: 0.0797 time to fit residues: 4.5559 Evaluate side-chains 46 residues out of total 541 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 41 time to evaluate : 0.174 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 98 THR Chi-restraints excluded: chain B residue 8 LEU Chi-restraints excluded: chain B residue 36 ILE Chi-restraints excluded: chain B residue 70 VAL Chi-restraints excluded: chain C residue 317 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 58 random chunks: chunk 36 optimal weight: 1.9990 chunk 12 optimal weight: 0.3980 chunk 33 optimal weight: 0.9980 chunk 7 optimal weight: 0.6980 chunk 50 optimal weight: 0.8980 chunk 52 optimal weight: 1.9990 chunk 16 optimal weight: 0.7980 chunk 8 optimal weight: 0.8980 chunk 57 optimal weight: 0.9990 chunk 44 optimal weight: 0.9990 chunk 17 optimal weight: 0.5980 overall best weight: 0.6780 ------------------------------------------------------------------------------- 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 = 0.3558 r_free = 0.3558 target = 0.125810 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3005 r_free = 0.3005 target = 0.084329 restraints weight = 11155.029| |-----------------------------------------------------------------------------| r_work (start): 0.3011 rms_B_bonded: 4.47 r_work: 0.2787 rms_B_bonded: 4.97 restraints_weight: 0.5000 r_work (final): 0.2787 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2805 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2805 r_free = 0.2805 target_work(ls_wunit_k1) = 0.072 | | occupancies: max = 1.00 min = 0.46 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2805 r_free = 0.2805 target_work(ls_wunit_k1) = 0.072 | | occupancies: max = 1.00 min = 0.46 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2805 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7815 moved from start: 0.1534 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 4985 Z= 0.175 Angle : 0.496 8.182 6747 Z= 0.257 Chirality : 0.042 0.136 737 Planarity : 0.004 0.034 873 Dihedral : 4.276 29.598 660 Min Nonbonded Distance : 2.414 Molprobity Statistics. All-atom Clashscore : 4.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.05 % Favored : 95.95 % Rotamer: Outliers : 1.10 % Allowed : 9.58 % Favored : 89.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.23 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.13 (0.36), residues: 594 helix: 1.79 (0.33), residues: 254 sheet: 1.30 (0.59), residues: 82 loop : -0.47 (0.41), residues: 258 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG C 351 TYR 0.010 0.001 TYR C 367 PHE 0.012 0.001 PHE C 407 TRP 0.010 0.001 TRP C 581 HIS 0.002 0.001 HIS A 75 Details of bonding type rmsd covalent geometry : bond 0.00439 ( 4983) covalent geometry : angle 0.49559 ( 6747) hydrogen bonds : bond 0.03656 ( 222) hydrogen bonds : angle 4.35803 ( 623) Misc. bond : bond 0.00040 ( 2) ********************** 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 48 residues out of total 541 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 42 time to evaluate : 0.181 Fit side-chains revert: symmetry clash REVERT: A 72 ARG cc_start: 0.8544 (mtp-110) cc_final: 0.8159 (mtp85) REVERT: A 112 ASP cc_start: 0.8741 (m-30) cc_final: 0.8222 (m-30) REVERT: C 294 MET cc_start: 0.4465 (tpp) cc_final: 0.4088 (tpp) REVERT: C 347 LEU cc_start: 0.8208 (tp) cc_final: 0.7999 (tt) outliers start: 6 outliers final: 5 residues processed: 44 average time/residue: 0.0821 time to fit residues: 4.5815 Evaluate side-chains 47 residues out of total 541 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 42 time to evaluate : 0.145 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 98 THR Chi-restraints excluded: chain B residue 8 LEU Chi-restraints excluded: chain B residue 36 ILE Chi-restraints excluded: chain B residue 70 VAL Chi-restraints excluded: chain C residue 317 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 58 random chunks: chunk 5 optimal weight: 0.9980 chunk 20 optimal weight: 0.9990 chunk 2 optimal weight: 0.0060 chunk 28 optimal weight: 0.5980 chunk 51 optimal weight: 0.7980 chunk 7 optimal weight: 0.4980 chunk 9 optimal weight: 0.9990 chunk 26 optimal weight: 0.6980 chunk 8 optimal weight: 0.3980 chunk 54 optimal weight: 0.4980 chunk 4 optimal weight: 0.2980 overall best weight: 0.3396 ------------------------------------------------------------------------------- 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 = 0.3576 r_free = 0.3576 target = 0.127320 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3041 r_free = 0.3041 target = 0.086735 restraints weight = 9180.985| |-----------------------------------------------------------------------------| r_work (start): 0.3046 rms_B_bonded: 4.11 r_work: 0.2830 rms_B_bonded: 4.69 restraints_weight: 0.5000 r_work (final): 0.2830 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2850 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2850 r_free = 0.2850 target_work(ls_wunit_k1) = 0.074 | | occupancies: max = 1.00 min = 0.46 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2850 r_free = 0.2850 target_work(ls_wunit_k1) = 0.074 | | occupancies: max = 1.00 min = 0.46 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2850 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7776 moved from start: 0.1579 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 4985 Z= 0.110 Angle : 0.471 7.895 6747 Z= 0.244 Chirality : 0.040 0.137 737 Planarity : 0.003 0.035 873 Dihedral : 4.251 30.721 660 Min Nonbonded Distance : 2.482 Molprobity Statistics. All-atom Clashscore : 4.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.71 % Favored : 96.29 % Rotamer: Outliers : 0.92 % Allowed : 9.94 % Favored : 89.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.23 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.23 (0.36), residues: 594 helix: 1.85 (0.33), residues: 254 sheet: 1.31 (0.59), residues: 82 loop : -0.39 (0.41), residues: 258 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG C 351 TYR 0.011 0.001 TYR C 389 PHE 0.009 0.001 PHE C 522 TRP 0.008 0.001 TRP C 581 HIS 0.002 0.000 HIS C 420 Details of bonding type rmsd covalent geometry : bond 0.00261 ( 4983) covalent geometry : angle 0.47056 ( 6747) hydrogen bonds : bond 0.03306 ( 222) hydrogen bonds : angle 4.27575 ( 623) Misc. bond : bond 0.00013 ( 2) Origin is already at (0, 0, 0), no shifts will be applied Model does not fit in PDB format. =============================================================================== Job complete usr+sys time: 1099.37 seconds wall clock time: 19 minutes 16.61 seconds (1156.61 seconds total)