Starting phenix.real_space_refine on Wed Sep 17 05:14:33 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9b58_44203/09_2025/9b58_44203.cif Found real_map, /net/cci-nas-00/data/ceres_data/9b58_44203/09_2025/9b58_44203.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.39 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/9b58_44203/09_2025/9b58_44203.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9b58_44203/09_2025/9b58_44203.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9b58_44203/09_2025/9b58_44203.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9b58_44203/09_2025/9b58_44203.map" } resolution = 3.39 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= 0.041 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 14 5.16 5 C 3110 2.51 5 N 824 2.21 5 O 923 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 1 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5805/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: 2.15, per 1000 atoms: 0.44 Number of scatterers: 4871 At special positions: 0 Unit cell: (69.16, 82.992, 101.08, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 14 16.00 O 923 8.00 N 824 7.00 C 3110 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=2, symmetry=0 Number of additional bonds: simple=2, symmetry=0 Coordination: Other bonds: Time building additional restraints: 0.56 Conformation dependent library (CDL) restraints added in 319.7 milliseconds Enol-peptide restraints added in 953.7 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: 30 helices and 6 sheets defined 50.3% alpha, 12.2% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.34 Creating SS restraints... Processing helix chain 'A' and resid 3 through 16 Processing helix chain 'A' and resid 86 through 91 Processing helix chain 'A' and resid 98 through 110 removed outlier: 4.094A pdb=" N VAL A 102 " --> pdb=" O THR A 98 " (cutoff:3.500A) Processing helix chain 'A' and resid 120 through 130 Processing helix chain 'A' and resid 130 through 146 Processing helix chain 'B' and resid 22 through 35 Processing helix chain 'B' and resid 37 through 41 Processing helix chain 'B' and resid 56 through 60 Processing helix chain 'C' and resid 293 through 306 Processing helix chain 'C' and resid 307 through 311 removed outlier: 4.057A pdb=" N ALA C 311 " --> pdb=" O PRO C 308 " (cutoff:3.500A) Processing helix chain 'C' and resid 325 through 335 removed outlier: 3.518A pdb=" N SER C 335 " --> pdb=" O TYR C 331 " (cutoff:3.500A) Processing helix chain 'C' and resid 338 through 343 Processing helix chain 'C' and resid 357 through 374 removed outlier: 3.518A pdb=" N PHE C 374 " --> pdb=" O SER C 370 " (cutoff:3.500A) Processing helix chain 'C' and resid 375 through 379 Processing helix chain 'C' and resid 395 through 400 removed outlier: 3.582A pdb=" N SER C 398 " --> pdb=" O PRO C 395 " (cutoff:3.500A) Processing helix chain 'C' and resid 402 through 420 removed outlier: 4.395A pdb=" N TYR C 406 " --> pdb=" O ASP C 402 " (cutoff:3.500A) Processing helix chain 'C' and resid 429 through 437 removed outlier: 3.567A pdb=" N TYR C 433 " --> pdb=" O VAL C 429 " (cutoff:3.500A) Processing helix chain 'C' and resid 442 through 444 No H-bonds generated for 'chain 'C' and resid 442 through 444' Processing helix chain 'C' and resid 445 through 450 removed outlier: 3.857A pdb=" N VAL C 449 " --> pdb=" O ASP C 445 " (cutoff:3.500A) Processing helix chain 'C' and resid 450 through 463 Processing helix chain 'C' and resid 491 through 495 removed outlier: 3.820A pdb=" N ASN C 494 " --> pdb=" O ASN C 491 " (cutoff:3.500A) removed outlier: 3.671A pdb=" N ILE C 495 " --> pdb=" O GLY C 492 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 491 through 495' Processing helix chain 'C' and resid 501 through 515 Processing helix chain 'C' and resid 518 through 533 removed outlier: 4.284A pdb=" N LEU C 532 " --> pdb=" O GLY C 528 " (cutoff:3.500A) Processing helix chain 'C' and resid 534 through 539 Processing helix chain 'C' and resid 544 through 552 Processing helix chain 'C' and resid 558 through 564 Processing helix chain 'C' and resid 574 through 586 removed outlier: 3.937A pdb=" N PHE C 580 " --> pdb=" O ILE C 576 " (cutoff:3.500A) Processing helix chain 'C' and resid 588 through 600 Processing helix chain 'C' and resid 638 through 640 No H-bonds generated for 'chain 'C' and resid 638 through 640' Processing helix chain 'C' and resid 650 through 662 removed outlier: 3.591A pdb=" N ILE C 662 " --> pdb=" O LEU C 658 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 22 through 25 Processing sheet with id=AA2, first strand: chain 'B' and resid 12 through 16 removed outlier: 3.885A pdb=" N SER B 65 " --> pdb=" O GLN B 2 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'C' and resid 316 through 321 removed outlier: 3.703A pdb=" N VAL C 321 " --> pdb=" O ARG C 349 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'C' and resid 381 through 385 removed outlier: 6.764A pdb=" N GLY C 390 " --> pdb=" O ALA C 384 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'C' and resid 474 through 479 Processing sheet with id=AA6, first strand: chain 'C' and resid 565 through 568 224 hydrogen bonds defined for protein. 626 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 0.74 Time building geometry restraints manager: 0.73 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.13 - 1.27: 820 1.27 - 1.41: 1234 1.41 - 1.54: 2889 1.54 - 1.68: 16 1.68 - 1.81: 24 Bond restraints: 4983 Sorted by residual: bond pdb=" C04 A1AIV B 101 " pdb=" C05 A1AIV B 101 " ideal model delta sigma weight residual 1.453 1.527 -0.074 2.00e-02 2.50e+03 1.36e+01 bond pdb=" N MET B 1 " pdb=" CA MET B 1 " ideal model delta sigma weight residual 1.458 1.489 -0.031 1.90e-02 2.77e+03 2.75e+00 bond pdb=" N MET A 1 " pdb=" CA MET A 1 " ideal model delta sigma weight residual 1.458 1.489 -0.031 1.90e-02 2.77e+03 2.69e+00 bond pdb=" C05 A1AIV B 101 " pdb=" N06 A1AIV B 101 " ideal model delta sigma weight residual 1.151 1.133 0.018 2.00e-02 2.50e+03 8.00e-01 bond pdb=" CG LEU C 595 " pdb=" CD2 LEU C 595 " ideal model delta sigma weight residual 1.521 1.500 0.021 3.30e-02 9.18e+02 4.21e-01 ... (remaining 4978 not shown) Histogram of bond angle deviations from ideal: 0.00 - 0.78: 6321 0.78 - 1.56: 350 1.56 - 2.34: 36 2.34 - 3.12: 13 3.12 - 3.90: 27 Bond angle restraints: 6747 Sorted by residual: angle pdb=" N LEU C 424 " pdb=" CA LEU C 424 " pdb=" C LEU C 424 " ideal model delta sigma weight residual 110.35 108.22 2.13 1.38e+00 5.25e-01 2.39e+00 angle pdb=" N VAL C 515 " pdb=" CA VAL C 515 " pdb=" C VAL C 515 " ideal model delta sigma weight residual 109.34 111.91 -2.57 2.08e+00 2.31e-01 1.52e+00 angle pdb=" CA TRP C 561 " pdb=" CB TRP C 561 " pdb=" CG TRP C 561 " ideal model delta sigma weight residual 113.60 115.65 -2.05 1.90e+00 2.77e-01 1.16e+00 angle pdb=" C LEU A 89 " pdb=" N ARG A 90 " pdb=" CA ARG A 90 " ideal model delta sigma weight residual 121.54 119.51 2.03 1.91e+00 2.74e-01 1.13e+00 angle pdb=" N SER C 569 " pdb=" CA SER C 569 " pdb=" CB SER C 569 " ideal model delta sigma weight residual 112.78 111.20 1.58 1.53e+00 4.27e-01 1.06e+00 ... (remaining 6742 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 15.54: 2802 15.54 - 31.07: 186 31.07 - 46.61: 24 46.61 - 62.15: 4 62.15 - 77.68: 2 Dihedral angle restraints: 3018 sinusoidal: 1254 harmonic: 1764 Sorted by residual: dihedral pdb=" CA TYR A 145 " pdb=" C TYR A 145 " pdb=" N ALA A 146 " pdb=" CA ALA A 146 " ideal model delta harmonic sigma weight residual 180.00 -161.78 -18.22 0 5.00e+00 4.00e-02 1.33e+01 dihedral pdb=" CA TYR C 423 " pdb=" C TYR C 423 " pdb=" N LEU C 424 " pdb=" CA LEU C 424 " ideal model delta harmonic sigma weight residual 180.00 163.25 16.75 0 5.00e+00 4.00e-02 1.12e+01 dihedral pdb=" CA LEU A 119 " pdb=" C LEU A 119 " pdb=" N VAL A 120 " pdb=" CA VAL A 120 " ideal model delta harmonic sigma weight residual 180.00 164.00 16.00 0 5.00e+00 4.00e-02 1.02e+01 ... (remaining 3015 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.028: 441 0.028 - 0.055: 197 0.055 - 0.082: 57 0.082 - 0.110: 27 0.110 - 0.137: 15 Chirality restraints: 737 Sorted by residual: chirality pdb=" CA ILE A 54 " pdb=" N ILE A 54 " pdb=" C ILE A 54 " pdb=" CB ILE A 54 " both_signs ideal model delta sigma weight residual False 2.43 2.57 -0.14 2.00e-01 2.50e+01 4.72e-01 chirality pdb=" CA ILE C 533 " pdb=" N ILE C 533 " pdb=" C ILE C 533 " pdb=" CB ILE C 533 " both_signs ideal model delta sigma weight residual False 2.43 2.57 -0.14 2.00e-01 2.50e+01 4.62e-01 chirality pdb=" CA ILE C 645 " pdb=" N ILE C 645 " pdb=" C ILE C 645 " pdb=" CB ILE C 645 " both_signs ideal model delta sigma weight residual False 2.43 2.56 -0.13 2.00e-01 2.50e+01 4.14e-01 ... (remaining 734 not shown) Planarity restraints: 873 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ASP A 117 " -0.022 5.00e-02 4.00e+02 3.32e-02 1.76e+00 pdb=" N PRO A 118 " 0.057 5.00e-02 4.00e+02 pdb=" CA PRO A 118 " -0.017 5.00e-02 4.00e+02 pdb=" CD PRO A 118 " -0.018 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C LEU C 430 " 0.020 5.00e-02 4.00e+02 2.98e-02 1.42e+00 pdb=" N PRO C 431 " -0.052 5.00e-02 4.00e+02 pdb=" CA PRO C 431 " 0.015 5.00e-02 4.00e+02 pdb=" CD PRO C 431 " 0.017 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C PRO C 646 " -0.018 5.00e-02 4.00e+02 2.80e-02 1.26e+00 pdb=" N PRO C 647 " 0.048 5.00e-02 4.00e+02 pdb=" CA PRO C 647 " -0.014 5.00e-02 4.00e+02 pdb=" CD PRO C 647 " -0.016 5.00e-02 4.00e+02 ... (remaining 870 not shown) Histogram of nonbonded interaction distances: 1.81 - 2.43: 16 2.43 - 3.05: 3104 3.05 - 3.66: 6734 3.66 - 4.28: 10344 4.28 - 4.90: 17704 Nonbonded interactions: 37902 Sorted by model distance: nonbonded pdb=" SG CYS C 639 " pdb=" C03 A1AIV B 101 " model vdw 1.812 3.800 nonbonded pdb=" OD1 ASN B 25 " pdb=" NZ LYS B 29 " model vdw 2.221 3.120 nonbonded pdb=" OG SER C 608 " pdb=" OD2 ASP C 612 " model vdw 2.303 3.040 nonbonded pdb=" OG SER C 397 " pdb=" OE1 GLN C 521 " model vdw 2.304 3.040 nonbonded pdb=" OD1 ASN C 478 " pdb=" OG SER C 483 " model vdw 2.316 3.040 ... (remaining 37897 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=0.39 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 3.250 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: 0.090 Check model and map are aligned: 0.010 Set scattering table: 0.020 Process input model: 8.250 Find NCS groups from input model: 0.020 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: 0.000 Load rotamer database and sin/cos tables:1.360 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 13.030 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7794 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.107 4985 Z= 0.194 Angle : 0.453 3.898 6747 Z= 0.226 Chirality : 0.039 0.137 737 Planarity : 0.003 0.033 873 Dihedral : 10.328 77.683 1878 Min Nonbonded Distance : 1.812 Molprobity Statistics. All-atom Clashscore : 3.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.22 % Favored : 95.78 % Rotamer: Outliers : 1.10 % Allowed : 6.08 % Favored : 92.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.23 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z 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: 0.81 (0.37), residues: 594 helix: 1.28 (0.33), residues: 257 sheet: 0.66 (0.61), residues: 85 loop : -0.19 (0.43), residues: 252 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG C 404 TYR 0.010 0.001 TYR C 367 PHE 0.009 0.001 PHE C 407 TRP 0.006 0.001 TRP C 581 HIS 0.001 0.000 HIS A 125 Details of bonding type rmsd covalent geometry : bond 0.00261 ( 4983) covalent geometry : angle 0.45320 ( 6747) hydrogen bonds : bond 0.13788 ( 224) hydrogen bonds : angle 5.53918 ( 626) Misc. bond : bond 0.07835 ( 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 75 residues out of total 541 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 69 time to evaluate : 0.200 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 131 ARG cc_start: 0.7889 (tpp80) cc_final: 0.7679 (ttt90) REVERT: C 318 GLN cc_start: 0.8449 (pt0) cc_final: 0.8232 (pm20) REVERT: C 347 LEU cc_start: 0.8076 (tp) cc_final: 0.7834 (mt) outliers start: 6 outliers final: 2 residues processed: 73 average time/residue: 0.1316 time to fit residues: 11.3270 Evaluate side-chains 50 residues out of total 541 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 48 time to evaluate : 0.215 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 73 ILE Chi-restraints excluded: chain C residue 385 THR Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 58 random chunks: chunk 54 optimal weight: 1.9990 chunk 24 optimal weight: 1.9990 chunk 48 optimal weight: 0.7980 chunk 56 optimal weight: 0.5980 chunk 26 optimal weight: 0.9990 chunk 2 optimal weight: 0.8980 chunk 16 optimal weight: 3.9990 chunk 32 optimal weight: 0.5980 chunk 31 optimal weight: 0.9990 chunk 25 optimal weight: 0.9980 chunk 50 optimal weight: 0.0010 overall best weight: 0.5786 ------------------------------------------------------------------------------- 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 = 0.3990 r_free = 0.3990 target = 0.147676 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 28)----------------| | r_work = 0.3577 r_free = 0.3577 target = 0.113858 restraints weight = 16576.920| |-----------------------------------------------------------------------------| r_work (start): 0.3570 rms_B_bonded: 5.27 r_work (final): 0.3570 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3569 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3569 r_free = 0.3569 target_work(ls_wunit_k1) = 0.114 | | occupancies: max = 1.00 min = 0.39 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3569 r_free = 0.3569 target_work(ls_wunit_k1) = 0.114 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3569 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7898 moved from start: 0.1407 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 4985 Z= 0.152 Angle : 0.546 8.363 6747 Z= 0.281 Chirality : 0.041 0.148 737 Planarity : 0.004 0.043 873 Dihedral : 4.475 40.831 663 Min Nonbonded Distance : 2.477 Molprobity Statistics. All-atom Clashscore : 6.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.72 % Favored : 95.28 % Rotamer: Outliers : 1.47 % Allowed : 10.31 % Favored : 88.21 % 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: 0.76 (0.36), residues: 594 helix: 1.20 (0.33), residues: 262 sheet: 0.80 (0.61), residues: 82 loop : -0.25 (0.43), residues: 250 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG C 568 TYR 0.008 0.001 TYR C 419 PHE 0.016 0.001 PHE C 564 TRP 0.008 0.001 TRP C 581 HIS 0.002 0.001 HIS C 420 Details of bonding type rmsd covalent geometry : bond 0.00365 ( 4983) covalent geometry : angle 0.54586 ( 6747) hydrogen bonds : bond 0.03794 ( 224) hydrogen bonds : angle 4.62983 ( 626) Misc. bond : bond 0.00040 ( 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 65 residues out of total 541 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 57 time to evaluate : 0.216 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 572 GLU cc_start: 0.7535 (tp30) cc_final: 0.7208 (tp30) outliers start: 8 outliers final: 6 residues processed: 61 average time/residue: 0.1024 time to fit residues: 7.7301 Evaluate side-chains 53 residues out of total 541 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 47 time to evaluate : 0.138 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 73 ILE Chi-restraints excluded: chain B residue 4 PHE Chi-restraints excluded: chain C residue 310 MET Chi-restraints excluded: chain C residue 385 THR Chi-restraints excluded: chain C residue 389 TYR Chi-restraints excluded: chain C residue 627 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 58 random chunks: chunk 53 optimal weight: 0.5980 chunk 3 optimal weight: 1.9990 chunk 33 optimal weight: 0.2980 chunk 2 optimal weight: 0.9990 chunk 44 optimal weight: 0.7980 chunk 47 optimal weight: 0.0770 chunk 5 optimal weight: 0.5980 chunk 50 optimal weight: 0.9990 chunk 46 optimal weight: 0.5980 chunk 6 optimal weight: 0.7980 chunk 56 optimal weight: 0.9980 overall best weight: 0.4338 ------------------------------------------------------------------------------- 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 = 0.3992 r_free = 0.3992 target = 0.148152 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3553 r_free = 0.3553 target = 0.113965 restraints weight = 15226.739| |-----------------------------------------------------------------------------| r_work (start): 0.3559 rms_B_bonded: 4.77 r_work: 0.3245 rms_B_bonded: 4.59 restraints_weight: 0.5000 r_work (final): 0.3245 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3270 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3270 r_free = 0.3270 target_work(ls_wunit_k1) = 0.095 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3270 r_free = 0.3270 target_work(ls_wunit_k1) = 0.095 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3270 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8219 moved from start: 0.1596 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= 0.122 Angle : 0.499 6.416 6747 Z= 0.256 Chirality : 0.040 0.131 737 Planarity : 0.004 0.035 873 Dihedral : 4.315 35.922 663 Min Nonbonded Distance : 2.478 Molprobity Statistics. All-atom Clashscore : 7.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.88 % Favored : 96.12 % Rotamer: Outliers : 2.39 % Allowed : 10.13 % Favored : 87.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.23 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z 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: 0.90 (0.36), residues: 594 helix: 1.32 (0.33), residues: 260 sheet: 0.81 (0.61), residues: 84 loop : -0.17 (0.43), residues: 250 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG C 568 TYR 0.009 0.001 TYR A 127 PHE 0.011 0.001 PHE C 564 TRP 0.007 0.001 TRP C 581 HIS 0.002 0.000 HIS C 420 Details of bonding type rmsd covalent geometry : bond 0.00289 ( 4983) covalent geometry : angle 0.49875 ( 6747) hydrogen bonds : bond 0.03408 ( 224) hydrogen bonds : angle 4.41447 ( 626) Misc. bond : bond 0.00015 ( 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 62 residues out of total 541 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 49 time to evaluate : 0.206 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 1 MET cc_start: 0.5876 (tmm) cc_final: 0.5433 (tmm) REVERT: B 74 ARG cc_start: 0.7251 (mmm-85) cc_final: 0.6690 (mtt180) outliers start: 13 outliers final: 10 residues processed: 57 average time/residue: 0.1055 time to fit residues: 7.4343 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 : 0.133 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 73 ILE Chi-restraints excluded: chain A residue 109 LEU Chi-restraints excluded: chain B residue 4 PHE Chi-restraints excluded: chain B residue 14 THR Chi-restraints excluded: chain B residue 50 LEU Chi-restraints excluded: chain C residue 310 MET Chi-restraints excluded: chain C residue 385 THR Chi-restraints excluded: chain C residue 389 TYR Chi-restraints excluded: chain C residue 587 TRP Chi-restraints excluded: chain C residue 627 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 58 random chunks: chunk 44 optimal weight: 0.9990 chunk 50 optimal weight: 0.7980 chunk 29 optimal weight: 0.9980 chunk 49 optimal weight: 0.5980 chunk 47 optimal weight: 0.9980 chunk 45 optimal weight: 0.9980 chunk 39 optimal weight: 0.8980 chunk 40 optimal weight: 0.9990 chunk 33 optimal weight: 0.1980 chunk 22 optimal weight: 0.4980 chunk 52 optimal weight: 1.9990 overall best weight: 0.5980 ------------------------------------------------------------------------------- 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 = 0.3956 r_free = 0.3956 target = 0.145577 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3542 r_free = 0.3542 target = 0.111834 restraints weight = 16615.479| |-----------------------------------------------------------------------------| r_work (start): 0.3570 rms_B_bonded: 5.52 r_work: 0.3184 rms_B_bonded: 5.22 restraints_weight: 2.0000 r_work (final): 0.3184 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3203 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3203 r_free = 0.3203 target_work(ls_wunit_k1) = 0.091 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3203 r_free = 0.3203 target_work(ls_wunit_k1) = 0.091 | | occupancies: max = 1.00 min = 0.49 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3203 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8265 moved from start: 0.1817 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.034 4985 Z= 0.148 Angle : 0.525 6.787 6747 Z= 0.271 Chirality : 0.041 0.164 737 Planarity : 0.004 0.034 873 Dihedral : 4.342 35.742 663 Min Nonbonded Distance : 2.472 Molprobity Statistics. All-atom Clashscore : 7.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.22 % Favored : 95.78 % Rotamer: Outliers : 2.39 % Allowed : 11.79 % Favored : 85.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.23 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z 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: 0.83 (0.36), residues: 594 helix: 1.23 (0.33), residues: 261 sheet: 1.04 (0.60), residues: 82 loop : -0.26 (0.42), residues: 251 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG C 568 TYR 0.010 0.001 TYR A 127 PHE 0.009 0.001 PHE C 428 TRP 0.007 0.001 TRP A 141 HIS 0.002 0.000 HIS C 420 Details of bonding type rmsd covalent geometry : bond 0.00358 ( 4983) covalent geometry : angle 0.52464 ( 6747) hydrogen bonds : bond 0.03374 ( 224) hydrogen bonds : angle 4.49195 ( 626) Misc. bond : bond 0.00035 ( 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 56 residues out of total 541 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 43 time to evaluate : 0.194 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 1 MET cc_start: 0.6549 (tmm) cc_final: 0.6168 (tmm) outliers start: 13 outliers final: 10 residues processed: 51 average time/residue: 0.1130 time to fit residues: 7.0797 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 : 0.193 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 73 ILE Chi-restraints excluded: chain A residue 109 LEU Chi-restraints excluded: chain B residue 4 PHE Chi-restraints excluded: chain B residue 14 THR Chi-restraints excluded: chain B residue 50 LEU Chi-restraints excluded: chain C residue 310 MET Chi-restraints excluded: chain C residue 385 THR Chi-restraints excluded: chain C residue 389 TYR Chi-restraints excluded: chain C residue 587 TRP Chi-restraints excluded: chain C residue 627 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 58 random chunks: chunk 30 optimal weight: 0.8980 chunk 26 optimal weight: 1.9990 chunk 41 optimal weight: 1.9990 chunk 18 optimal weight: 3.9990 chunk 15 optimal weight: 8.9990 chunk 10 optimal weight: 0.5980 chunk 9 optimal weight: 0.8980 chunk 42 optimal weight: 0.6980 chunk 47 optimal weight: 1.9990 chunk 52 optimal weight: 0.9980 chunk 2 optimal weight: 1.9990 overall best weight: 0.8180 ------------------------------------------------------------------------------- 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 = 0.3932 r_free = 0.3932 target = 0.143926 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3503 r_free = 0.3503 target = 0.109907 restraints weight = 11812.986| |-----------------------------------------------------------------------------| r_work (start): 0.3550 rms_B_bonded: 3.53 r_work: 0.3293 rms_B_bonded: 3.71 restraints_weight: 0.5000 r_work (final): 0.3293 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3295 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3295 r_free = 0.3295 target_work(ls_wunit_k1) = 0.096 | | occupancies: max = 1.00 min = 0.49 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3295 r_free = 0.3295 target_work(ls_wunit_k1) = 0.096 | | occupancies: max = 1.00 min = 0.49 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3295 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8191 moved from start: 0.1893 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.033 4985 Z= 0.186 Angle : 0.530 6.933 6747 Z= 0.276 Chirality : 0.042 0.153 737 Planarity : 0.004 0.034 873 Dihedral : 4.425 36.343 663 Min Nonbonded Distance : 2.483 Molprobity Statistics. All-atom Clashscore : 7.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.05 % Favored : 95.95 % Rotamer: Outliers : 2.95 % Allowed : 11.42 % Favored : 85.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.23 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z 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: 0.76 (0.36), residues: 594 helix: 1.25 (0.33), residues: 260 sheet: 0.95 (0.59), residues: 82 loop : -0.36 (0.42), residues: 252 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG C 568 TYR 0.017 0.001 TYR A 74 PHE 0.011 0.002 PHE C 598 TRP 0.008 0.001 TRP C 581 HIS 0.002 0.001 HIS C 420 Details of bonding type rmsd covalent geometry : bond 0.00456 ( 4983) covalent geometry : angle 0.53046 ( 6747) hydrogen bonds : bond 0.03530 ( 224) hydrogen bonds : angle 4.45134 ( 626) Misc. bond : bond 0.00032 ( 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 60 residues out of total 541 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 44 time to evaluate : 0.129 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 99 ILE cc_start: 0.8551 (OUTLIER) cc_final: 0.7875 (tp) REVERT: B 1 MET cc_start: 0.6006 (tmm) cc_final: 0.5255 (tmm) outliers start: 16 outliers final: 12 residues processed: 54 average time/residue: 0.1100 time to fit residues: 7.3160 Evaluate side-chains 54 residues out of total 541 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 41 time to evaluate : 0.205 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 73 ILE Chi-restraints excluded: chain A residue 99 ILE Chi-restraints excluded: chain A residue 109 LEU Chi-restraints excluded: chain A residue 123 ILE Chi-restraints excluded: chain B residue 4 PHE Chi-restraints excluded: chain B residue 14 THR Chi-restraints excluded: chain B residue 50 LEU Chi-restraints excluded: chain C residue 310 MET Chi-restraints excluded: chain C residue 385 THR Chi-restraints excluded: chain C residue 389 TYR Chi-restraints excluded: chain C residue 584 LEU Chi-restraints excluded: chain C residue 587 TRP Chi-restraints excluded: chain C residue 627 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 58 random chunks: chunk 35 optimal weight: 0.9980 chunk 34 optimal weight: 0.9990 chunk 21 optimal weight: 0.2980 chunk 24 optimal weight: 0.0980 chunk 26 optimal weight: 0.7980 chunk 37 optimal weight: 0.4980 chunk 29 optimal weight: 0.5980 chunk 23 optimal weight: 1.9990 chunk 1 optimal weight: 0.0060 chunk 5 optimal weight: 0.0970 chunk 4 optimal weight: 0.9990 overall best weight: 0.1994 ------------------------------------------------------------------------------- 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 = 0.3972 r_free = 0.3972 target = 0.147100 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3549 r_free = 0.3549 target = 0.112926 restraints weight = 15376.037| |-----------------------------------------------------------------------------| r_work (start): 0.3592 rms_B_bonded: 5.00 r_work: 0.3265 rms_B_bonded: 4.61 restraints_weight: 0.5000 r_work (final): 0.3265 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3262 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3262 r_free = 0.3262 target_work(ls_wunit_k1) = 0.094 | | occupancies: max = 1.00 min = 0.49 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3262 r_free = 0.3262 target_work(ls_wunit_k1) = 0.094 | | occupancies: max = 1.00 min = 0.49 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3262 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8183 moved from start: 0.2018 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.032 4985 Z= 0.092 Angle : 0.503 12.068 6747 Z= 0.254 Chirality : 0.039 0.160 737 Planarity : 0.004 0.036 873 Dihedral : 4.185 31.371 663 Min Nonbonded Distance : 2.483 Molprobity Statistics. All-atom Clashscore : 6.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.54 % Favored : 96.46 % Rotamer: Outliers : 2.03 % Allowed : 12.89 % Favored : 85.08 % 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: 0.94 (0.36), residues: 594 helix: 1.38 (0.33), residues: 265 sheet: 1.09 (0.59), residues: 82 loop : -0.30 (0.42), residues: 247 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG C 568 TYR 0.007 0.001 TYR C 419 PHE 0.010 0.001 PHE C 564 TRP 0.005 0.001 TRP C 581 HIS 0.002 0.000 HIS B 68 Details of bonding type rmsd covalent geometry : bond 0.00207 ( 4983) covalent geometry : angle 0.50345 ( 6747) hydrogen bonds : bond 0.02918 ( 224) hydrogen bonds : angle 4.24695 ( 626) Misc. bond : bond 0.00011 ( 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 59 residues out of total 541 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 48 time to evaluate : 0.257 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 1 MET cc_start: 0.6185 (tmm) cc_final: 0.5357 (tmm) REVERT: B 74 ARG cc_start: 0.5299 (mtt180) cc_final: 0.4838 (ttm110) outliers start: 11 outliers final: 6 residues processed: 55 average time/residue: 0.1073 time to fit residues: 7.3216 Evaluate side-chains 50 residues out of total 541 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 44 time to evaluate : 0.152 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 109 LEU Chi-restraints excluded: chain B residue 4 PHE Chi-restraints excluded: chain B residue 14 THR Chi-restraints excluded: chain C residue 385 THR Chi-restraints excluded: chain C residue 389 TYR Chi-restraints excluded: chain C residue 627 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 58 random chunks: chunk 7 optimal weight: 0.9990 chunk 50 optimal weight: 0.6980 chunk 42 optimal weight: 0.8980 chunk 48 optimal weight: 0.9990 chunk 11 optimal weight: 0.0030 chunk 2 optimal weight: 0.8980 chunk 12 optimal weight: 0.7980 chunk 16 optimal weight: 3.9990 chunk 45 optimal weight: 0.9990 chunk 6 optimal weight: 0.6980 chunk 23 optimal weight: 1.9990 overall best weight: 0.6190 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3943 r_free = 0.3943 target = 0.144874 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3520 r_free = 0.3520 target = 0.110853 restraints weight = 15508.518| |-----------------------------------------------------------------------------| r_work (start): 0.3563 rms_B_bonded: 5.18 r_work: 0.3204 rms_B_bonded: 4.99 restraints_weight: 0.5000 r_work (final): 0.3204 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3208 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3208 r_free = 0.3208 target_work(ls_wunit_k1) = 0.090 | | occupancies: max = 1.00 min = 0.49 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3208 r_free = 0.3208 target_work(ls_wunit_k1) = 0.090 | | occupancies: max = 1.00 min = 0.49 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3208 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8261 moved from start: 0.2160 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.025 4985 Z= 0.151 Angle : 0.529 9.882 6747 Z= 0.270 Chirality : 0.041 0.168 737 Planarity : 0.004 0.038 873 Dihedral : 4.186 31.937 661 Min Nonbonded Distance : 2.431 Molprobity Statistics. All-atom Clashscore : 7.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.22 % Favored : 95.78 % Rotamer: Outliers : 2.21 % Allowed : 12.52 % Favored : 85.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.23 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z 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 (0.36), residues: 594 helix: 1.29 (0.33), residues: 265 sheet: 1.03 (0.58), residues: 82 loop : -0.39 (0.42), residues: 247 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG C 412 TYR 0.014 0.001 TYR A 74 PHE 0.019 0.002 PHE C 327 TRP 0.007 0.001 TRP C 581 HIS 0.004 0.001 HIS A 125 Details of bonding type rmsd covalent geometry : bond 0.00366 ( 4983) covalent geometry : angle 0.52890 ( 6747) hydrogen bonds : bond 0.03311 ( 224) hydrogen bonds : angle 4.25877 ( 626) Misc. bond : bond 0.00031 ( 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 54 residues out of total 541 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 42 time to evaluate : 0.205 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 99 ILE cc_start: 0.8596 (OUTLIER) cc_final: 0.7883 (tp) REVERT: B 1 MET cc_start: 0.6445 (tmm) cc_final: 0.5529 (tmm) REVERT: B 74 ARG cc_start: 0.5219 (mtt180) cc_final: 0.4717 (ttm110) outliers start: 12 outliers final: 11 residues processed: 49 average time/residue: 0.1152 time to fit residues: 6.9461 Evaluate side-chains 53 residues out of total 541 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 41 time to evaluate : 0.201 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 73 ILE Chi-restraints excluded: chain A residue 99 ILE Chi-restraints excluded: chain A residue 109 LEU Chi-restraints excluded: chain A residue 123 ILE Chi-restraints excluded: chain A residue 132 SER Chi-restraints excluded: chain B residue 4 PHE Chi-restraints excluded: chain B residue 14 THR Chi-restraints excluded: chain C residue 385 THR Chi-restraints excluded: chain C residue 389 TYR Chi-restraints excluded: chain C residue 442 CYS Chi-restraints excluded: chain C residue 587 TRP Chi-restraints excluded: chain C residue 627 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 58 random chunks: chunk 23 optimal weight: 1.9990 chunk 38 optimal weight: 0.4980 chunk 5 optimal weight: 0.3980 chunk 41 optimal weight: 0.5980 chunk 26 optimal weight: 0.8980 chunk 54 optimal weight: 1.9990 chunk 33 optimal weight: 0.5980 chunk 21 optimal weight: 0.5980 chunk 31 optimal weight: 0.3980 chunk 55 optimal weight: 0.0270 chunk 43 optimal weight: 1.9990 overall best weight: 0.3838 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3958 r_free = 0.3958 target = 0.145808 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.3482 r_free = 0.3482 target = 0.109113 restraints weight = 7590.622| |-----------------------------------------------------------------------------| r_work (start): 0.3490 rms_B_bonded: 2.13 r_work: 0.3348 rms_B_bonded: 2.92 restraints_weight: 0.5000 r_work: 0.3184 rms_B_bonded: 4.96 restraints_weight: 0.2500 r_work (final): 0.3184 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3233 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3233 r_free = 0.3233 target_work(ls_wunit_k1) = 0.092 | | occupancies: max = 1.00 min = 0.49 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3233 r_free = 0.3233 target_work(ls_wunit_k1) = 0.092 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3233 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8248 moved from start: 0.2224 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 4985 Z= 0.116 Angle : 0.522 9.642 6747 Z= 0.265 Chirality : 0.040 0.171 737 Planarity : 0.004 0.035 873 Dihedral : 4.119 29.623 661 Min Nonbonded Distance : 2.434 Molprobity Statistics. All-atom Clashscore : 6.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.71 % Favored : 96.29 % Rotamer: Outliers : 2.39 % Allowed : 12.89 % Favored : 84.71 % 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: 0.78 (0.35), residues: 594 helix: 1.26 (0.33), residues: 265 sheet: 1.01 (0.61), residues: 75 loop : -0.37 (0.41), residues: 254 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 133 TYR 0.008 0.001 TYR C 419 PHE 0.018 0.001 PHE C 327 TRP 0.006 0.001 TRP C 581 HIS 0.002 0.000 HIS A 125 Details of bonding type rmsd covalent geometry : bond 0.00274 ( 4983) covalent geometry : angle 0.52229 ( 6747) hydrogen bonds : bond 0.03114 ( 224) hydrogen bonds : angle 4.24328 ( 626) Misc. bond : bond 0.00007 ( 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 56 residues out of total 541 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 43 time to evaluate : 0.206 Fit side-chains revert: symmetry clash REVERT: B 1 MET cc_start: 0.6433 (tmm) cc_final: 0.5452 (tmm) outliers start: 13 outliers final: 10 residues processed: 51 average time/residue: 0.1105 time to fit residues: 6.9658 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 : 0.150 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 73 ILE Chi-restraints excluded: chain A residue 109 LEU Chi-restraints excluded: chain A residue 123 ILE Chi-restraints excluded: chain B residue 4 PHE Chi-restraints excluded: chain B residue 14 THR Chi-restraints excluded: chain C residue 385 THR Chi-restraints excluded: chain C residue 389 TYR Chi-restraints excluded: chain C residue 442 CYS Chi-restraints excluded: chain C residue 587 TRP Chi-restraints excluded: chain C residue 627 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 58 random chunks: chunk 54 optimal weight: 1.9990 chunk 45 optimal weight: 0.5980 chunk 37 optimal weight: 0.6980 chunk 41 optimal weight: 0.9980 chunk 38 optimal weight: 0.7980 chunk 2 optimal weight: 0.0670 chunk 56 optimal weight: 0.6980 chunk 51 optimal weight: 0.0980 chunk 48 optimal weight: 0.1980 chunk 19 optimal weight: 0.9980 chunk 53 optimal weight: 0.9980 overall best weight: 0.3318 ------------------------------------------------------------------------------- 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 = 0.3967 r_free = 0.3967 target = 0.146642 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3533 r_free = 0.3533 target = 0.112667 restraints weight = 12223.603| |-----------------------------------------------------------------------------| r_work (start): 0.3575 rms_B_bonded: 3.76 r_work: 0.3338 rms_B_bonded: 3.68 restraints_weight: 0.5000 r_work (final): 0.3338 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3339 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3339 r_free = 0.3339 target_work(ls_wunit_k1) = 0.099 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3339 r_free = 0.3339 target_work(ls_wunit_k1) = 0.099 | | occupancies: max = 1.00 min = 0.49 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3339 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8132 moved from start: 0.2254 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= 0.110 Angle : 0.542 12.620 6747 Z= 0.273 Chirality : 0.041 0.167 737 Planarity : 0.004 0.035 873 Dihedral : 4.058 28.293 661 Min Nonbonded Distance : 2.441 Molprobity Statistics. All-atom Clashscore : 7.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.05 % Favored : 95.95 % Rotamer: Outliers : 2.21 % Allowed : 13.44 % Favored : 84.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.23 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z 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: 0.81 (0.36), residues: 594 helix: 1.29 (0.33), residues: 265 sheet: 1.04 (0.61), residues: 75 loop : -0.36 (0.41), residues: 254 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.001 ARG A 143 TYR 0.017 0.001 TYR A 74 PHE 0.018 0.001 PHE C 327 TRP 0.006 0.001 TRP C 581 HIS 0.001 0.000 HIS B 68 Details of bonding type rmsd covalent geometry : bond 0.00257 ( 4983) covalent geometry : angle 0.54194 ( 6747) hydrogen bonds : bond 0.03057 ( 224) hydrogen bonds : angle 4.13891 ( 626) Misc. bond : bond 0.00020 ( 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 55 residues out of total 541 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 43 time to evaluate : 0.208 Fit side-chains revert: symmetry clash REVERT: A 99 ILE cc_start: 0.8482 (OUTLIER) cc_final: 0.7776 (tp) REVERT: A 133 ARG cc_start: 0.7543 (ptt-90) cc_final: 0.7249 (ptt90) REVERT: B 1 MET cc_start: 0.6042 (tmm) cc_final: 0.4364 (tmm) outliers start: 12 outliers final: 11 residues processed: 50 average time/residue: 0.1190 time to fit residues: 7.3361 Evaluate side-chains 54 residues out of total 541 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 42 time to evaluate : 0.187 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 73 ILE Chi-restraints excluded: chain A residue 99 ILE Chi-restraints excluded: chain A residue 109 LEU Chi-restraints excluded: chain A residue 123 ILE Chi-restraints excluded: chain A residue 132 SER Chi-restraints excluded: chain B residue 4 PHE Chi-restraints excluded: chain B residue 14 THR Chi-restraints excluded: chain C residue 385 THR Chi-restraints excluded: chain C residue 389 TYR Chi-restraints excluded: chain C residue 442 CYS Chi-restraints excluded: chain C residue 587 TRP Chi-restraints excluded: chain C residue 627 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 58 random chunks: chunk 36 optimal weight: 0.2980 chunk 12 optimal weight: 0.8980 chunk 33 optimal weight: 0.9980 chunk 7 optimal weight: 0.9990 chunk 50 optimal weight: 0.8980 chunk 52 optimal weight: 2.9990 chunk 16 optimal weight: 3.9990 chunk 8 optimal weight: 0.7980 chunk 57 optimal weight: 0.5980 chunk 44 optimal weight: 0.9990 chunk 17 optimal weight: 0.1980 overall best weight: 0.5580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3954 r_free = 0.3954 target = 0.145412 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3522 r_free = 0.3522 target = 0.111627 restraints weight = 12609.767| |-----------------------------------------------------------------------------| r_work (start): 0.3557 rms_B_bonded: 4.11 r_work: 0.3281 rms_B_bonded: 4.05 restraints_weight: 0.5000 r_work (final): 0.3281 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3288 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3288 r_free = 0.3288 target_work(ls_wunit_k1) = 0.095 | | occupancies: max = 1.00 min = 0.49 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3288 r_free = 0.3288 target_work(ls_wunit_k1) = 0.095 | | occupancies: max = 1.00 min = 0.49 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3288 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8192 moved from start: 0.2290 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 4985 Z= 0.140 Angle : 0.551 11.993 6747 Z= 0.279 Chirality : 0.041 0.166 737 Planarity : 0.004 0.035 873 Dihedral : 4.086 28.147 661 Min Nonbonded Distance : 2.446 Molprobity Statistics. All-atom Clashscore : 7.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.22 % Favored : 95.78 % Rotamer: Outliers : 2.21 % Allowed : 13.44 % Favored : 84.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.23 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z 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: 0.72 (0.36), residues: 594 helix: 1.23 (0.33), residues: 265 sheet: 0.95 (0.60), residues: 75 loop : -0.42 (0.41), residues: 254 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 72 TYR 0.018 0.001 TYR A 145 PHE 0.018 0.001 PHE C 327 TRP 0.007 0.001 TRP C 581 HIS 0.002 0.000 HIS C 420 Details of bonding type rmsd covalent geometry : bond 0.00336 ( 4983) covalent geometry : angle 0.55082 ( 6747) hydrogen bonds : bond 0.03236 ( 224) hydrogen bonds : angle 4.18234 ( 626) Misc. bond : bond 0.00016 ( 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 56 residues out of total 541 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 44 time to evaluate : 0.202 Fit side-chains revert: symmetry clash REVERT: A 99 ILE cc_start: 0.8535 (OUTLIER) cc_final: 0.7813 (tp) REVERT: A 133 ARG cc_start: 0.7638 (ptt-90) cc_final: 0.7331 (ptt90) REVERT: B 1 MET cc_start: 0.6341 (tmm) cc_final: 0.4679 (tmm) outliers start: 12 outliers final: 10 residues processed: 50 average time/residue: 0.1072 time to fit residues: 6.6216 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 : 0.206 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 73 ILE Chi-restraints excluded: chain A residue 99 ILE Chi-restraints excluded: chain A residue 109 LEU Chi-restraints excluded: chain A residue 123 ILE Chi-restraints excluded: chain B residue 4 PHE Chi-restraints excluded: chain B residue 14 THR Chi-restraints excluded: chain C residue 385 THR Chi-restraints excluded: chain C residue 389 TYR Chi-restraints excluded: chain C residue 442 CYS Chi-restraints excluded: chain C residue 587 TRP Chi-restraints excluded: chain C residue 627 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 58 random chunks: chunk 5 optimal weight: 0.9990 chunk 20 optimal weight: 7.9990 chunk 2 optimal weight: 3.9990 chunk 28 optimal weight: 0.7980 chunk 51 optimal weight: 0.9990 chunk 7 optimal weight: 0.8980 chunk 9 optimal weight: 0.6980 chunk 26 optimal weight: 0.9980 chunk 8 optimal weight: 0.7980 chunk 54 optimal weight: 0.8980 chunk 4 optimal weight: 0.5980 overall best weight: 0.7580 ------------------------------------------------------------------------------- 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 = 0.3940 r_free = 0.3940 target = 0.144184 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3509 r_free = 0.3509 target = 0.109307 restraints weight = 10455.287| |-----------------------------------------------------------------------------| r_work (start): 0.3540 rms_B_bonded: 2.83 r_work: 0.3318 rms_B_bonded: 3.41 restraints_weight: 0.5000 r_work (final): 0.3318 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3322 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3322 r_free = 0.3322 target_work(ls_wunit_k1) = 0.097 | | occupancies: max = 1.00 min = 0.49 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3322 r_free = 0.3322 target_work(ls_wunit_k1) = 0.097 | | occupancies: max = 1.00 min = 0.49 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3322 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8159 moved from start: 0.2343 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.031 4985 Z= 0.177 Angle : 0.572 11.850 6747 Z= 0.291 Chirality : 0.042 0.167 737 Planarity : 0.004 0.034 873 Dihedral : 4.219 29.347 661 Min Nonbonded Distance : 2.453 Molprobity Statistics. All-atom Clashscore : 7.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.88 % Favored : 96.12 % Rotamer: Outliers : 2.39 % Allowed : 13.44 % Favored : 84.16 % 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: 0.55 (0.36), residues: 594 helix: 1.01 (0.33), residues: 265 sheet: 0.89 (0.57), residues: 82 loop : -0.45 (0.42), residues: 247 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 143 TYR 0.016 0.001 TYR A 74 PHE 0.018 0.002 PHE C 327 TRP 0.038 0.002 TRP A 141 HIS 0.002 0.001 HIS C 420 Details of bonding type rmsd covalent geometry : bond 0.00430 ( 4983) covalent geometry : angle 0.57213 ( 6747) hydrogen bonds : bond 0.03545 ( 224) hydrogen bonds : angle 4.27535 ( 626) Misc. bond : bond 0.00048 ( 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: 1446.57 seconds wall clock time: 25 minutes 17.74 seconds (1517.74 seconds total)