Starting phenix.real_space_refine on Tue Aug 4 13:32:49 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/36bb_77348/08_2026/36bb_77348.cif Found real_map, /net/cci-nas-00/data/ceres_data/36bb_77348/08_2026/36bb_77348.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.6 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/36bb_77348/08_2026/36bb_77348.map" default_real_map = "/net/cci-nas-00/data/ceres_data/36bb_77348/08_2026/36bb_77348.map" model { file = "/net/cci-nas-00/data/ceres_data/36bb_77348/08_2026/36bb_77348.cif" } default_model = "/net/cci-nas-00/data/ceres_data/36bb_77348/08_2026/36bb_77348.cif" } resolution = 3.6 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= -0.047 sd= 0.081 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 20 5.16 5 C 2090 2.51 5 N 562 2.21 5 O 620 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 24 residue(s): 0.00s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.2rc3-6140/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 3292 Number of models: 1 Model: "" Number of chains: 3 Chain: "H" Number of atoms: 955 Number of conformers: 1 Conformer: "" Number of residues, atoms: 122, 955 Classifications: {'peptide': 122} Link IDs: {'PTRANS': 3, 'TRANS': 118} Chain: "L" Number of atoms: 829 Number of conformers: 1 Conformer: "" Number of residues, atoms: 108, 829 Classifications: {'peptide': 108} Link IDs: {'PTRANS': 6, 'TRANS': 101} Chain: "A" Number of atoms: 1508 Number of conformers: 1 Conformer: "" Number of residues, atoms: 188, 1508 Classifications: {'peptide': 188} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 10, 'TRANS': 177} Chain breaks: 1 Time building chain proxies: 1.10, per 1000 atoms: 0.33 Number of scatterers: 3292 At special positions: 0 Unit cell: (53, 74.2, 110.24, 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 20 16.00 O 620 8.00 N 562 7.00 C 2090 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=7, symmetry=0 Simple disulfide: pdb=" SG CYS H 22 " - pdb=" SG CYS H 92 " distance=2.03 Simple disulfide: pdb=" SG CYS H 97 " - pdb=" SG CYS H 100B" distance=2.21 Simple disulfide: pdb=" SG CYS L 23 " - pdb=" SG CYS L 88 " distance=2.15 Simple disulfide: pdb=" SG CYS A 336 " - pdb=" SG CYS A 361 " distance=2.06 Simple disulfide: pdb=" SG CYS A 379 " - pdb=" SG CYS A 432 " distance=2.02 Simple disulfide: pdb=" SG CYS A 391 " - pdb=" SG CYS A 525 " distance=2.03 Simple disulfide: pdb=" SG CYS A 480 " - pdb=" SG CYS A 488 " distance=2.03 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=0, symmetry=0 Time building additional restraints: 0.20 Conformation dependent library (CDL) restraints added in 78.8 milliseconds 820 Ramachandran restraints generated. 410 Oldfield, 0 Emsley, 410 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 768 Finding SS restraints... Secondary structure from input PDB file: 6 helices and 8 sheets defined 8.4% alpha, 16.7% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.11 Creating SS restraints... Processing helix chain 'H' and resid 60 through 65 removed outlier: 4.271A pdb=" N GLU H 65 " --> pdb=" O GLN H 61 " (cutoff:3.500A) Processing helix chain 'H' and resid 83 through 87 Processing helix chain 'A' and resid 337 through 341 Processing helix chain 'A' and resid 364 through 371 removed outlier: 3.842A pdb=" N LEU A 368 " --> pdb=" O TYR A 365 " (cutoff:3.500A) Processing helix chain 'A' and resid 416 through 421 removed outlier: 3.804A pdb=" N TYR A 421 " --> pdb=" O ASN A 417 " (cutoff:3.500A) Processing helix chain 'A' and resid 498 through 502 Processing sheet with id=AA1, first strand: chain 'H' and resid 3 through 6 Processing sheet with id=AA2, first strand: chain 'H' and resid 10 through 12 removed outlier: 3.763A pdb=" N GLU H 10 " --> pdb=" O MET H 108 " (cutoff:3.500A) removed outlier: 3.621A pdb=" N GLY H 49 " --> pdb=" O TRP H 36 " (cutoff:3.500A) removed outlier: 6.226A pdb=" N ARG H 38 " --> pdb=" O TRP H 47 " (cutoff:3.500A) removed outlier: 5.147A pdb=" N TRP H 47 " --> pdb=" O ARG H 38 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'L' and resid 11 through 12 removed outlier: 7.913A pdb=" N LEU L 11 " --> pdb=" O GLU L 105 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA3 Processing sheet with id=AA4, first strand: chain 'L' and resid 33 through 35 Processing sheet with id=AA5, first strand: chain 'A' and resid 334 through 335 removed outlier: 6.704A pdb=" N ASN A 334 " --> pdb=" O VAL A 362 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA5 Processing sheet with id=AA6, first strand: chain 'A' and resid 401 through 402 Processing sheet with id=AA7, first strand: chain 'A' and resid 453 through 454 removed outlier: 3.555A pdb=" N GLN A 493 " --> pdb=" O TYR A 453 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 473 through 474 58 hydrogen bonds defined for protein. 117 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: 0.44 Time building geometry restraints manager: 0.28 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.17 - 1.31: 525 1.31 - 1.44: 1015 1.44 - 1.58: 1810 1.58 - 1.71: 0 1.71 - 1.85: 26 Bond restraints: 3376 Sorted by residual: bond pdb=" N PRO A 507 " pdb=" CD PRO A 507 " ideal model delta sigma weight residual 1.473 1.386 0.087 1.40e-02 5.10e+03 3.82e+01 bond pdb=" N PRO A 412 " pdb=" CD PRO A 412 " ideal model delta sigma weight residual 1.473 1.398 0.075 1.40e-02 5.10e+03 2.87e+01 bond pdb=" N PRO A 463 " pdb=" CD PRO A 463 " ideal model delta sigma weight residual 1.473 1.407 0.066 1.40e-02 5.10e+03 2.26e+01 bond pdb=" C GLN A 506 " pdb=" O GLN A 506 " ideal model delta sigma weight residual 1.235 1.173 0.062 1.35e-02 5.49e+03 2.12e+01 bond pdb=" N PRO H 9 " pdb=" CD PRO H 9 " ideal model delta sigma weight residual 1.473 1.409 0.064 1.40e-02 5.10e+03 2.07e+01 ... (remaining 3371 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.37: 4167 2.37 - 4.74: 348 4.74 - 7.11: 53 7.11 - 9.48: 10 9.48 - 11.85: 2 Bond angle restraints: 4580 Sorted by residual: angle pdb=" C ALA H 94 " pdb=" N PRO H 95 " pdb=" CA PRO H 95 " ideal model delta sigma weight residual 119.85 128.15 -8.30 1.01e+00 9.80e-01 6.75e+01 angle pdb=" C ALA L 43 " pdb=" N PRO L 44 " pdb=" CA PRO L 44 " ideal model delta sigma weight residual 119.56 127.69 -8.13 1.02e+00 9.61e-01 6.35e+01 angle pdb=" N TYR A 508 " pdb=" CA TYR A 508 " pdb=" C TYR A 508 " ideal model delta sigma weight residual 109.24 121.09 -11.85 1.51e+00 4.39e-01 6.16e+01 angle pdb=" C GLY H 8 " pdb=" N PRO H 9 " pdb=" CA PRO H 9 " ideal model delta sigma weight residual 119.85 127.34 -7.49 1.01e+00 9.80e-01 5.50e+01 angle pdb=" C PHE A 490 " pdb=" N PRO A 491 " pdb=" CA PRO A 491 " ideal model delta sigma weight residual 119.56 126.75 -7.19 1.01e+00 9.80e-01 5.06e+01 ... (remaining 4575 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.01: 1891 17.01 - 34.02: 77 34.02 - 51.02: 18 51.02 - 68.03: 6 68.03 - 85.04: 3 Dihedral angle restraints: 1995 sinusoidal: 787 harmonic: 1208 Sorted by residual: dihedral pdb=" CA PHE A 497 " pdb=" C PHE A 497 " pdb=" N ARG A 498 " pdb=" CA ARG A 498 " ideal model delta harmonic sigma weight residual 180.00 125.64 54.36 0 5.00e+00 4.00e-02 1.18e+02 dihedral pdb=" CB CYS A 391 " pdb=" SG CYS A 391 " pdb=" SG CYS A 525 " pdb=" CB CYS A 525 " ideal model delta sinusoidal sigma weight residual 93.00 157.89 -64.89 1 1.00e+01 1.00e-02 5.53e+01 dihedral pdb=" CB CYS A 480 " pdb=" SG CYS A 480 " pdb=" SG CYS A 488 " pdb=" CB CYS A 488 " ideal model delta sinusoidal sigma weight residual -86.00 -134.54 48.54 1 1.00e+01 1.00e-02 3.24e+01 ... (remaining 1992 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.040: 278 0.040 - 0.080: 114 0.080 - 0.121: 67 0.121 - 0.161: 23 0.161 - 0.201: 2 Chirality restraints: 484 Sorted by residual: chirality pdb=" CA ILE L 58 " pdb=" N ILE L 58 " pdb=" C ILE L 58 " pdb=" CB ILE L 58 " both_signs ideal model delta sigma weight residual False 2.43 2.63 -0.20 2.00e-01 2.50e+01 1.01e+00 chirality pdb=" CA SER A 496 " pdb=" N SER A 496 " pdb=" C SER A 496 " pdb=" CB SER A 496 " both_signs ideal model delta sigma weight residual False 2.51 2.34 0.17 2.00e-01 2.50e+01 6.85e-01 chirality pdb=" CA TYR A 421 " pdb=" N TYR A 421 " pdb=" C TYR A 421 " pdb=" CB TYR A 421 " both_signs ideal model delta sigma weight residual False 2.51 2.35 0.16 2.00e-01 2.50e+01 6.43e-01 ... (remaining 481 not shown) Planarity restraints: 592 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA PHE A 497 " -0.056 2.00e-02 2.50e+03 1.18e-01 1.39e+02 pdb=" C PHE A 497 " 0.203 2.00e-02 2.50e+03 pdb=" O PHE A 497 " -0.079 2.00e-02 2.50e+03 pdb=" N ARG A 498 " -0.068 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA GLN A 506 " 0.026 2.00e-02 2.50e+03 5.26e-02 2.77e+01 pdb=" C GLN A 506 " -0.091 2.00e-02 2.50e+03 pdb=" O GLN A 506 " 0.034 2.00e-02 2.50e+03 pdb=" N PRO A 507 " 0.031 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA TYR L 36 " 0.014 2.00e-02 2.50e+03 2.79e-02 7.78e+00 pdb=" C TYR L 36 " -0.048 2.00e-02 2.50e+03 pdb=" O TYR L 36 " 0.018 2.00e-02 2.50e+03 pdb=" N GLN L 37 " 0.016 2.00e-02 2.50e+03 ... (remaining 589 not shown) Histogram of nonbonded interaction distances: 1.91 - 2.51: 10 2.51 - 3.11: 2474 3.11 - 3.71: 4667 3.71 - 4.30: 6777 4.30 - 4.90: 10608 Nonbonded interactions: 24536 Sorted by model distance: nonbonded pdb=" CE2 TYR L 87 " pdb=" O GLN L 100 " model vdw 1.914 3.340 nonbonded pdb=" OH TYR H 91 " pdb=" NE2 GLN L 38 " model vdw 2.031 3.120 nonbonded pdb=" O GLN A 506 " pdb=" CE1 TYR A 508 " model vdw 2.151 3.340 nonbonded pdb=" O GLY L 92 " pdb=" NE1 TRP L 96 " model vdw 2.310 3.120 nonbonded pdb=" O GLN A 506 " pdb=" CD1 TYR A 508 " model vdw 2.340 3.340 ... (remaining 24531 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=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue 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: 15.620 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: 0.050 Check model and map are aligned: 0.020 Set scattering table: 0.010 Process input model: 4.740 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: 21.710 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5664 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 : 0.011 0.179 3383 Z= 0.658 Angle : 1.452 14.074 4594 Z= 0.999 Chirality : 0.058 0.201 484 Planarity : 0.008 0.118 592 Dihedral : 11.112 85.039 1206 Min Nonbonded Distance : 1.914 Molprobity Statistics. All-atom Clashscore : 7.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.41 % Favored : 96.59 % Rotamer: Outliers : 0.00 % Allowed : 0.28 % Favored : 99.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.25 % 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 are not related in a simple way. whole: 2.50 (0.43), residues: 410 helix: -4.00 (0.54), residues: 7 sheet: 1.25 (0.53), residues: 99 loop : 2.23 (0.37), residues: 304 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG L 54 TYR 0.031 0.001 TYR A 421 PHE 0.016 0.001 PHE L 62 TRP 0.001 0.000 TRP L 35 HIS 0.001 0.001 HIS A 505 Details of bonding type rmsd/Z covalent geometry : bond 0.01037 / 0.63 ( 3376) covalent geometry : angle 1.42733 / 0.99 ( 4580) SS BOND : bond 0.08138 / 3.94 ( 7) SS BOND : angle 4.99878 / 4.22 ( 14) hydrogen bonds : bond 0.22932 / 15.75 ( 58) hydrogen bonds : angle 9.47398 / 6.29 ( 117) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 820 Ramachandran restraints generated. 410 Oldfield, 0 Emsley, 410 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 820 Ramachandran restraints generated. 410 Oldfield, 0 Emsley, 410 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 148 residues out of total 356 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 148 time to evaluate : 0.128 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: H 29 PHE cc_start: 0.5384 (t80) cc_final: 0.5024 (t80) REVERT: H 71 ARG cc_start: 0.8712 (ptt90) cc_final: 0.8482 (ptt-90) REVERT: H 72 ASP cc_start: 0.8279 (t0) cc_final: 0.7983 (t0) REVERT: H 90 TYR cc_start: 0.7263 (m-80) cc_final: 0.6982 (m-80) REVERT: H 91 TYR cc_start: 0.7059 (p90) cc_final: 0.6084 (p90) REVERT: L 103 LYS cc_start: 0.8782 (mttt) cc_final: 0.8563 (mmtt) REVERT: L 106 ILE cc_start: 0.5483 (tt) cc_final: 0.5203 (pt) REVERT: A 428 ASP cc_start: 0.6787 (t0) cc_final: 0.6271 (m-30) outliers start: 0 outliers final: 0 residues processed: 148 average time/residue: 0.1004 time to fit residues: 16.9731 Evaluate side-chains 100 residues out of total 356 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 100 time to evaluate : 0.158 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 40 random chunks: chunk 24 optimal weight: 0.6980 chunk 26 optimal weight: 0.5980 chunk 2 optimal weight: 0.8980 chunk 16 optimal weight: 0.0470 chunk 32 optimal weight: 0.6980 chunk 31 optimal weight: 0.5980 chunk 25 optimal weight: 0.0870 chunk 19 optimal weight: 0.4980 chunk 30 optimal weight: 0.6980 chunk 22 optimal weight: 0.0570 chunk 37 optimal weight: 0.6980 overall best weight: 0.2574 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 334 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4527 r_free = 0.4527 target = 0.144497 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.4395 r_free = 0.4395 target = 0.132990 restraints weight = 17473.255| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.4407 r_free = 0.4407 target = 0.134043 restraints weight = 14882.502| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 42)----------------| | r_work = 0.4415 r_free = 0.4415 target = 0.134787 restraints weight = 12765.339| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.4421 r_free = 0.4421 target = 0.135307 restraints weight = 11382.981| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 18)----------------| | r_work = 0.4424 r_free = 0.4424 target = 0.135559 restraints weight = 10441.951| |-----------------------------------------------------------------------------| r_work (final): 0.4403 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5578 moved from start: 0.5548 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 3383 Z= 0.162 Angle : 0.781 7.203 4594 Z= 0.433 Chirality : 0.048 0.183 484 Planarity : 0.006 0.040 592 Dihedral : 7.058 25.647 465 Min Nonbonded Distance : 2.465 Molprobity Statistics. All-atom Clashscore : 15.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.90 % Favored : 96.10 % Rotamer: Outliers : 3.93 % Allowed : 12.36 % Favored : 83.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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 are not related in a simple way. whole: 0.78 (0.41), residues: 410 helix: -4.86 (0.37), residues: 6 sheet: 0.56 (0.56), residues: 94 loop : 0.75 (0.35), residues: 310 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG L 77 TYR 0.023 0.002 TYR L 87 PHE 0.021 0.002 PHE A 490 TRP 0.029 0.002 TRP L 35 HIS 0.006 0.002 HIS A 505 Details of bonding type rmsd/Z covalent geometry : bond 0.00348 / 0.16 ( 3376) covalent geometry : angle 0.77374 / 0.43 ( 4580) SS BOND : bond 0.00323 / 0.17 ( 7) SS BOND : angle 2.03081 / 1.59 ( 14) hydrogen bonds : bond 0.03614 / 2.23 ( 58) hydrogen bonds : angle 7.53729 / 5.06 ( 117) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 820 Ramachandran restraints generated. 410 Oldfield, 0 Emsley, 410 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 820 Ramachandran restraints generated. 410 Oldfield, 0 Emsley, 410 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 127 residues out of total 356 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 113 time to evaluate : 0.145 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: H 27 PHE cc_start: 0.5391 (p90) cc_final: 0.4875 (p90) REVERT: H 59 TYR cc_start: 0.7481 (m-80) cc_final: 0.7087 (m-80) REVERT: H 69 ILE cc_start: 0.8775 (mt) cc_final: 0.8528 (mm) REVERT: H 90 TYR cc_start: 0.7178 (m-80) cc_final: 0.6569 (m-80) REVERT: H 91 TYR cc_start: 0.7018 (p90) cc_final: 0.6249 (p90) REVERT: L 46 LEU cc_start: 0.6416 (OUTLIER) cc_final: 0.6019 (pp) REVERT: L 70 ASP cc_start: 0.6789 (t0) cc_final: 0.6566 (t0) REVERT: A 351 TYR cc_start: 0.5803 (t80) cc_final: 0.5534 (t80) REVERT: A 353 TRP cc_start: 0.5929 (m100) cc_final: 0.4237 (m-10) REVERT: A 410 ILE cc_start: 0.6844 (mm) cc_final: 0.6553 (tp) REVERT: A 458 LYS cc_start: 0.8549 (tptp) cc_final: 0.8140 (tptp) REVERT: A 464 PHE cc_start: 0.7079 (m-80) cc_final: 0.6477 (m-10) REVERT: A 471 GLU cc_start: 0.8171 (tp30) cc_final: 0.7953 (tp30) REVERT: A 490 PHE cc_start: 0.8219 (t80) cc_final: 0.7875 (m-80) outliers start: 14 outliers final: 8 residues processed: 120 average time/residue: 0.0971 time to fit residues: 13.4708 Evaluate side-chains 101 residues out of total 356 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 92 time to evaluate : 0.139 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 18 VAL Chi-restraints excluded: chain H residue 41 ARG Chi-restraints excluded: chain H residue 109 VAL Chi-restraints excluded: chain L residue 46 LEU Chi-restraints excluded: chain L residue 73 LEU Chi-restraints excluded: chain L residue 83 PHE Chi-restraints excluded: chain A residue 342 PHE Chi-restraints excluded: chain A residue 362 VAL Chi-restraints excluded: chain A residue 466 ARG Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 40 random chunks: chunk 39 optimal weight: 1.9990 chunk 9 optimal weight: 0.8980 chunk 20 optimal weight: 0.2980 chunk 15 optimal weight: 0.9990 chunk 16 optimal weight: 1.9990 chunk 35 optimal weight: 0.3980 chunk 11 optimal weight: 0.9990 chunk 34 optimal weight: 0.9980 chunk 38 optimal weight: 0.3980 chunk 7 optimal weight: 1.9990 chunk 28 optimal weight: 0.6980 overall best weight: 0.5380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... H 6 GLN H 43 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4445 r_free = 0.4445 target = 0.139480 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.4311 r_free = 0.4311 target = 0.126892 restraints weight = 16333.537| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.4316 r_free = 0.4316 target = 0.127242 restraints weight = 15843.442| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 23)----------------| | r_work = 0.4325 r_free = 0.4325 target = 0.127928 restraints weight = 14071.534| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.4327 r_free = 0.4327 target = 0.128060 restraints weight = 13044.243| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 34)----------------| | r_work = 0.4330 r_free = 0.4330 target = 0.128347 restraints weight = 12548.848| |-----------------------------------------------------------------------------| r_work (final): 0.4303 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5869 moved from start: 0.7429 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.034 3383 Z= 0.210 Angle : 0.841 8.593 4594 Z= 0.451 Chirality : 0.051 0.232 484 Planarity : 0.007 0.065 592 Dihedral : 7.600 31.322 465 Min Nonbonded Distance : 2.439 Molprobity Statistics. All-atom Clashscore : 23.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.83 % Favored : 93.17 % Rotamer: Outliers : 4.78 % Allowed : 13.48 % Favored : 81.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.25 % 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 are not related in a simple way. whole: -0.38 (0.40), residues: 410 helix: -5.05 (0.31), residues: 6 sheet: 0.04 (0.56), residues: 93 loop : -0.22 (0.34), residues: 311 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG L 77 TYR 0.015 0.002 TYR L 87 PHE 0.032 0.003 PHE A 456 TRP 0.044 0.003 TRP L 35 HIS 0.003 0.002 HIS A 505 Details of bonding type rmsd/Z covalent geometry : bond 0.00451 / 0.21 ( 3376) covalent geometry : angle 0.83641 / 0.45 ( 4580) SS BOND : bond 0.00432 / 0.21 ( 7) SS BOND : angle 1.73077 / 1.36 ( 14) hydrogen bonds : bond 0.04004 / 2.51 ( 58) hydrogen bonds : angle 7.62787 / 5.14 ( 117) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 820 Ramachandran restraints generated. 410 Oldfield, 0 Emsley, 410 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 820 Ramachandran restraints generated. 410 Oldfield, 0 Emsley, 410 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 105 residues out of total 356 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 88 time to evaluate : 0.130 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: H 52 ILE cc_start: 0.8253 (mm) cc_final: 0.7687 (mm) REVERT: H 69 ILE cc_start: 0.8809 (mt) cc_final: 0.8604 (mm) REVERT: H 72 ASP cc_start: 0.8162 (t0) cc_final: 0.7466 (p0) REVERT: H 73 MET cc_start: 0.8531 (mmm) cc_final: 0.8168 (mmt) REVERT: H 79 TYR cc_start: 0.7102 (m-80) cc_final: 0.6499 (m-80) REVERT: H 80 MET cc_start: 0.7682 (ttp) cc_final: 0.7052 (ttp) REVERT: H 90 TYR cc_start: 0.7336 (m-80) cc_final: 0.6774 (m-80) REVERT: H 91 TYR cc_start: 0.6989 (p90) cc_final: 0.6280 (p90) REVERT: L 46 LEU cc_start: 0.7099 (OUTLIER) cc_final: 0.6793 (pp) REVERT: A 355 ARG cc_start: 0.7567 (ptm-80) cc_final: 0.7283 (ptp-110) REVERT: A 471 GLU cc_start: 0.8221 (tp30) cc_final: 0.7814 (tp30) REVERT: A 490 PHE cc_start: 0.8479 (t80) cc_final: 0.8195 (t80) REVERT: A 493 GLN cc_start: 0.8271 (pt0) cc_final: 0.8017 (pm20) outliers start: 17 outliers final: 12 residues processed: 98 average time/residue: 0.0870 time to fit residues: 10.0160 Evaluate side-chains 91 residues out of total 356 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 78 time to evaluate : 0.134 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 18 VAL Chi-restraints excluded: chain H residue 25 SER Chi-restraints excluded: chain H residue 41 ARG Chi-restraints excluded: chain H residue 63 PHE Chi-restraints excluded: chain L residue 46 LEU Chi-restraints excluded: chain L residue 73 LEU Chi-restraints excluded: chain L residue 83 PHE Chi-restraints excluded: chain A residue 342 PHE Chi-restraints excluded: chain A residue 362 VAL Chi-restraints excluded: chain A residue 453 TYR Chi-restraints excluded: chain A residue 466 ARG Chi-restraints excluded: chain A residue 498 ARG Chi-restraints excluded: chain A residue 513 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 40 random chunks: chunk 26 optimal weight: 0.8980 chunk 29 optimal weight: 1.9990 chunk 4 optimal weight: 1.9990 chunk 6 optimal weight: 0.6980 chunk 9 optimal weight: 1.9990 chunk 24 optimal weight: 0.2980 chunk 11 optimal weight: 1.9990 chunk 35 optimal weight: 0.8980 chunk 2 optimal weight: 0.8980 chunk 22 optimal weight: 0.0980 chunk 27 optimal weight: 1.9990 overall best weight: 0.5780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4415 r_free = 0.4415 target = 0.137764 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.4284 r_free = 0.4284 target = 0.125676 restraints weight = 16077.883| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.4292 r_free = 0.4292 target = 0.126137 restraints weight = 14088.398| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.4297 r_free = 0.4297 target = 0.126621 restraints weight = 12761.149| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 32)----------------| | r_work = 0.4304 r_free = 0.4304 target = 0.127164 restraints weight = 11866.353| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 31)----------------| | r_work = 0.4307 r_free = 0.4307 target = 0.127400 restraints weight = 11015.470| |-----------------------------------------------------------------------------| r_work (final): 0.4280 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5948 moved from start: 0.8351 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.044 3383 Z= 0.217 Angle : 0.838 7.898 4594 Z= 0.455 Chirality : 0.052 0.265 484 Planarity : 0.007 0.052 592 Dihedral : 7.735 32.850 465 Min Nonbonded Distance : 2.460 Molprobity Statistics. All-atom Clashscore : 23.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.02 % Favored : 90.98 % Rotamer: Outliers : 6.74 % Allowed : 14.89 % Favored : 78.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.25 % 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 are not related in a simple way. whole: -1.35 (0.38), residues: 410 helix: -5.09 (0.31), residues: 6 sheet: -0.07 (0.54), residues: 93 loop : -1.15 (0.32), residues: 311 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG L 77 TYR 0.014 0.002 TYR A 369 PHE 0.034 0.003 PHE A 456 TRP 0.046 0.003 TRP L 35 HIS 0.003 0.001 HIS L 90 Details of bonding type rmsd/Z covalent geometry : bond 0.00471 / 0.22 ( 3376) covalent geometry : angle 0.83013 / 0.45 ( 4580) SS BOND : bond 0.00617 / 0.30 ( 7) SS BOND : angle 2.22934 / 1.65 ( 14) hydrogen bonds : bond 0.03971 / 2.36 ( 58) hydrogen bonds : angle 7.98693 / 5.43 ( 117) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 820 Ramachandran restraints generated. 410 Oldfield, 0 Emsley, 410 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 820 Ramachandran restraints generated. 410 Oldfield, 0 Emsley, 410 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 112 residues out of total 356 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 88 time to evaluate : 0.096 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: H 19 LYS cc_start: 0.8973 (tptm) cc_final: 0.8752 (tptp) REVERT: H 43 GLN cc_start: 0.8652 (mp10) cc_final: 0.8426 (mp10) REVERT: H 52 ILE cc_start: 0.8211 (mm) cc_final: 0.7983 (mm) REVERT: H 72 ASP cc_start: 0.7526 (t0) cc_final: 0.6750 (p0) REVERT: H 73 MET cc_start: 0.8468 (mmm) cc_final: 0.8093 (tpt) REVERT: H 80 MET cc_start: 0.8006 (ttp) cc_final: 0.7796 (tmm) REVERT: H 91 TYR cc_start: 0.6832 (p90) cc_final: 0.5852 (p90) REVERT: H 96 TYR cc_start: 0.6548 (t80) cc_final: 0.5939 (t80) REVERT: A 453 TYR cc_start: 0.6735 (OUTLIER) cc_final: 0.5944 (p90) REVERT: A 469 SER cc_start: 0.9242 (m) cc_final: 0.8964 (p) REVERT: A 471 GLU cc_start: 0.8327 (tp30) cc_final: 0.7981 (tp30) REVERT: A 490 PHE cc_start: 0.8442 (t80) cc_final: 0.8025 (t80) REVERT: A 495 TYR cc_start: 0.6262 (p90) cc_final: 0.6032 (p90) outliers start: 24 outliers final: 18 residues processed: 103 average time/residue: 0.0776 time to fit residues: 9.5516 Evaluate side-chains 102 residues out of total 356 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 83 time to evaluate : 0.125 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 18 VAL Chi-restraints excluded: chain H residue 25 SER Chi-restraints excluded: chain H residue 28 THR Chi-restraints excluded: chain H residue 41 ARG Chi-restraints excluded: chain H residue 63 PHE Chi-restraints excluded: chain H residue 77 THR Chi-restraints excluded: chain H residue 100 ASN Chi-restraints excluded: chain L residue 4 LEU Chi-restraints excluded: chain L residue 31 MET Chi-restraints excluded: chain L residue 73 LEU Chi-restraints excluded: chain L residue 83 PHE Chi-restraints excluded: chain L residue 91 TYR Chi-restraints excluded: chain L residue 102 THR Chi-restraints excluded: chain A residue 342 PHE Chi-restraints excluded: chain A residue 382 VAL Chi-restraints excluded: chain A residue 395 VAL Chi-restraints excluded: chain A residue 453 TYR Chi-restraints excluded: chain A residue 455 LEU Chi-restraints excluded: chain A residue 498 ARG Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 40 random chunks: chunk 20 optimal weight: 0.4980 chunk 24 optimal weight: 0.7980 chunk 29 optimal weight: 2.9990 chunk 6 optimal weight: 0.5980 chunk 8 optimal weight: 0.3980 chunk 31 optimal weight: 0.3980 chunk 30 optimal weight: 0.0970 chunk 28 optimal weight: 0.9990 chunk 11 optimal weight: 1.9990 chunk 13 optimal weight: 0.0570 chunk 7 optimal weight: 0.8980 overall best weight: 0.2896 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 493 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4446 r_free = 0.4446 target = 0.140280 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.4330 r_free = 0.4330 target = 0.128377 restraints weight = 15670.824| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.4334 r_free = 0.4334 target = 0.128488 restraints weight = 14009.663| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.4338 r_free = 0.4338 target = 0.128947 restraints weight = 13263.407| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.4343 r_free = 0.4343 target = 0.129364 restraints weight = 12150.696| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 21)----------------| | r_work = 0.4344 r_free = 0.4344 target = 0.129437 restraints weight = 11596.166| |-----------------------------------------------------------------------------| r_work (final): 0.4313 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5870 moved from start: 0.8542 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 3383 Z= 0.154 Angle : 0.788 9.165 4594 Z= 0.416 Chirality : 0.049 0.245 484 Planarity : 0.006 0.079 592 Dihedral : 7.162 30.067 465 Min Nonbonded Distance : 2.460 Molprobity Statistics. All-atom Clashscore : 19.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.00 % Favored : 90.00 % Rotamer: Outliers : 5.62 % Allowed : 18.82 % Favored : 75.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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 are not related in a simple way. whole: -1.49 (0.40), residues: 410 helix: -5.06 (0.20), residues: 12 sheet: -0.15 (0.58), residues: 86 loop : -1.14 (0.33), residues: 312 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG A 466 TYR 0.039 0.002 TYR A 369 PHE 0.017 0.002 PHE H 29 TRP 0.048 0.003 TRP L 35 HIS 0.001 0.000 HIS A 505 Details of bonding type rmsd/Z covalent geometry : bond 0.00337 / 0.15 ( 3376) covalent geometry : angle 0.78449 / 0.41 ( 4580) SS BOND : bond 0.00450 / 0.22 ( 7) SS BOND : angle 1.62688 / 1.21 ( 14) hydrogen bonds : bond 0.03466 / 2.18 ( 58) hydrogen bonds : angle 7.59312 / 5.09 ( 117) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 820 Ramachandran restraints generated. 410 Oldfield, 0 Emsley, 410 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 820 Ramachandran restraints generated. 410 Oldfield, 0 Emsley, 410 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 106 residues out of total 356 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 86 time to evaluate : 0.074 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: H 52 ILE cc_start: 0.8193 (mm) cc_final: 0.7927 (mm) REVERT: H 72 ASP cc_start: 0.8078 (t0) cc_final: 0.7247 (p0) REVERT: H 73 MET cc_start: 0.8483 (mmm) cc_final: 0.8026 (tpt) REVERT: H 91 TYR cc_start: 0.6871 (p90) cc_final: 0.5847 (p90) REVERT: A 453 TYR cc_start: 0.6693 (OUTLIER) cc_final: 0.5592 (p90) REVERT: A 457 ARG cc_start: 0.7288 (OUTLIER) cc_final: 0.6930 (ttt180) REVERT: A 469 SER cc_start: 0.9370 (m) cc_final: 0.9098 (p) REVERT: A 471 GLU cc_start: 0.8331 (tp30) cc_final: 0.7893 (tp30) REVERT: A 490 PHE cc_start: 0.8440 (t80) cc_final: 0.8031 (t80) outliers start: 20 outliers final: 13 residues processed: 99 average time/residue: 0.0502 time to fit residues: 5.9268 Evaluate side-chains 98 residues out of total 356 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 83 time to evaluate : 0.072 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 18 VAL Chi-restraints excluded: chain H residue 25 SER Chi-restraints excluded: chain H residue 41 ARG Chi-restraints excluded: chain H residue 77 THR Chi-restraints excluded: chain L residue 4 LEU Chi-restraints excluded: chain L residue 73 LEU Chi-restraints excluded: chain L residue 83 PHE Chi-restraints excluded: chain L residue 102 THR Chi-restraints excluded: chain A residue 342 PHE Chi-restraints excluded: chain A residue 382 VAL Chi-restraints excluded: chain A residue 395 VAL Chi-restraints excluded: chain A residue 453 TYR Chi-restraints excluded: chain A residue 457 ARG Chi-restraints excluded: chain A residue 498 ARG Chi-restraints excluded: chain A residue 510 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 40 random chunks: chunk 24 optimal weight: 0.7980 chunk 1 optimal weight: 0.2980 chunk 37 optimal weight: 1.9990 chunk 29 optimal weight: 0.6980 chunk 5 optimal weight: 1.9990 chunk 27 optimal weight: 0.8980 chunk 7 optimal weight: 1.9990 chunk 35 optimal weight: 0.4980 chunk 2 optimal weight: 0.8980 chunk 23 optimal weight: 0.9990 chunk 26 optimal weight: 0.6980 overall best weight: 0.5980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... L 89 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4402 r_free = 0.4402 target = 0.137311 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.4271 r_free = 0.4271 target = 0.124518 restraints weight = 15823.767| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.4278 r_free = 0.4278 target = 0.124862 restraints weight = 13902.827| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.4287 r_free = 0.4287 target = 0.125555 restraints weight = 12647.248| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 31)----------------| | r_work = 0.4289 r_free = 0.4289 target = 0.125770 restraints weight = 11667.817| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.4291 r_free = 0.4291 target = 0.125908 restraints weight = 11071.870| |-----------------------------------------------------------------------------| r_work (final): 0.4259 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5964 moved from start: 0.9232 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.046 3383 Z= 0.228 Angle : 0.901 9.501 4594 Z= 0.477 Chirality : 0.053 0.307 484 Planarity : 0.007 0.069 592 Dihedral : 7.748 35.651 465 Min Nonbonded Distance : 2.444 Molprobity Statistics. All-atom Clashscore : 28.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 13.17 % Favored : 86.83 % Rotamer: Outliers : 7.02 % Allowed : 21.35 % Favored : 71.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.25 % 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 are not related in a simple way. whole: -2.09 (0.38), residues: 410 helix: -5.16 (0.30), residues: 6 sheet: 0.06 (0.58), residues: 86 loop : -1.90 (0.31), residues: 318 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG L 77 TYR 0.024 0.002 TYR A 396 PHE 0.028 0.003 PHE A 377 TRP 0.051 0.003 TRP L 35 HIS 0.001 0.000 HIS L 90 Details of bonding type rmsd/Z covalent geometry : bond 0.00497 / 0.23 ( 3376) covalent geometry : angle 0.89722 / 0.48 ( 4580) SS BOND : bond 0.00554 / 0.27 ( 7) SS BOND : angle 1.67301 / 1.22 ( 14) hydrogen bonds : bond 0.04103 / 2.49 ( 58) hydrogen bonds : angle 7.84943 / 5.29 ( 117) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 820 Ramachandran restraints generated. 410 Oldfield, 0 Emsley, 410 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 820 Ramachandran restraints generated. 410 Oldfield, 0 Emsley, 410 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 113 residues out of total 356 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 88 time to evaluate : 0.124 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: H 43 GLN cc_start: 0.8606 (mp10) cc_final: 0.8377 (mp10) REVERT: H 72 ASP cc_start: 0.8304 (t0) cc_final: 0.7520 (p0) REVERT: H 73 MET cc_start: 0.8378 (mmm) cc_final: 0.8052 (tpp) REVERT: H 91 TYR cc_start: 0.6965 (p90) cc_final: 0.5879 (p90) REVERT: A 453 TYR cc_start: 0.7181 (OUTLIER) cc_final: 0.4998 (p90) REVERT: A 469 SER cc_start: 0.9352 (m) cc_final: 0.9039 (p) REVERT: A 471 GLU cc_start: 0.8348 (tp30) cc_final: 0.7984 (tp30) REVERT: A 490 PHE cc_start: 0.8386 (t80) cc_final: 0.7934 (t80) REVERT: A 493 GLN cc_start: 0.8188 (pt0) cc_final: 0.7775 (pt0) REVERT: A 495 TYR cc_start: 0.6401 (p90) cc_final: 0.6151 (p90) outliers start: 25 outliers final: 18 residues processed: 102 average time/residue: 0.0769 time to fit residues: 9.3618 Evaluate side-chains 105 residues out of total 356 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 86 time to evaluate : 0.140 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 18 VAL Chi-restraints excluded: chain H residue 25 SER Chi-restraints excluded: chain H residue 28 THR Chi-restraints excluded: chain H residue 41 ARG Chi-restraints excluded: chain H residue 63 PHE Chi-restraints excluded: chain H residue 77 THR Chi-restraints excluded: chain L residue 4 LEU Chi-restraints excluded: chain L residue 27 SER Chi-restraints excluded: chain L residue 31 MET Chi-restraints excluded: chain L residue 35 TRP Chi-restraints excluded: chain L residue 73 LEU Chi-restraints excluded: chain L residue 83 PHE Chi-restraints excluded: chain L residue 102 THR Chi-restraints excluded: chain A residue 342 PHE Chi-restraints excluded: chain A residue 382 VAL Chi-restraints excluded: chain A residue 453 TYR Chi-restraints excluded: chain A residue 455 LEU Chi-restraints excluded: chain A residue 498 ARG Chi-restraints excluded: chain A residue 510 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 40 random chunks: chunk 30 optimal weight: 0.2980 chunk 31 optimal weight: 0.9990 chunk 14 optimal weight: 0.9980 chunk 15 optimal weight: 0.9980 chunk 39 optimal weight: 0.0070 chunk 8 optimal weight: 0.7980 chunk 36 optimal weight: 3.9990 chunk 12 optimal weight: 0.8980 chunk 18 optimal weight: 0.6980 chunk 35 optimal weight: 0.0870 chunk 3 optimal weight: 1.9990 overall best weight: 0.3776 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4427 r_free = 0.4427 target = 0.139127 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.4300 r_free = 0.4300 target = 0.126415 restraints weight = 16003.325| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.4315 r_free = 0.4315 target = 0.127283 restraints weight = 13959.942| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 20)----------------| | r_work = 0.4318 r_free = 0.4318 target = 0.127587 restraints weight = 12197.265| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.4325 r_free = 0.4325 target = 0.128139 restraints weight = 11400.725| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 22)----------------| | r_work = 0.4325 r_free = 0.4325 target = 0.128139 restraints weight = 10708.377| |-----------------------------------------------------------------------------| r_work (final): 0.4290 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5898 moved from start: 0.9479 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 3383 Z= 0.177 Angle : 0.867 11.237 4594 Z= 0.452 Chirality : 0.051 0.273 484 Planarity : 0.006 0.046 592 Dihedral : 7.323 35.597 465 Min Nonbonded Distance : 2.436 Molprobity Statistics. All-atom Clashscore : 24.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 13.66 % Favored : 86.34 % Rotamer: Outliers : 6.18 % Allowed : 21.91 % Favored : 71.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.25 % 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 are not related in a simple way. whole: -2.28 (0.38), residues: 410 helix: -5.24 (0.20), residues: 12 sheet: -0.36 (0.59), residues: 86 loop : -1.85 (0.32), residues: 312 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG L 77 TYR 0.021 0.002 TYR A 423 PHE 0.022 0.002 PHE H 29 TRP 0.034 0.002 TRP L 35 HIS 0.001 0.000 HIS A 505 Details of bonding type rmsd/Z covalent geometry : bond 0.00396 / 0.18 ( 3376) covalent geometry : angle 0.85949 / 0.45 ( 4580) SS BOND : bond 0.00497 / 0.26 ( 7) SS BOND : angle 2.24408 / 1.60 ( 14) hydrogen bonds : bond 0.03882 / 2.31 ( 58) hydrogen bonds : angle 7.79459 / 5.18 ( 117) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 820 Ramachandran restraints generated. 410 Oldfield, 0 Emsley, 410 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 820 Ramachandran restraints generated. 410 Oldfield, 0 Emsley, 410 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 107 residues out of total 356 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 85 time to evaluate : 0.127 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: H 72 ASP cc_start: 0.8284 (t0) cc_final: 0.7524 (p0) REVERT: H 73 MET cc_start: 0.8378 (mmm) cc_final: 0.7768 (tpt) REVERT: H 86 ASP cc_start: 0.7425 (m-30) cc_final: 0.7212 (t0) REVERT: H 90 TYR cc_start: 0.7076 (m-80) cc_final: 0.6785 (m-80) REVERT: H 91 TYR cc_start: 0.6863 (p90) cc_final: 0.5727 (p90) REVERT: A 453 TYR cc_start: 0.7380 (OUTLIER) cc_final: 0.5184 (p90) REVERT: A 469 SER cc_start: 0.9307 (m) cc_final: 0.8934 (p) REVERT: A 471 GLU cc_start: 0.8388 (tp30) cc_final: 0.7729 (tm-30) REVERT: A 490 PHE cc_start: 0.8366 (t80) cc_final: 0.7890 (t80) REVERT: A 495 TYR cc_start: 0.5976 (p90) cc_final: 0.5679 (p90) outliers start: 22 outliers final: 15 residues processed: 98 average time/residue: 0.0827 time to fit residues: 9.5796 Evaluate side-chains 97 residues out of total 356 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 81 time to evaluate : 0.126 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 18 VAL Chi-restraints excluded: chain H residue 25 SER Chi-restraints excluded: chain H residue 28 THR Chi-restraints excluded: chain H residue 41 ARG Chi-restraints excluded: chain H residue 77 THR Chi-restraints excluded: chain H residue 79 TYR Chi-restraints excluded: chain L residue 4 LEU Chi-restraints excluded: chain L residue 31 MET Chi-restraints excluded: chain L residue 35 TRP Chi-restraints excluded: chain L residue 73 LEU Chi-restraints excluded: chain L residue 83 PHE Chi-restraints excluded: chain L residue 102 THR Chi-restraints excluded: chain A residue 342 PHE Chi-restraints excluded: chain A residue 382 VAL Chi-restraints excluded: chain A residue 453 TYR Chi-restraints excluded: chain A residue 498 ARG Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 40 random chunks: chunk 35 optimal weight: 0.7980 chunk 38 optimal weight: 0.9980 chunk 15 optimal weight: 0.8980 chunk 27 optimal weight: 0.2980 chunk 20 optimal weight: 0.8980 chunk 3 optimal weight: 0.0980 chunk 8 optimal weight: 0.6980 chunk 11 optimal weight: 1.9990 chunk 6 optimal weight: 0.4980 chunk 25 optimal weight: 0.9990 chunk 30 optimal weight: 0.1980 overall best weight: 0.3580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... L 89 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4424 r_free = 0.4424 target = 0.138982 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.4293 r_free = 0.4293 target = 0.126588 restraints weight = 15902.024| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.4298 r_free = 0.4298 target = 0.126741 restraints weight = 14102.560| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 22)----------------| | r_work = 0.4303 r_free = 0.4303 target = 0.127139 restraints weight = 13512.612| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.4306 r_free = 0.4306 target = 0.127402 restraints weight = 12632.293| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.4306 r_free = 0.4306 target = 0.127411 restraints weight = 12243.066| |-----------------------------------------------------------------------------| r_work (final): 0.4278 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5969 moved from start: 0.9746 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 3383 Z= 0.182 Angle : 0.912 12.304 4594 Z= 0.473 Chirality : 0.051 0.284 484 Planarity : 0.006 0.052 592 Dihedral : 7.307 36.065 465 Min Nonbonded Distance : 2.451 Molprobity Statistics. All-atom Clashscore : 24.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 13.66 % Favored : 86.34 % Rotamer: Outliers : 5.62 % Allowed : 25.56 % Favored : 68.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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 are not related in a simple way. whole: -2.41 (0.38), residues: 410 helix: -5.24 (0.20), residues: 12 sheet: 0.01 (0.59), residues: 89 loop : -2.13 (0.31), residues: 309 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG A 457 TYR 0.018 0.002 TYR H 91 PHE 0.026 0.002 PHE H 29 TRP 0.024 0.002 TRP L 35 HIS 0.001 0.000 HIS A 505 Details of bonding type rmsd/Z covalent geometry : bond 0.00410 / 0.18 ( 3376) covalent geometry : angle 0.90676 / 0.47 ( 4580) SS BOND : bond 0.00468 / 0.24 ( 7) SS BOND : angle 2.02297 / 1.45 ( 14) hydrogen bonds : bond 0.04140 / 2.42 ( 58) hydrogen bonds : angle 7.90586 / 5.20 ( 117) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 820 Ramachandran restraints generated. 410 Oldfield, 0 Emsley, 410 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 820 Ramachandran restraints generated. 410 Oldfield, 0 Emsley, 410 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 107 residues out of total 356 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 87 time to evaluate : 0.126 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: H 10 GLU cc_start: 0.7770 (mm-30) cc_final: 0.7415 (mm-30) REVERT: H 19 LYS cc_start: 0.8962 (tptp) cc_final: 0.8638 (tptp) REVERT: H 72 ASP cc_start: 0.8317 (t0) cc_final: 0.7559 (p0) REVERT: H 73 MET cc_start: 0.8353 (mmm) cc_final: 0.7745 (tpt) REVERT: H 91 TYR cc_start: 0.6889 (p90) cc_final: 0.5729 (p90) REVERT: L 86 TYR cc_start: 0.7568 (p90) cc_final: 0.7270 (p90) REVERT: A 453 TYR cc_start: 0.7500 (OUTLIER) cc_final: 0.5266 (p90) REVERT: A 469 SER cc_start: 0.9316 (m) cc_final: 0.8946 (p) REVERT: A 471 GLU cc_start: 0.8360 (tp30) cc_final: 0.8050 (tp30) REVERT: A 490 PHE cc_start: 0.8255 (t80) cc_final: 0.7774 (t80) outliers start: 20 outliers final: 17 residues processed: 99 average time/residue: 0.0816 time to fit residues: 9.5615 Evaluate side-chains 101 residues out of total 356 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 83 time to evaluate : 0.125 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 18 VAL Chi-restraints excluded: chain H residue 25 SER Chi-restraints excluded: chain H residue 41 ARG Chi-restraints excluded: chain H residue 59 TYR Chi-restraints excluded: chain H residue 63 PHE Chi-restraints excluded: chain H residue 77 THR Chi-restraints excluded: chain H residue 79 TYR Chi-restraints excluded: chain L residue 4 LEU Chi-restraints excluded: chain L residue 31 MET Chi-restraints excluded: chain L residue 35 TRP Chi-restraints excluded: chain L residue 73 LEU Chi-restraints excluded: chain L residue 83 PHE Chi-restraints excluded: chain L residue 102 THR Chi-restraints excluded: chain A residue 342 PHE Chi-restraints excluded: chain A residue 382 VAL Chi-restraints excluded: chain A residue 453 TYR Chi-restraints excluded: chain A residue 455 LEU Chi-restraints excluded: chain A residue 498 ARG Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 40 random chunks: chunk 18 optimal weight: 0.9980 chunk 20 optimal weight: 0.9990 chunk 2 optimal weight: 1.9990 chunk 38 optimal weight: 0.0980 chunk 35 optimal weight: 0.4980 chunk 12 optimal weight: 0.1980 chunk 17 optimal weight: 0.6980 chunk 21 optimal weight: 0.3980 chunk 39 optimal weight: 0.7980 chunk 4 optimal weight: 0.1980 chunk 0 optimal weight: 1.9990 overall best weight: 0.2780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** H 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 37 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 89 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4434 r_free = 0.4434 target = 0.139706 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.4307 r_free = 0.4307 target = 0.127106 restraints weight = 15743.897| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.4314 r_free = 0.4314 target = 0.127359 restraints weight = 13769.761| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 25)----------------| | r_work = 0.4317 r_free = 0.4317 target = 0.127690 restraints weight = 12448.317| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 31)----------------| | r_work = 0.4326 r_free = 0.4326 target = 0.128324 restraints weight = 11774.116| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.4325 r_free = 0.4325 target = 0.128259 restraints weight = 11209.985| |-----------------------------------------------------------------------------| r_work (final): 0.4298 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5858 moved from start: 0.9980 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 3383 Z= 0.168 Angle : 0.885 12.250 4594 Z= 0.456 Chirality : 0.050 0.269 484 Planarity : 0.006 0.043 592 Dihedral : 7.079 33.519 465 Min Nonbonded Distance : 2.470 Molprobity Statistics. All-atom Clashscore : 22.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 12.68 % Favored : 87.32 % Rotamer: Outliers : 4.21 % Allowed : 26.40 % Favored : 69.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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 are not related in a simple way. whole: -2.42 (0.38), residues: 410 helix: -5.27 (0.20), residues: 12 sheet: -0.01 (0.59), residues: 89 loop : -2.13 (0.32), residues: 309 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG A 457 TYR 0.023 0.002 TYR A 495 PHE 0.027 0.002 PHE H 29 TRP 0.051 0.003 TRP H 36 HIS 0.001 0.000 HIS A 505 Details of bonding type rmsd/Z covalent geometry : bond 0.00383 / 0.17 ( 3376) covalent geometry : angle 0.87769 / 0.45 ( 4580) SS BOND : bond 0.00597 / 0.31 ( 7) SS BOND : angle 2.20410 / 1.54 ( 14) hydrogen bonds : bond 0.03767 / 2.20 ( 58) hydrogen bonds : angle 7.51950 / 4.99 ( 117) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 820 Ramachandran restraints generated. 410 Oldfield, 0 Emsley, 410 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 820 Ramachandran restraints generated. 410 Oldfield, 0 Emsley, 410 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 99 residues out of total 356 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 84 time to evaluate : 0.129 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: H 10 GLU cc_start: 0.7484 (mm-30) cc_final: 0.7195 (mm-30) REVERT: H 19 LYS cc_start: 0.8859 (tptp) cc_final: 0.8535 (tptp) REVERT: H 72 ASP cc_start: 0.8346 (t0) cc_final: 0.7506 (p0) REVERT: H 73 MET cc_start: 0.8379 (mmm) cc_final: 0.7845 (tpt) REVERT: L 86 TYR cc_start: 0.7522 (p90) cc_final: 0.7298 (p90) REVERT: A 452 ARG cc_start: 0.5786 (OUTLIER) cc_final: 0.5523 (mtm-85) REVERT: A 453 TYR cc_start: 0.7529 (OUTLIER) cc_final: 0.5277 (p90) REVERT: A 469 SER cc_start: 0.9320 (m) cc_final: 0.8959 (p) REVERT: A 471 GLU cc_start: 0.8363 (tp30) cc_final: 0.7833 (tm-30) REVERT: A 490 PHE cc_start: 0.8260 (t80) cc_final: 0.7706 (t80) outliers start: 15 outliers final: 13 residues processed: 94 average time/residue: 0.0864 time to fit residues: 9.5181 Evaluate side-chains 97 residues out of total 356 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 82 time to evaluate : 0.126 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 25 SER Chi-restraints excluded: chain H residue 41 ARG Chi-restraints excluded: chain H residue 59 TYR Chi-restraints excluded: chain H residue 77 THR Chi-restraints excluded: chain H residue 79 TYR Chi-restraints excluded: chain L residue 31 MET Chi-restraints excluded: chain L residue 35 TRP Chi-restraints excluded: chain L residue 73 LEU Chi-restraints excluded: chain L residue 83 PHE Chi-restraints excluded: chain L residue 102 THR Chi-restraints excluded: chain A residue 342 PHE Chi-restraints excluded: chain A residue 452 ARG Chi-restraints excluded: chain A residue 453 TYR Chi-restraints excluded: chain A residue 455 LEU Chi-restraints excluded: chain A residue 498 ARG Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 40 random chunks: chunk 35 optimal weight: 0.9980 chunk 6 optimal weight: 0.5980 chunk 30 optimal weight: 0.3980 chunk 36 optimal weight: 1.9990 chunk 11 optimal weight: 1.9990 chunk 0 optimal weight: 0.9990 chunk 24 optimal weight: 0.6980 chunk 31 optimal weight: 0.6980 chunk 34 optimal weight: 1.9990 chunk 18 optimal weight: 0.9980 chunk 4 optimal weight: 0.9990 overall best weight: 0.6780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** H 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4373 r_free = 0.4373 target = 0.135389 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.4233 r_free = 0.4233 target = 0.122780 restraints weight = 15803.413| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 21)----------------| | r_work = 0.4240 r_free = 0.4240 target = 0.123218 restraints weight = 14156.544| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 22)----------------| | r_work = 0.4240 r_free = 0.4240 target = 0.123218 restraints weight = 12833.842| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 22)----------------| | r_work = 0.4240 r_free = 0.4240 target = 0.123218 restraints weight = 12833.841| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 22)----------------| | r_work = 0.4240 r_free = 0.4240 target = 0.123218 restraints weight = 12833.841| |-----------------------------------------------------------------------------| r_work (final): 0.4213 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6084 moved from start: 1.0536 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.041 3383 Z= 0.254 Angle : 1.013 11.575 4594 Z= 0.529 Chirality : 0.055 0.403 484 Planarity : 0.008 0.072 592 Dihedral : 8.209 45.564 465 Min Nonbonded Distance : 2.454 Molprobity Statistics. All-atom Clashscore : 34.28 Ramachandran Plot: Outliers : 0.24 % Allowed : 15.12 % Favored : 84.63 % Rotamer: Outliers : 5.34 % Allowed : 26.40 % Favored : 68.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.25 % 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 are not related in a simple way. whole: -2.69 (0.39), residues: 410 helix: -5.23 (0.31), residues: 6 sheet: -0.29 (0.70), residues: 76 loop : -2.31 (0.30), residues: 328 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG A 457 TYR 0.029 0.003 TYR A 495 PHE 0.031 0.003 PHE H 29 TRP 0.038 0.003 TRP H 36 HIS 0.002 0.001 HIS L 90 Details of bonding type rmsd/Z covalent geometry : bond 0.00559 / 0.25 ( 3376) covalent geometry : angle 1.00644 / 0.53 ( 4580) SS BOND : bond 0.00556 / 0.29 ( 7) SS BOND : angle 2.26475 / 1.58 ( 14) hydrogen bonds : bond 0.04368 / 2.59 ( 58) hydrogen bonds : angle 7.77996 / 5.25 ( 117) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 820 Ramachandran restraints generated. 410 Oldfield, 0 Emsley, 410 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 820 Ramachandran restraints generated. 410 Oldfield, 0 Emsley, 410 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 106 residues out of total 356 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 87 time to evaluate : 0.132 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: H 10 GLU cc_start: 0.7603 (mm-30) cc_final: 0.7186 (mm-30) REVERT: H 19 LYS cc_start: 0.8790 (tptp) cc_final: 0.8476 (tptp) REVERT: H 29 PHE cc_start: 0.5559 (t80) cc_final: 0.5246 (t80) REVERT: H 72 ASP cc_start: 0.8307 (t0) cc_final: 0.7339 (p0) REVERT: H 73 MET cc_start: 0.8267 (mmm) cc_final: 0.7344 (tpt) REVERT: L 86 TYR cc_start: 0.7657 (p90) cc_final: 0.7286 (p90) REVERT: A 452 ARG cc_start: 0.5737 (OUTLIER) cc_final: 0.5394 (mtm-85) REVERT: A 453 TYR cc_start: 0.7345 (OUTLIER) cc_final: 0.5021 (p90) REVERT: A 469 SER cc_start: 0.9313 (m) cc_final: 0.8899 (p) REVERT: A 471 GLU cc_start: 0.8338 (tp30) cc_final: 0.8131 (tp30) outliers start: 19 outliers final: 15 residues processed: 98 average time/residue: 0.0874 time to fit residues: 10.1276 Evaluate side-chains 102 residues out of total 356 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 85 time to evaluate : 0.132 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 25 SER Chi-restraints excluded: chain H residue 41 ARG Chi-restraints excluded: chain H residue 59 TYR Chi-restraints excluded: chain H residue 63 PHE Chi-restraints excluded: chain H residue 77 THR Chi-restraints excluded: chain H residue 79 TYR Chi-restraints excluded: chain L residue 4 LEU Chi-restraints excluded: chain L residue 27 SER Chi-restraints excluded: chain L residue 31 MET Chi-restraints excluded: chain L residue 35 TRP Chi-restraints excluded: chain L residue 73 LEU Chi-restraints excluded: chain L residue 83 PHE Chi-restraints excluded: chain L residue 102 THR Chi-restraints excluded: chain A residue 342 PHE Chi-restraints excluded: chain A residue 452 ARG Chi-restraints excluded: chain A residue 453 TYR Chi-restraints excluded: chain A residue 498 ARG Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 40 random chunks: chunk 31 optimal weight: 0.3980 chunk 36 optimal weight: 0.9980 chunk 11 optimal weight: 0.9990 chunk 0 optimal weight: 1.9990 chunk 12 optimal weight: 0.5980 chunk 33 optimal weight: 0.7980 chunk 6 optimal weight: 0.4980 chunk 34 optimal weight: 0.5980 chunk 10 optimal weight: 1.9990 chunk 24 optimal weight: 0.7980 chunk 28 optimal weight: 0.6980 overall best weight: 0.5580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** H 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 405 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4385 r_free = 0.4385 target = 0.136470 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.4243 r_free = 0.4243 target = 0.123808 restraints weight = 16209.653| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.4250 r_free = 0.4250 target = 0.124257 restraints weight = 14356.030| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.4255 r_free = 0.4255 target = 0.124674 restraints weight = 13174.239| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 22)----------------| | r_work = 0.4259 r_free = 0.4259 target = 0.124964 restraints weight = 12274.379| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 22)----------------| | r_work = 0.4259 r_free = 0.4259 target = 0.124964 restraints weight = 11939.173| |-----------------------------------------------------------------------------| r_work (final): 0.4230 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5999 moved from start: 1.0660 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.038 3383 Z= 0.224 Angle : 1.019 11.458 4594 Z= 0.524 Chirality : 0.053 0.210 484 Planarity : 0.007 0.057 592 Dihedral : 7.958 40.461 465 Min Nonbonded Distance : 2.451 Molprobity Statistics. All-atom Clashscore : 30.72 Ramachandran Plot: Outliers : 0.24 % Allowed : 15.85 % Favored : 83.90 % Rotamer: Outliers : 4.49 % Allowed : 29.21 % Favored : 66.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.25 % 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 are not related in a simple way. whole: -2.92 (0.39), residues: 410 helix: -5.30 (0.21), residues: 12 sheet: -0.76 (0.64), residues: 90 loop : -2.36 (0.31), residues: 308 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.002 ARG H 38 TYR 0.027 0.002 TYR A 495 PHE 0.025 0.003 PHE H 29 TRP 0.032 0.003 TRP H 36 HIS 0.000 0.000 HIS L 90 Details of bonding type rmsd/Z covalent geometry : bond 0.00504 / 0.22 ( 3376) covalent geometry : angle 1.01328 / 0.52 ( 4580) SS BOND : bond 0.00503 / 0.27 ( 7) SS BOND : angle 2.17293 / 1.52 ( 14) hydrogen bonds : bond 0.04085 / 2.44 ( 58) hydrogen bonds : angle 7.75516 / 5.18 ( 117) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1123.58 seconds wall clock time: 20 minutes 0.27 seconds (1200.27 seconds total)