Starting phenix.real_space_refine on Wed Jul 1 22:16:53 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/7wp5_32669/07_2026/7wp5_32669.cif Found real_map, /net/cci-nas-00/data/ceres_data/7wp5_32669/07_2026/7wp5_32669.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.9 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/7wp5_32669/07_2026/7wp5_32669.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7wp5_32669/07_2026/7wp5_32669.cif" restraint_files = "/net/cci-nas-00/data/ceres_data/7wp5_32669/07_2026/7wp5_32669.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/7wp5_32669/07_2026/7wp5_32669.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/7wp5_32669/07_2026/7wp5_32669.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7wp5_32669/07_2026/7wp5_32669.map" } resolution = 3.9 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= 0.008 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 15 5.16 5 C 2118 2.51 5 N 563 2.21 5 O 644 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 5 residue(s): 0.00s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 3340 Number of models: 1 Model: "" Number of chains: 4 Chain: "L" Number of atoms: 811 Number of conformers: 1 Conformer: "" Number of residues, atoms: 111, 811 Classifications: {'peptide': 111} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 7, 'TRANS': 103} Chain: "H" Number of atoms: 1017 Number of conformers: 1 Conformer: "" Number of residues, atoms: 131, 1017 Classifications: {'peptide': 131} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 2, 'TRANS': 128} Chain: "F" Number of atoms: 1484 Number of conformers: 1 Conformer: "" Number of residues, atoms: 183, 1484 Classifications: {'peptide': 183} Link IDs: {'PTRANS': 10, 'TRANS': 172} Chain: "A" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Time building chain proxies: 0.64, per 1000 atoms: 0.19 Number of scatterers: 3340 At special positions: 0 Unit cell: (77.022, 80.912, 81.69, 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 15 16.00 O 644 8.00 N 563 7.00 C 2118 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=3, symmetry=0 Simple disulfide: pdb=" SG CYS L 22 " - pdb=" SG CYS L 90 " distance=2.04 Simple disulfide: pdb=" SG CYS H 22 " - pdb=" SG CYS H 96 " distance=2.04 Simple disulfide: pdb=" SG CYS F 379 " - pdb=" SG CYS F 432 " 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 Links applied BETA1-4 " NAG A 1 " - " NAG A 2 " NAG-ASN " NAG A 1 " - " ASN F 343 " Time building additional restraints: 0.18 Conformation dependent library (CDL) restraints added in 76.8 milliseconds 838 Ramachandran restraints generated. 419 Oldfield, 0 Emsley, 419 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 766 Finding SS restraints... Secondary structure from input PDB file: 2 helices and 7 sheets defined 2.4% alpha, 21.4% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.05 Creating SS restraints... Processing helix chain 'F' and resid 336 through 340 removed outlier: 3.688A pdb=" N ASP F 339 " --> pdb=" O CYS F 336 " (cutoff:3.500A) removed outlier: 4.112A pdb=" N GLU F 340 " --> pdb=" O PRO F 337 " (cutoff:3.500A) No H-bonds generated for 'chain 'F' and resid 336 through 340' Processing helix chain 'F' and resid 406 through 410 Processing sheet with id=AA1, first strand: chain 'L' and resid 17 through 23 removed outlier: 3.750A pdb=" N SER L 74 " --> pdb=" O SER L 67 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'L' and resid 47 through 50 removed outlier: 5.740A pdb=" N LEU L 48 " --> pdb=" O GLN L 39 " (cutoff:3.500A) removed outlier: 6.151A pdb=" N GLN L 39 " --> pdb=" O LEU L 48 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'H' and resid 3 through 7 removed outlier: 3.600A pdb=" N VAL H 5 " --> pdb=" O ALA H 23 " (cutoff:3.500A) removed outlier: 3.790A pdb=" N SER H 71 " --> pdb=" O TYR H 80 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'H' and resid 10 through 12 removed outlier: 3.618A pdb=" N GLY H 10 " --> pdb=" O THR H 126 " (cutoff:3.500A) removed outlier: 3.570A pdb=" N THR H 125 " --> pdb=" O TYR H 94 " (cutoff:3.500A) removed outlier: 6.020A pdb=" N ARG H 38 " --> pdb=" O TRP H 47 " (cutoff:3.500A) removed outlier: 5.152A pdb=" N TRP H 47 " --> pdb=" O ARG H 38 " (cutoff:3.500A) removed outlier: 3.629A pdb=" N VAL H 50 " --> pdb=" O TYR H 59 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'H' and resid 103 through 104 removed outlier: 3.606A pdb=" N TYR H 103 " --> pdb=" O ASN H 111 " (cutoff:3.500A) removed outlier: 3.602A pdb=" N ASN H 111 " --> pdb=" O TYR H 103 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA5 Processing sheet with id=AA6, first strand: chain 'F' and resid 358 through 359 removed outlier: 3.735A pdb=" N VAL F 395 " --> pdb=" O ILE F 358 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'F' and resid 376 through 379 removed outlier: 3.527A pdb=" N THR F 376 " --> pdb=" O ALA F 435 " (cutoff:3.500A) 63 hydrogen bonds defined for protein. 153 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: 0.23 Time building geometry restraints manager: 0.25 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 1052 1.34 - 1.46: 852 1.46 - 1.58: 1503 1.58 - 1.70: 0 1.70 - 1.82: 19 Bond restraints: 3426 Sorted by residual: bond pdb=" CA SER F 446 " pdb=" C SER F 446 " ideal model delta sigma weight residual 1.522 1.544 -0.022 1.37e-02 5.33e+03 2.59e+00 bond pdb=" CA CYS F 336 " pdb=" C CYS F 336 " ideal model delta sigma weight residual 1.525 1.557 -0.032 2.10e-02 2.27e+03 2.31e+00 bond pdb=" C3 NAG A 1 " pdb=" O3 NAG A 1 " ideal model delta sigma weight residual 1.403 1.432 -0.029 2.00e-02 2.50e+03 2.16e+00 bond pdb=" C3 NAG A 2 " pdb=" O3 NAG A 2 " ideal model delta sigma weight residual 1.403 1.431 -0.028 2.00e-02 2.50e+03 2.02e+00 bond pdb=" C4 NAG A 1 " pdb=" O4 NAG A 1 " ideal model delta sigma weight residual 1.409 1.435 -0.026 2.00e-02 2.50e+03 1.75e+00 ... (remaining 3421 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.60: 4522 2.60 - 5.21: 110 5.21 - 7.81: 17 7.81 - 10.41: 1 10.41 - 13.01: 4 Bond angle restraints: 4654 Sorted by residual: angle pdb=" C ASN F 477 " pdb=" N LYS F 478 " pdb=" CA LYS F 478 " ideal model delta sigma weight residual 121.80 132.91 -11.11 2.44e+00 1.68e-01 2.07e+01 angle pdb=" C GLY L 52 " pdb=" N ASN L 53 " pdb=" CA ASN L 53 " ideal model delta sigma weight residual 121.54 130.03 -8.49 1.91e+00 2.74e-01 1.98e+01 angle pdb=" C TYR F 369 " pdb=" N ASN F 370 " pdb=" CA ASN F 370 " ideal model delta sigma weight residual 122.19 128.42 -6.23 1.41e+00 5.03e-01 1.95e+01 angle pdb=" C SER F 359 " pdb=" N ASN F 360 " pdb=" CA ASN F 360 " ideal model delta sigma weight residual 122.46 128.68 -6.22 1.41e+00 5.03e-01 1.95e+01 angle pdb=" CA LEU F 371 " pdb=" CB LEU F 371 " pdb=" CG LEU F 371 " ideal model delta sigma weight residual 116.30 129.31 -13.01 3.50e+00 8.16e-02 1.38e+01 ... (remaining 4649 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 14.85: 1693 14.85 - 29.70: 218 29.70 - 44.55: 56 44.55 - 59.41: 6 59.41 - 74.26: 5 Dihedral angle restraints: 1978 sinusoidal: 758 harmonic: 1220 Sorted by residual: dihedral pdb=" CA ASN F 460 " pdb=" C ASN F 460 " pdb=" N LEU F 461 " pdb=" CA LEU F 461 " ideal model delta harmonic sigma weight residual -180.00 -147.27 -32.73 0 5.00e+00 4.00e-02 4.29e+01 dihedral pdb=" CA ASN F 477 " pdb=" C ASN F 477 " pdb=" N LYS F 478 " pdb=" CA LYS F 478 " ideal model delta harmonic sigma weight residual -180.00 -155.90 -24.10 0 5.00e+00 4.00e-02 2.32e+01 dihedral pdb=" CA ASN H 115 " pdb=" C ASN H 115 " pdb=" N TYR H 116 " pdb=" CA TYR H 116 " ideal model delta harmonic sigma weight residual -180.00 -159.61 -20.39 0 5.00e+00 4.00e-02 1.66e+01 ... (remaining 1975 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.066: 392 0.066 - 0.132: 80 0.132 - 0.198: 21 0.198 - 0.264: 1 0.264 - 0.329: 1 Chirality restraints: 495 Sorted by residual: chirality pdb=" C1 NAG A 1 " pdb=" ND2 ASN F 343 " pdb=" C2 NAG A 1 " pdb=" O5 NAG A 1 " both_signs ideal model delta sigma weight residual False -2.40 -2.07 -0.33 2.00e-01 2.50e+01 2.71e+00 chirality pdb=" C1 NAG A 2 " pdb=" O4 NAG A 1 " pdb=" C2 NAG A 2 " pdb=" O5 NAG A 2 " both_signs ideal model delta sigma weight residual False -2.40 -2.37 -0.03 2.00e-02 2.50e+03 2.11e+00 chirality pdb=" CB THR H 91 " pdb=" CA THR H 91 " pdb=" OG1 THR H 91 " pdb=" CG2 THR H 91 " both_signs ideal model delta sigma weight residual False 2.55 2.35 0.20 2.00e-01 2.50e+01 9.87e-01 ... (remaining 492 not shown) Planarity restraints: 604 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C2 NAG A 1 " -0.278 2.00e-02 2.50e+03 2.38e-01 7.10e+02 pdb=" C7 NAG A 1 " 0.061 2.00e-02 2.50e+03 pdb=" C8 NAG A 1 " 0.016 2.00e-02 2.50e+03 pdb=" N2 NAG A 1 " 0.402 2.00e-02 2.50e+03 pdb=" O7 NAG A 1 " -0.202 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C2 NAG A 2 " 0.028 2.00e-02 2.50e+03 2.34e-02 6.84e+00 pdb=" C7 NAG A 2 " -0.007 2.00e-02 2.50e+03 pdb=" C8 NAG A 2 " 0.021 2.00e-02 2.50e+03 pdb=" N2 NAG A 2 " -0.037 2.00e-02 2.50e+03 pdb=" O7 NAG A 2 " -0.005 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C ALA F 411 " 0.034 5.00e-02 4.00e+02 5.16e-02 4.26e+00 pdb=" N PRO F 412 " -0.089 5.00e-02 4.00e+02 pdb=" CA PRO F 412 " 0.026 5.00e-02 4.00e+02 pdb=" CD PRO F 412 " 0.029 5.00e-02 4.00e+02 ... (remaining 601 not shown) Histogram of nonbonded interaction distances: 2.28 - 2.80: 935 2.80 - 3.33: 2725 3.33 - 3.85: 5189 3.85 - 4.38: 5630 4.38 - 4.90: 9998 Nonbonded interactions: 24477 Sorted by model distance: nonbonded pdb=" OD2 ASP F 442 " pdb=" OH TYR F 451 " model vdw 2.278 3.040 nonbonded pdb=" OD2 ASP F 398 " pdb=" OH TYR F 423 " model vdw 2.305 3.040 nonbonded pdb=" NE2 HIS L 36 " pdb=" O ASN H 115 " model vdw 2.326 3.120 nonbonded pdb=" NE2 GLN L 39 " pdb=" OD1 ASP L 84 " model vdw 2.364 3.120 nonbonded pdb=" OG SER H 130 " pdb=" N SER H 131 " model vdw 2.373 3.120 ... (remaining 24472 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=0.00 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: 15.120 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: 0.070 Check model and map are aligned: 0.010 Set scattering table: 0.010 Process input model: 3.310 Find NCS groups from input model: 0.010 Set up NCS constraints: 0.000 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:0.810 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 19.350 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7366 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 : 0.005 0.039 3431 Z= 0.250 Angle : 1.027 13.015 4666 Z= 0.561 Chirality : 0.060 0.329 495 Planarity : 0.012 0.238 603 Dihedral : 14.109 74.258 1203 Min Nonbonded Distance : 2.278 Molprobity Statistics. All-atom Clashscore : 4.75 Ramachandran Plot: Outliers : 0.24 % Allowed : 9.07 % Favored : 90.69 % Rotamer: Outliers : 0.56 % Allowed : 10.64 % Favored : 88.80 % 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: -4.27 (0.34), residues: 419 helix: -5.34 (0.29), residues: 11 sheet: -1.85 (0.43), residues: 135 loop : -3.47 (0.29), residues: 273 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG L 56 TYR 0.018 0.002 TYR F 508 PHE 0.017 0.003 PHE F 515 TRP 0.011 0.002 TRP H 47 HIS 0.005 0.002 HIS L 36 Details of bonding type rmsd/Z covalent geometry : bond 0.00511 / 0.25 ( 3426) covalent geometry : angle 1.02540 / 0.56 ( 4654) SS BOND : bond 0.00438 / 0.22 ( 3) SS BOND : angle 0.69593 / 0.37 ( 6) hydrogen bonds : bond 0.30171 / 22.56 ( 63) hydrogen bonds : angle 11.42120 / 8.85 ( 153) link_BETA1-4 : bond 0.00664 / 0.35 ( 1) link_BETA1-4 : angle 1.18892 / 0.66 ( 3) link_NAG-ASN : bond 0.00320 / 0.17 ( 1) link_NAG-ASN : angle 2.42326 / 1.27 ( 3) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 838 Ramachandran restraints generated. 419 Oldfield, 0 Emsley, 419 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 838 Ramachandran restraints generated. 419 Oldfield, 0 Emsley, 419 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 113 residues out of total 357 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 111 time to evaluate : 0.120 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: L 108 LEU cc_start: 0.8612 (tp) cc_final: 0.8355 (tt) REVERT: H 51 MET cc_start: 0.8021 (ttp) cc_final: 0.7744 (ttm) REVERT: F 339 ASP cc_start: 0.7344 (t70) cc_final: 0.6809 (t70) REVERT: F 368 LEU cc_start: 0.8505 (mt) cc_final: 0.8287 (mt) REVERT: F 406 GLU cc_start: 0.8286 (mm-30) cc_final: 0.7871 (mm-30) outliers start: 2 outliers final: 1 residues processed: 113 average time/residue: 0.0563 time to fit residues: 7.5838 Evaluate side-chains 84 residues out of total 357 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 83 time to evaluate : 0.095 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain F residue 497 PHE Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 42 random chunks: chunk 24 optimal weight: 0.9980 chunk 26 optimal weight: 2.9990 chunk 2 optimal weight: 1.9990 chunk 16 optimal weight: 0.9980 chunk 32 optimal weight: 1.9990 chunk 31 optimal weight: 0.8980 chunk 25 optimal weight: 0.3980 chunk 19 optimal weight: 1.9990 chunk 30 optimal weight: 0.5980 chunk 22 optimal weight: 0.2980 chunk 37 optimal weight: 0.5980 overall best weight: 0.5580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... L 81 GLN H 115 ASN F 417 ASN F 448 ASN F 450 ASN F 474 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4019 r_free = 0.4019 target = 0.170488 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3833 r_free = 0.3833 target = 0.154478 restraints weight = 6549.418| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 24)----------------| | r_work = 0.3879 r_free = 0.3879 target = 0.158864 restraints weight = 4921.465| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 25)----------------| | r_work = 0.3907 r_free = 0.3907 target = 0.161213 restraints weight = 2330.711| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 33)----------------| | r_work = 0.3917 r_free = 0.3917 target = 0.162179 restraints weight = 1715.628| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.3922 r_free = 0.3922 target = 0.162541 restraints weight = 1409.803| |-----------------------------------------------------------------------------| r_work (final): 0.3921 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3922 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3922 r_free = 0.3922 target_work(ls_wunit_k1) = 0.162 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 3 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3921 r_free = 0.3921 target_work(ls_wunit_k1) = 0.162 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 3 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 6 (11 function evaluations) r_final: 0.3921 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7291 moved from start: 0.1957 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.021 3431 Z= 0.156 Angle : 0.741 8.618 4666 Z= 0.375 Chirality : 0.048 0.209 495 Planarity : 0.005 0.035 603 Dihedral : 6.719 38.015 480 Min Nonbonded Distance : 2.549 Molprobity Statistics. All-atom Clashscore : 8.89 Ramachandran Plot: Outliers : 0.24 % Allowed : 9.55 % Favored : 90.21 % Rotamer: Outliers : 4.20 % Allowed : 18.49 % Favored : 77.31 % 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: -3.72 (0.36), residues: 419 helix: -4.09 (1.01), residues: 13 sheet: -1.50 (0.42), residues: 143 loop : -3.12 (0.33), residues: 263 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG F 457 TYR 0.024 0.001 TYR F 369 PHE 0.012 0.002 PHE F 338 TRP 0.008 0.001 TRP L 100 HIS 0.002 0.000 HIS H 35 Details of bonding type rmsd/Z covalent geometry : bond 0.00335 / 0.16 ( 3426) covalent geometry : angle 0.73653 / 0.37 ( 4654) SS BOND : bond 0.00480 / 0.23 ( 3) SS BOND : angle 1.85708 / 1.01 ( 6) hydrogen bonds : bond 0.04726 / 3.70 ( 63) hydrogen bonds : angle 7.79174 / 5.78 ( 153) link_BETA1-4 : bond 0.00517 / 0.27 ( 1) link_BETA1-4 : angle 1.14371 / 0.64 ( 3) link_NAG-ASN : bond 0.00283 / 0.15 ( 1) link_NAG-ASN : angle 2.18834 / 1.16 ( 3) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 838 Ramachandran restraints generated. 419 Oldfield, 0 Emsley, 419 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 838 Ramachandran restraints generated. 419 Oldfield, 0 Emsley, 419 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 98 residues out of total 357 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 83 time to evaluate : 0.078 Fit side-chains revert: symmetry clash REVERT: L 108 LEU cc_start: 0.8541 (tp) cc_final: 0.8234 (tt) REVERT: H 38 ARG cc_start: 0.8229 (ptt180) cc_final: 0.7958 (ptm-80) REVERT: H 51 MET cc_start: 0.7669 (ttp) cc_final: 0.7331 (ttm) REVERT: H 116 TYR cc_start: 0.8558 (m-80) cc_final: 0.8272 (m-80) REVERT: F 365 TYR cc_start: 0.8086 (m-10) cc_final: 0.7864 (m-10) REVERT: F 406 GLU cc_start: 0.8705 (mm-30) cc_final: 0.7637 (mm-30) outliers start: 15 outliers final: 11 residues processed: 88 average time/residue: 0.0413 time to fit residues: 4.6218 Evaluate side-chains 92 residues out of total 357 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 81 time to evaluate : 0.073 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain L residue 23 THR Chi-restraints excluded: chain L residue 110 VAL Chi-restraints excluded: chain H residue 25 SER Chi-restraints excluded: chain H residue 30 SER Chi-restraints excluded: chain H residue 53 PHE Chi-restraints excluded: chain H residue 96 CYS Chi-restraints excluded: chain F residue 371 LEU Chi-restraints excluded: chain F residue 401 VAL Chi-restraints excluded: chain F residue 470 THR Chi-restraints excluded: chain F residue 497 PHE Chi-restraints excluded: chain F residue 511 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 42 random chunks: chunk 18 optimal weight: 2.9990 chunk 31 optimal weight: 0.9990 chunk 26 optimal weight: 2.9990 chunk 20 optimal weight: 0.9980 chunk 24 optimal weight: 0.6980 chunk 3 optimal weight: 1.9990 chunk 7 optimal weight: 2.9990 chunk 21 optimal weight: 2.9990 chunk 10 optimal weight: 0.6980 chunk 17 optimal weight: 0.6980 chunk 39 optimal weight: 2.9990 overall best weight: 0.8182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** H 35 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 115 ASN F 370 ASN ** F 409 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 448 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3989 r_free = 0.3989 target = 0.167657 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3807 r_free = 0.3807 target = 0.152212 restraints weight = 6612.082| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 24)----------------| | r_work = 0.3853 r_free = 0.3853 target = 0.156491 restraints weight = 5057.316| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3874 r_free = 0.3874 target = 0.158317 restraints weight = 2318.598| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 31)----------------| | r_work = 0.3895 r_free = 0.3895 target = 0.160096 restraints weight = 1682.632| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.3898 r_free = 0.3898 target = 0.160327 restraints weight = 1358.395| |-----------------------------------------------------------------------------| r_work (final): 0.3900 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3900 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3900 r_free = 0.3900 target_work(ls_wunit_k1) = 0.160 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 3 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3900 r_free = 0.3900 target_work(ls_wunit_k1) = 0.160 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 3 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 5 (10 function evaluations) r_final: 0.3900 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7331 moved from start: 0.2346 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.026 3431 Z= 0.182 Angle : 0.721 7.812 4666 Z= 0.364 Chirality : 0.047 0.176 495 Planarity : 0.004 0.037 603 Dihedral : 6.534 33.019 480 Min Nonbonded Distance : 2.452 Molprobity Statistics. All-atom Clashscore : 9.04 Ramachandran Plot: Outliers : 0.24 % Allowed : 10.02 % Favored : 89.74 % Rotamer: Outliers : 6.44 % Allowed : 18.21 % Favored : 75.35 % 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: -3.61 (0.36), residues: 419 helix: -4.32 (0.83), residues: 13 sheet: -1.32 (0.43), residues: 136 loop : -3.07 (0.33), residues: 270 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG F 355 TYR 0.017 0.001 TYR F 369 PHE 0.012 0.002 PHE F 338 TRP 0.009 0.001 TRP L 37 HIS 0.003 0.001 HIS H 35 Details of bonding type rmsd/Z covalent geometry : bond 0.00400 / 0.18 ( 3426) covalent geometry : angle 0.71824 / 0.36 ( 4654) SS BOND : bond 0.00532 / 0.26 ( 3) SS BOND : angle 1.57420 / 0.84 ( 6) hydrogen bonds : bond 0.04009 / 3.15 ( 63) hydrogen bonds : angle 6.93337 / 5.08 ( 153) link_BETA1-4 : bond 0.00500 / 0.26 ( 1) link_BETA1-4 : angle 1.22009 / 0.65 ( 3) link_NAG-ASN : bond 0.00091 / 0.05 ( 1) link_NAG-ASN : angle 1.08240 / 0.57 ( 3) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 838 Ramachandran restraints generated. 419 Oldfield, 0 Emsley, 419 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 838 Ramachandran restraints generated. 419 Oldfield, 0 Emsley, 419 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 107 residues out of total 357 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 84 time to evaluate : 0.146 Fit side-chains revert: symmetry clash REVERT: L 108 LEU cc_start: 0.8555 (tp) cc_final: 0.8232 (tt) REVERT: L 111 LEU cc_start: 0.7540 (OUTLIER) cc_final: 0.7303 (mt) REVERT: H 51 MET cc_start: 0.7719 (ttp) cc_final: 0.7425 (ttm) REVERT: F 365 TYR cc_start: 0.8116 (m-10) cc_final: 0.7870 (m-10) REVERT: F 406 GLU cc_start: 0.8853 (mm-30) cc_final: 0.8550 (mm-30) REVERT: F 425 LEU cc_start: 0.8550 (OUTLIER) cc_final: 0.8308 (mp) outliers start: 23 outliers final: 13 residues processed: 94 average time/residue: 0.0471 time to fit residues: 5.6374 Evaluate side-chains 96 residues out of total 357 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 81 time to evaluate : 0.090 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain L residue 5 THR Chi-restraints excluded: chain L residue 10 VAL Chi-restraints excluded: chain L residue 23 THR Chi-restraints excluded: chain L residue 110 VAL Chi-restraints excluded: chain L residue 111 LEU Chi-restraints excluded: chain H residue 30 SER Chi-restraints excluded: chain H residue 53 PHE Chi-restraints excluded: chain H residue 96 CYS Chi-restraints excluded: chain F residue 362 VAL Chi-restraints excluded: chain F residue 371 LEU Chi-restraints excluded: chain F residue 418 ILE Chi-restraints excluded: chain F residue 425 LEU Chi-restraints excluded: chain F residue 430 THR Chi-restraints excluded: chain F residue 470 THR Chi-restraints excluded: chain F residue 511 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 42 random chunks: chunk 15 optimal weight: 1.9990 chunk 36 optimal weight: 1.9990 chunk 37 optimal weight: 0.0980 chunk 2 optimal weight: 0.0170 chunk 31 optimal weight: 0.2980 chunk 13 optimal weight: 2.9990 chunk 17 optimal weight: 0.9990 chunk 10 optimal weight: 0.8980 chunk 11 optimal weight: 1.9990 chunk 28 optimal weight: 2.9990 chunk 14 optimal weight: 0.9990 overall best weight: 0.4620 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... H 115 ASN ** F 409 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 448 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4008 r_free = 0.4008 target = 0.169306 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3809 r_free = 0.3809 target = 0.152819 restraints weight = 6411.577| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3849 r_free = 0.3849 target = 0.156042 restraints weight = 3687.749| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3873 r_free = 0.3873 target = 0.158099 restraints weight = 2414.104| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 33)----------------| | r_work = 0.3892 r_free = 0.3892 target = 0.159611 restraints weight = 1772.775| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.3905 r_free = 0.3905 target = 0.160644 restraints weight = 1410.494| |-----------------------------------------------------------------------------| r_work (final): 0.3907 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3907 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3907 r_free = 0.3907 target_work(ls_wunit_k1) = 0.161 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 3 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3907 r_free = 0.3907 target_work(ls_wunit_k1) = 0.161 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 3 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (8 function evaluations) r_final: 0.3907 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7332 moved from start: 0.2565 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.023 3431 Z= 0.135 Angle : 0.666 7.579 4666 Z= 0.337 Chirality : 0.045 0.162 495 Planarity : 0.004 0.034 603 Dihedral : 5.970 25.399 478 Min Nonbonded Distance : 2.510 Molprobity Statistics. All-atom Clashscore : 8.59 Ramachandran Plot: Outliers : 0.24 % Allowed : 8.59 % Favored : 91.17 % Rotamer: Outliers : 6.72 % Allowed : 20.17 % Favored : 73.11 % 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: -3.40 (0.37), residues: 419 helix: -4.14 (0.94), residues: 13 sheet: -1.02 (0.44), residues: 136 loop : -3.03 (0.33), residues: 270 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG F 355 TYR 0.016 0.001 TYR F 369 PHE 0.009 0.001 PHE F 374 TRP 0.008 0.001 TRP F 436 HIS 0.003 0.001 HIS L 36 Details of bonding type rmsd/Z covalent geometry : bond 0.00297 / 0.13 ( 3426) covalent geometry : angle 0.66450 / 0.34 ( 4654) SS BOND : bond 0.00347 / 0.17 ( 3) SS BOND : angle 1.16847 / 0.62 ( 6) hydrogen bonds : bond 0.03435 / 2.71 ( 63) hydrogen bonds : angle 6.58700 / 4.81 ( 153) link_BETA1-4 : bond 0.00531 / 0.28 ( 1) link_BETA1-4 : angle 1.17133 / 0.62 ( 3) link_NAG-ASN : bond 0.00272 / 0.14 ( 1) link_NAG-ASN : angle 1.15830 / 0.62 ( 3) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 838 Ramachandran restraints generated. 419 Oldfield, 0 Emsley, 419 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 838 Ramachandran restraints generated. 419 Oldfield, 0 Emsley, 419 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 107 residues out of total 357 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 83 time to evaluate : 0.086 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: L 91 GLN cc_start: 0.8044 (tt0) cc_final: 0.7836 (tt0) REVERT: L 108 LEU cc_start: 0.8485 (tp) cc_final: 0.8198 (tt) REVERT: F 365 TYR cc_start: 0.8073 (m-10) cc_final: 0.7831 (m-10) REVERT: F 406 GLU cc_start: 0.8837 (mm-30) cc_final: 0.8479 (mm-30) REVERT: F 425 LEU cc_start: 0.8466 (OUTLIER) cc_final: 0.8224 (mp) REVERT: F 495 TYR cc_start: 0.6469 (OUTLIER) cc_final: 0.5678 (t80) outliers start: 24 outliers final: 16 residues processed: 97 average time/residue: 0.0360 time to fit residues: 4.5415 Evaluate side-chains 97 residues out of total 357 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 79 time to evaluate : 0.087 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain L residue 5 THR Chi-restraints excluded: chain L residue 23 THR Chi-restraints excluded: chain L residue 35 VAL Chi-restraints excluded: chain L residue 53 ASN Chi-restraints excluded: chain L residue 110 VAL Chi-restraints excluded: chain H residue 30 SER Chi-restraints excluded: chain H residue 53 PHE Chi-restraints excluded: chain H residue 96 CYS Chi-restraints excluded: chain H residue 127 VAL Chi-restraints excluded: chain F residue 362 VAL Chi-restraints excluded: chain F residue 371 LEU Chi-restraints excluded: chain F residue 401 VAL Chi-restraints excluded: chain F residue 418 ILE Chi-restraints excluded: chain F residue 425 LEU Chi-restraints excluded: chain F residue 430 THR Chi-restraints excluded: chain F residue 470 THR Chi-restraints excluded: chain F residue 495 TYR Chi-restraints excluded: chain F residue 511 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 42 random chunks: chunk 3 optimal weight: 1.9990 chunk 38 optimal weight: 0.0370 chunk 15 optimal weight: 0.0570 chunk 32 optimal weight: 2.9990 chunk 21 optimal weight: 0.7980 chunk 23 optimal weight: 1.9990 chunk 22 optimal weight: 0.6980 chunk 5 optimal weight: 0.9980 chunk 37 optimal weight: 0.5980 chunk 17 optimal weight: 0.0980 chunk 1 optimal weight: 0.0770 overall best weight: 0.1734 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... H 115 ASN ** F 409 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 422 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4063 r_free = 0.4063 target = 0.173065 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3873 r_free = 0.3873 target = 0.157132 restraints weight = 6351.390| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.3915 r_free = 0.3915 target = 0.160412 restraints weight = 3605.636| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 43)----------------| | r_work = 0.3942 r_free = 0.3942 target = 0.162633 restraints weight = 2352.764| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 37)----------------| | r_work = 0.3960 r_free = 0.3960 target = 0.164160 restraints weight = 1687.934| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 31)----------------| | r_work = 0.3971 r_free = 0.3971 target = 0.165142 restraints weight = 1302.941| |-----------------------------------------------------------------------------| r_work (final): 0.3966 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7245 moved from start: 0.2861 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.023 3431 Z= 0.104 Angle : 0.624 7.210 4666 Z= 0.314 Chirality : 0.044 0.154 495 Planarity : 0.004 0.030 603 Dihedral : 5.547 25.606 478 Min Nonbonded Distance : 2.553 Molprobity Statistics. All-atom Clashscore : 7.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.88 % Favored : 92.12 % Rotamer: Outliers : 5.04 % Allowed : 22.41 % Favored : 72.55 % 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: -3.17 (0.38), residues: 419 helix: -4.04 (1.00), residues: 13 sheet: -0.75 (0.44), residues: 137 loop : -2.94 (0.33), residues: 269 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG F 454 TYR 0.012 0.001 TYR F 369 PHE 0.008 0.001 PHE F 374 TRP 0.009 0.001 TRP F 436 HIS 0.002 0.001 HIS L 36 Details of bonding type rmsd/Z covalent geometry : bond 0.00224 / 0.10 ( 3426) covalent geometry : angle 0.62217 / 0.31 ( 4654) SS BOND : bond 0.00192 / 0.09 ( 3) SS BOND : angle 0.88739 / 0.46 ( 6) hydrogen bonds : bond 0.02934 / 2.32 ( 63) hydrogen bonds : angle 6.11812 / 4.41 ( 153) link_BETA1-4 : bond 0.00450 / 0.24 ( 1) link_BETA1-4 : angle 1.21329 / 0.64 ( 3) link_NAG-ASN : bond 0.00366 / 0.19 ( 1) link_NAG-ASN : angle 1.13865 / 0.61 ( 3) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 838 Ramachandran restraints generated. 419 Oldfield, 0 Emsley, 419 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 838 Ramachandran restraints generated. 419 Oldfield, 0 Emsley, 419 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 99 residues out of total 357 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 81 time to evaluate : 0.074 Fit side-chains revert: symmetry clash REVERT: L 23 THR cc_start: 0.7551 (OUTLIER) cc_final: 0.7202 (p) REVERT: L 108 LEU cc_start: 0.8483 (tp) cc_final: 0.8230 (tt) REVERT: H 12 VAL cc_start: 0.5868 (t) cc_final: 0.5592 (p) REVERT: F 365 TYR cc_start: 0.7969 (m-80) cc_final: 0.7718 (m-10) REVERT: F 425 LEU cc_start: 0.8402 (OUTLIER) cc_final: 0.8166 (mp) outliers start: 18 outliers final: 13 residues processed: 91 average time/residue: 0.0384 time to fit residues: 4.5032 Evaluate side-chains 92 residues out of total 357 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 77 time to evaluate : 0.150 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain L residue 5 THR Chi-restraints excluded: chain L residue 23 THR Chi-restraints excluded: chain L residue 110 VAL Chi-restraints excluded: chain H residue 25 SER Chi-restraints excluded: chain H residue 30 SER Chi-restraints excluded: chain H residue 53 PHE Chi-restraints excluded: chain H residue 96 CYS Chi-restraints excluded: chain F residue 371 LEU Chi-restraints excluded: chain F residue 382 VAL Chi-restraints excluded: chain F residue 401 VAL Chi-restraints excluded: chain F residue 402 ILE Chi-restraints excluded: chain F residue 418 ILE Chi-restraints excluded: chain F residue 425 LEU Chi-restraints excluded: chain F residue 430 THR Chi-restraints excluded: chain F residue 511 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 42 random chunks: chunk 30 optimal weight: 2.9990 chunk 7 optimal weight: 5.9990 chunk 40 optimal weight: 1.9990 chunk 37 optimal weight: 0.8980 chunk 1 optimal weight: 3.9990 chunk 12 optimal weight: 0.1980 chunk 38 optimal weight: 0.6980 chunk 22 optimal weight: 1.9990 chunk 3 optimal weight: 0.6980 chunk 11 optimal weight: 0.9980 chunk 33 optimal weight: 0.9980 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** F 409 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 506 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4008 r_free = 0.4008 target = 0.169181 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.3815 r_free = 0.3815 target = 0.152829 restraints weight = 6614.173| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3873 r_free = 0.3873 target = 0.158083 restraints weight = 4094.281| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3888 r_free = 0.3888 target = 0.159344 restraints weight = 2168.871| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3904 r_free = 0.3904 target = 0.160649 restraints weight = 1515.777| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3907 r_free = 0.3907 target = 0.160915 restraints weight = 1513.094| |-----------------------------------------------------------------------------| r_work (final): 0.3906 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7322 moved from start: 0.3113 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.025 3431 Z= 0.164 Angle : 0.705 7.327 4666 Z= 0.350 Chirality : 0.045 0.135 495 Planarity : 0.004 0.032 603 Dihedral : 5.711 25.160 478 Min Nonbonded Distance : 2.453 Molprobity Statistics. All-atom Clashscore : 9.20 Ramachandran Plot: Outliers : 0.24 % Allowed : 10.02 % Favored : 89.74 % Rotamer: Outliers : 6.16 % Allowed : 22.13 % Favored : 71.71 % 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: -2.96 (0.39), residues: 419 helix: -5.85 (0.27), residues: 5 sheet: -0.70 (0.45), residues: 138 loop : -2.75 (0.34), residues: 276 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG F 454 TYR 0.013 0.001 TYR F 369 PHE 0.025 0.002 PHE H 27 TRP 0.008 0.001 TRP H 36 HIS 0.003 0.001 HIS H 35 Details of bonding type rmsd/Z covalent geometry : bond 0.00365 / 0.16 ( 3426) covalent geometry : angle 0.70168 / 0.35 ( 4654) SS BOND : bond 0.00387 / 0.19 ( 3) SS BOND : angle 1.13081 / 0.60 ( 6) hydrogen bonds : bond 0.03272 / 2.57 ( 63) hydrogen bonds : angle 6.16213 / 4.46 ( 153) link_BETA1-4 : bond 0.00837 / 0.44 ( 1) link_BETA1-4 : angle 1.37676 / 0.79 ( 3) link_NAG-ASN : bond 0.01562 / 0.82 ( 1) link_NAG-ASN : angle 2.34301 / 1.33 ( 3) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 838 Ramachandran restraints generated. 419 Oldfield, 0 Emsley, 419 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 838 Ramachandran restraints generated. 419 Oldfield, 0 Emsley, 419 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 102 residues out of total 357 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 80 time to evaluate : 0.098 Fit side-chains REVERT: L 108 LEU cc_start: 0.8558 (tp) cc_final: 0.8263 (tt) REVERT: H 46 GLU cc_start: 0.7604 (pt0) cc_final: 0.7364 (pt0) REVERT: F 365 TYR cc_start: 0.8114 (m-80) cc_final: 0.7824 (m-10) REVERT: F 406 GLU cc_start: 0.8867 (mm-30) cc_final: 0.8548 (mm-30) REVERT: F 425 LEU cc_start: 0.8453 (OUTLIER) cc_final: 0.8195 (mp) outliers start: 22 outliers final: 16 residues processed: 92 average time/residue: 0.0502 time to fit residues: 5.9843 Evaluate side-chains 92 residues out of total 357 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 75 time to evaluate : 0.102 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain L residue 5 THR Chi-restraints excluded: chain L residue 23 THR Chi-restraints excluded: chain L residue 35 VAL Chi-restraints excluded: chain L residue 110 VAL Chi-restraints excluded: chain L residue 111 LEU Chi-restraints excluded: chain H residue 30 SER Chi-restraints excluded: chain H residue 53 PHE Chi-restraints excluded: chain H residue 96 CYS Chi-restraints excluded: chain F residue 362 VAL Chi-restraints excluded: chain F residue 371 LEU Chi-restraints excluded: chain F residue 401 VAL Chi-restraints excluded: chain F residue 418 ILE Chi-restraints excluded: chain F residue 425 LEU Chi-restraints excluded: chain F residue 430 THR Chi-restraints excluded: chain F residue 480 CYS Chi-restraints excluded: chain F residue 495 TYR Chi-restraints excluded: chain F residue 511 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 42 random chunks: chunk 18 optimal weight: 0.8980 chunk 19 optimal weight: 0.5980 chunk 12 optimal weight: 0.5980 chunk 22 optimal weight: 2.9990 chunk 32 optimal weight: 0.5980 chunk 6 optimal weight: 1.9990 chunk 39 optimal weight: 2.9990 chunk 2 optimal weight: 0.6980 chunk 21 optimal weight: 0.5980 chunk 38 optimal weight: 0.0060 chunk 5 optimal weight: 0.6980 overall best weight: 0.4796 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** F 409 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 506 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4019 r_free = 0.4019 target = 0.170421 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.3834 r_free = 0.3834 target = 0.154414 restraints weight = 6551.548| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3886 r_free = 0.3886 target = 0.159467 restraints weight = 4031.632| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3901 r_free = 0.3901 target = 0.160692 restraints weight = 2165.772| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 31)----------------| | r_work = 0.3917 r_free = 0.3917 target = 0.162103 restraints weight = 1509.509| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3920 r_free = 0.3920 target = 0.162404 restraints weight = 1426.602| |-----------------------------------------------------------------------------| r_work (final): 0.3915 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7299 moved from start: 0.3258 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 3431 Z= 0.134 Angle : 0.665 7.432 4666 Z= 0.334 Chirality : 0.044 0.137 495 Planarity : 0.004 0.028 603 Dihedral : 5.578 24.672 478 Min Nonbonded Distance : 2.480 Molprobity Statistics. All-atom Clashscore : 9.66 Ramachandran Plot: Outliers : 0.24 % Allowed : 8.83 % Favored : 90.93 % Rotamer: Outliers : 5.60 % Allowed : 22.13 % Favored : 72.27 % 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: -2.92 (0.39), residues: 419 helix: -5.85 (0.27), residues: 5 sheet: -0.77 (0.45), residues: 138 loop : -2.67 (0.34), residues: 276 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG F 454 TYR 0.012 0.001 TYR F 369 PHE 0.025 0.002 PHE H 27 TRP 0.009 0.001 TRP F 436 HIS 0.002 0.001 HIS H 35 Details of bonding type rmsd/Z covalent geometry : bond 0.00299 / 0.13 ( 3426) covalent geometry : angle 0.66164 / 0.33 ( 4654) SS BOND : bond 0.00266 / 0.13 ( 3) SS BOND : angle 0.90411 / 0.48 ( 6) hydrogen bonds : bond 0.02998 / 2.38 ( 63) hydrogen bonds : angle 6.07285 / 4.42 ( 153) link_BETA1-4 : bond 0.00828 / 0.44 ( 1) link_BETA1-4 : angle 1.17896 / 0.67 ( 3) link_NAG-ASN : bond 0.00694 / 0.37 ( 1) link_NAG-ASN : angle 2.32281 / 1.28 ( 3) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 838 Ramachandran restraints generated. 419 Oldfield, 0 Emsley, 419 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 838 Ramachandran restraints generated. 419 Oldfield, 0 Emsley, 419 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 100 residues out of total 357 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 80 time to evaluate : 0.136 Fit side-chains REVERT: L 108 LEU cc_start: 0.8527 (tp) cc_final: 0.8229 (tt) REVERT: F 406 GLU cc_start: 0.8872 (mm-30) cc_final: 0.8539 (mm-30) REVERT: F 425 LEU cc_start: 0.8435 (OUTLIER) cc_final: 0.8169 (mp) outliers start: 20 outliers final: 16 residues processed: 91 average time/residue: 0.0351 time to fit residues: 4.3118 Evaluate side-chains 93 residues out of total 357 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 76 time to evaluate : 0.075 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain L residue 5 THR Chi-restraints excluded: chain L residue 19 THR Chi-restraints excluded: chain L residue 23 THR Chi-restraints excluded: chain L residue 35 VAL Chi-restraints excluded: chain L residue 110 VAL Chi-restraints excluded: chain H residue 53 PHE Chi-restraints excluded: chain H residue 96 CYS Chi-restraints excluded: chain F residue 362 VAL Chi-restraints excluded: chain F residue 371 LEU Chi-restraints excluded: chain F residue 401 VAL Chi-restraints excluded: chain F residue 402 ILE Chi-restraints excluded: chain F residue 418 ILE Chi-restraints excluded: chain F residue 425 LEU Chi-restraints excluded: chain F residue 430 THR Chi-restraints excluded: chain F residue 495 TYR Chi-restraints excluded: chain F residue 506 GLN Chi-restraints excluded: chain F residue 511 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 42 random chunks: chunk 31 optimal weight: 0.9990 chunk 10 optimal weight: 0.5980 chunk 40 optimal weight: 0.9980 chunk 6 optimal weight: 0.3980 chunk 8 optimal weight: 0.7980 chunk 35 optimal weight: 0.6980 chunk 38 optimal weight: 0.9990 chunk 1 optimal weight: 0.9990 chunk 37 optimal weight: 1.9990 chunk 18 optimal weight: 0.5980 chunk 39 optimal weight: 0.7980 overall best weight: 0.6180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** F 409 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 = 0.4003 r_free = 0.4003 target = 0.168731 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3826 r_free = 0.3826 target = 0.153354 restraints weight = 6612.342| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3874 r_free = 0.3874 target = 0.157819 restraints weight = 5091.033| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3895 r_free = 0.3895 target = 0.159710 restraints weight = 2281.196| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 31)----------------| | r_work = 0.3916 r_free = 0.3916 target = 0.161506 restraints weight = 1629.190| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3918 r_free = 0.3918 target = 0.161754 restraints weight = 1307.550| |-----------------------------------------------------------------------------| r_work (final): 0.3917 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7305 moved from start: 0.3338 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 3431 Z= 0.153 Angle : 0.677 7.512 4666 Z= 0.342 Chirality : 0.045 0.161 495 Planarity : 0.004 0.027 603 Dihedral : 5.597 24.768 478 Min Nonbonded Distance : 2.481 Molprobity Statistics. All-atom Clashscore : 10.12 Ramachandran Plot: Outliers : 0.24 % Allowed : 9.55 % Favored : 90.21 % Rotamer: Outliers : 6.16 % Allowed : 22.13 % Favored : 71.71 % 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: -2.93 (0.39), residues: 419 helix: -5.64 (0.19), residues: 11 sheet: -0.83 (0.45), residues: 139 loop : -2.55 (0.35), residues: 269 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG F 454 TYR 0.012 0.001 TYR F 369 PHE 0.024 0.002 PHE H 27 TRP 0.008 0.001 TRP F 436 HIS 0.003 0.001 HIS F 505 Details of bonding type rmsd/Z covalent geometry : bond 0.00345 / 0.15 ( 3426) covalent geometry : angle 0.67302 / 0.34 ( 4654) SS BOND : bond 0.00324 / 0.16 ( 3) SS BOND : angle 1.00512 / 0.53 ( 6) hydrogen bonds : bond 0.03174 / 2.52 ( 63) hydrogen bonds : angle 6.00063 / 4.38 ( 153) link_BETA1-4 : bond 0.00757 / 0.40 ( 1) link_BETA1-4 : angle 1.21007 / 0.70 ( 3) link_NAG-ASN : bond 0.00472 / 0.25 ( 1) link_NAG-ASN : angle 2.64431 / 1.47 ( 3) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 838 Ramachandran restraints generated. 419 Oldfield, 0 Emsley, 419 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 838 Ramachandran restraints generated. 419 Oldfield, 0 Emsley, 419 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 99 residues out of total 357 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 77 time to evaluate : 0.112 Fit side-chains REVERT: L 108 LEU cc_start: 0.8535 (tp) cc_final: 0.8258 (tt) REVERT: F 406 GLU cc_start: 0.8879 (mm-30) cc_final: 0.8486 (mm-30) REVERT: F 425 LEU cc_start: 0.8445 (OUTLIER) cc_final: 0.8176 (mp) outliers start: 22 outliers final: 18 residues processed: 91 average time/residue: 0.0394 time to fit residues: 4.7220 Evaluate side-chains 94 residues out of total 357 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 75 time to evaluate : 0.090 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain L residue 5 THR Chi-restraints excluded: chain L residue 19 THR Chi-restraints excluded: chain L residue 23 THR Chi-restraints excluded: chain L residue 35 VAL Chi-restraints excluded: chain L residue 110 VAL Chi-restraints excluded: chain L residue 111 LEU Chi-restraints excluded: chain H residue 53 PHE Chi-restraints excluded: chain H residue 96 CYS Chi-restraints excluded: chain H residue 127 VAL Chi-restraints excluded: chain F residue 362 VAL Chi-restraints excluded: chain F residue 371 LEU Chi-restraints excluded: chain F residue 401 VAL Chi-restraints excluded: chain F residue 418 ILE Chi-restraints excluded: chain F residue 425 LEU Chi-restraints excluded: chain F residue 430 THR Chi-restraints excluded: chain F residue 480 CYS Chi-restraints excluded: chain F residue 495 TYR Chi-restraints excluded: chain F residue 506 GLN Chi-restraints excluded: chain F residue 511 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 42 random chunks: chunk 8 optimal weight: 1.9990 chunk 13 optimal weight: 3.9990 chunk 6 optimal weight: 2.9990 chunk 39 optimal weight: 2.9990 chunk 12 optimal weight: 0.3980 chunk 35 optimal weight: 2.9990 chunk 30 optimal weight: 0.7980 chunk 15 optimal weight: 1.9990 chunk 40 optimal weight: 0.9990 chunk 4 optimal weight: 0.5980 chunk 14 optimal weight: 0.8980 overall best weight: 0.7382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** F 409 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 506 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3994 r_free = 0.3994 target = 0.167919 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3807 r_free = 0.3807 target = 0.151974 restraints weight = 6528.116| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 24)----------------| | r_work = 0.3856 r_free = 0.3856 target = 0.156366 restraints weight = 5136.372| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3880 r_free = 0.3880 target = 0.158459 restraints weight = 2405.150| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.3897 r_free = 0.3897 target = 0.159924 restraints weight = 1693.410| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.3900 r_free = 0.3900 target = 0.160213 restraints weight = 1388.805| |-----------------------------------------------------------------------------| r_work (final): 0.3902 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7349 moved from start: 0.3477 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.034 3431 Z= 0.171 Angle : 0.698 7.671 4666 Z= 0.354 Chirality : 0.045 0.152 495 Planarity : 0.004 0.029 603 Dihedral : 5.775 25.589 478 Min Nonbonded Distance : 2.490 Molprobity Statistics. All-atom Clashscore : 9.96 Ramachandran Plot: Outliers : 0.24 % Allowed : 10.74 % Favored : 89.02 % Rotamer: Outliers : 5.32 % Allowed : 23.53 % Favored : 71.15 % 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: -2.92 (0.39), residues: 419 helix: -5.84 (0.27), residues: 5 sheet: -0.90 (0.44), residues: 139 loop : -2.58 (0.35), residues: 275 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG F 457 TYR 0.013 0.002 TYR F 369 PHE 0.025 0.002 PHE H 27 TRP 0.008 0.001 TRP F 436 HIS 0.003 0.001 HIS H 35 Details of bonding type rmsd/Z covalent geometry : bond 0.00385 / 0.17 ( 3426) covalent geometry : angle 0.69320 / 0.35 ( 4654) SS BOND : bond 0.00380 / 0.19 ( 3) SS BOND : angle 1.15703 / 0.62 ( 6) hydrogen bonds : bond 0.03287 / 2.61 ( 63) hydrogen bonds : angle 5.97337 / 4.41 ( 153) link_BETA1-4 : bond 0.00821 / 0.43 ( 1) link_BETA1-4 : angle 1.19386 / 0.69 ( 3) link_NAG-ASN : bond 0.00467 / 0.25 ( 1) link_NAG-ASN : angle 2.66791 / 1.45 ( 3) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 838 Ramachandran restraints generated. 419 Oldfield, 0 Emsley, 419 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 838 Ramachandran restraints generated. 419 Oldfield, 0 Emsley, 419 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 94 residues out of total 357 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 75 time to evaluate : 0.123 Fit side-chains REVERT: L 108 LEU cc_start: 0.8467 (tp) cc_final: 0.8142 (tt) REVERT: H 28 THR cc_start: 0.8258 (m) cc_final: 0.7997 (p) REVERT: F 406 GLU cc_start: 0.8917 (mm-30) cc_final: 0.8545 (mm-30) REVERT: F 425 LEU cc_start: 0.8508 (OUTLIER) cc_final: 0.8245 (mp) outliers start: 19 outliers final: 18 residues processed: 86 average time/residue: 0.0384 time to fit residues: 4.4015 Evaluate side-chains 94 residues out of total 357 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 75 time to evaluate : 0.101 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain L residue 5 THR Chi-restraints excluded: chain L residue 19 THR Chi-restraints excluded: chain L residue 23 THR Chi-restraints excluded: chain L residue 35 VAL Chi-restraints excluded: chain L residue 110 VAL Chi-restraints excluded: chain L residue 111 LEU Chi-restraints excluded: chain H residue 53 PHE Chi-restraints excluded: chain H residue 96 CYS Chi-restraints excluded: chain H residue 127 VAL Chi-restraints excluded: chain F residue 362 VAL Chi-restraints excluded: chain F residue 371 LEU Chi-restraints excluded: chain F residue 401 VAL Chi-restraints excluded: chain F residue 418 ILE Chi-restraints excluded: chain F residue 425 LEU Chi-restraints excluded: chain F residue 430 THR Chi-restraints excluded: chain F residue 480 CYS Chi-restraints excluded: chain F residue 495 TYR Chi-restraints excluded: chain F residue 506 GLN Chi-restraints excluded: chain F residue 511 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 42 random chunks: chunk 14 optimal weight: 0.7980 chunk 2 optimal weight: 0.8980 chunk 34 optimal weight: 0.0970 chunk 24 optimal weight: 2.9990 chunk 19 optimal weight: 2.9990 chunk 17 optimal weight: 0.7980 chunk 40 optimal weight: 0.9980 chunk 20 optimal weight: 1.9990 chunk 12 optimal weight: 0.0980 chunk 33 optimal weight: 1.9990 chunk 32 optimal weight: 1.9990 overall best weight: 0.5378 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** F 409 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 = 0.4006 r_free = 0.4006 target = 0.168850 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3825 r_free = 0.3825 target = 0.153352 restraints weight = 6525.399| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 24)----------------| | r_work = 0.3871 r_free = 0.3871 target = 0.157579 restraints weight = 5071.206| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3894 r_free = 0.3894 target = 0.159553 restraints weight = 2358.134| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.3911 r_free = 0.3911 target = 0.161033 restraints weight = 1666.539| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.3914 r_free = 0.3914 target = 0.161261 restraints weight = 1415.389| |-----------------------------------------------------------------------------| r_work (final): 0.3914 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7330 moved from start: 0.3513 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 3431 Z= 0.147 Angle : 0.687 7.625 4666 Z= 0.347 Chirality : 0.045 0.141 495 Planarity : 0.004 0.037 603 Dihedral : 5.701 24.736 478 Min Nonbonded Distance : 2.487 Molprobity Statistics. All-atom Clashscore : 9.96 Ramachandran Plot: Outliers : 0.24 % Allowed : 9.55 % Favored : 90.21 % Rotamer: Outliers : 5.32 % Allowed : 23.81 % Favored : 70.87 % 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: -2.86 (0.39), residues: 419 helix: -5.84 (0.27), residues: 5 sheet: -0.87 (0.44), residues: 139 loop : -2.54 (0.35), residues: 275 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG F 457 TYR 0.016 0.002 TYR F 365 PHE 0.023 0.001 PHE H 27 TRP 0.008 0.001 TRP F 436 HIS 0.003 0.001 HIS H 35 Details of bonding type rmsd/Z covalent geometry : bond 0.00333 / 0.15 ( 3426) covalent geometry : angle 0.68257 / 0.35 ( 4654) SS BOND : bond 0.00329 / 0.16 ( 3) SS BOND : angle 1.11689 / 0.61 ( 6) hydrogen bonds : bond 0.03151 / 2.51 ( 63) hydrogen bonds : angle 5.97480 / 4.41 ( 153) link_BETA1-4 : bond 0.00757 / 0.40 ( 1) link_BETA1-4 : angle 1.22729 / 0.70 ( 3) link_NAG-ASN : bond 0.00415 / 0.22 ( 1) link_NAG-ASN : angle 2.67280 / 1.46 ( 3) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 838 Ramachandran restraints generated. 419 Oldfield, 0 Emsley, 419 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 838 Ramachandran restraints generated. 419 Oldfield, 0 Emsley, 419 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 93 residues out of total 357 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 74 time to evaluate : 0.079 Fit side-chains REVERT: L 108 LEU cc_start: 0.8460 (tp) cc_final: 0.8157 (tt) REVERT: H 28 THR cc_start: 0.8251 (m) cc_final: 0.8015 (p) REVERT: F 406 GLU cc_start: 0.8915 (mm-30) cc_final: 0.8496 (mm-30) REVERT: F 425 LEU cc_start: 0.8465 (OUTLIER) cc_final: 0.8195 (mp) outliers start: 19 outliers final: 18 residues processed: 85 average time/residue: 0.0366 time to fit residues: 4.1633 Evaluate side-chains 92 residues out of total 357 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 73 time to evaluate : 0.087 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain L residue 5 THR Chi-restraints excluded: chain L residue 19 THR Chi-restraints excluded: chain L residue 23 THR Chi-restraints excluded: chain L residue 35 VAL Chi-restraints excluded: chain L residue 110 VAL Chi-restraints excluded: chain L residue 111 LEU Chi-restraints excluded: chain H residue 53 PHE Chi-restraints excluded: chain H residue 96 CYS Chi-restraints excluded: chain H residue 127 VAL Chi-restraints excluded: chain F residue 362 VAL Chi-restraints excluded: chain F residue 371 LEU Chi-restraints excluded: chain F residue 401 VAL Chi-restraints excluded: chain F residue 418 ILE Chi-restraints excluded: chain F residue 425 LEU Chi-restraints excluded: chain F residue 430 THR Chi-restraints excluded: chain F residue 480 CYS Chi-restraints excluded: chain F residue 495 TYR Chi-restraints excluded: chain F residue 506 GLN Chi-restraints excluded: chain F residue 511 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 42 random chunks: chunk 24 optimal weight: 2.9990 chunk 29 optimal weight: 5.9990 chunk 27 optimal weight: 0.6980 chunk 23 optimal weight: 0.6980 chunk 0 optimal weight: 3.9990 chunk 7 optimal weight: 5.9990 chunk 12 optimal weight: 0.0070 chunk 36 optimal weight: 0.8980 chunk 18 optimal weight: 0.7980 chunk 17 optimal weight: 0.8980 chunk 28 optimal weight: 0.9990 overall best weight: 0.6198 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** F 409 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 506 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3997 r_free = 0.3997 target = 0.167861 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3811 r_free = 0.3811 target = 0.152096 restraints weight = 6632.929| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 24)----------------| | r_work = 0.3859 r_free = 0.3859 target = 0.156453 restraints weight = 5129.527| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3883 r_free = 0.3883 target = 0.158532 restraints weight = 2352.083| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.3898 r_free = 0.3898 target = 0.159798 restraints weight = 1651.905| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.3901 r_free = 0.3901 target = 0.160049 restraints weight = 1416.982| |-----------------------------------------------------------------------------| r_work (final): 0.3903 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7345 moved from start: 0.3644 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.029 3431 Z= 0.156 Angle : 0.710 8.307 4666 Z= 0.354 Chirality : 0.046 0.164 495 Planarity : 0.004 0.035 603 Dihedral : 5.747 24.659 478 Min Nonbonded Distance : 2.492 Molprobity Statistics. All-atom Clashscore : 10.58 Ramachandran Plot: Outliers : 0.24 % Allowed : 10.02 % Favored : 89.74 % Rotamer: Outliers : 5.88 % Allowed : 22.69 % Favored : 71.43 % 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: -2.80 (0.39), residues: 419 helix: -5.63 (0.19), residues: 11 sheet: -0.83 (0.44), residues: 139 loop : -2.39 (0.35), residues: 269 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG F 457 TYR 0.017 0.002 TYR F 365 PHE 0.022 0.002 PHE H 27 TRP 0.010 0.001 TRP L 37 HIS 0.002 0.001 HIS H 35 Details of bonding type rmsd/Z covalent geometry : bond 0.00353 / 0.16 ( 3426) covalent geometry : angle 0.70570 / 0.35 ( 4654) SS BOND : bond 0.00333 / 0.16 ( 3) SS BOND : angle 1.10305 / 0.60 ( 6) hydrogen bonds : bond 0.03171 / 2.53 ( 63) hydrogen bonds : angle 6.00271 / 4.41 ( 153) link_BETA1-4 : bond 0.00810 / 0.43 ( 1) link_BETA1-4 : angle 1.21625 / 0.70 ( 3) link_NAG-ASN : bond 0.00410 / 0.22 ( 1) link_NAG-ASN : angle 2.73401 / 1.48 ( 3) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 875.30 seconds wall clock time: 15 minutes 49.09 seconds (949.09 seconds total)