Starting phenix.real_space_refine on Wed Sep 17 06:22:08 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9jil_61509/09_2025/9jil_61509.cif Found real_map, /net/cci-nas-00/data/ceres_data/9jil_61509/09_2025/9jil_61509.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.44 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/9jil_61509/09_2025/9jil_61509.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9jil_61509/09_2025/9jil_61509.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9jil_61509/09_2025/9jil_61509.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9jil_61509/09_2025/9jil_61509.map" } resolution = 2.44 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= 0.001 sd= 0.021 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 18 5.16 5 C 3731 2.51 5 N 993 2.21 5 O 1174 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 3 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5805/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 5916 Number of models: 1 Model: "" Number of chains: 6 Chain: "A" Number of atoms: 1192 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 152, 1174 Classifications: {'peptide': 152} Link IDs: {'PCIS': 1, 'PTRANS': 7, 'TRANS': 143} Conformer: "B" Number of residues, atoms: 152, 1174 Classifications: {'peptide': 152} Link IDs: {'PCIS': 1, 'PTRANS': 7, 'TRANS': 143} bond proxies already assigned to first conformer: 1190 Chain: "B" Number of atoms: 1186 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 152, 1174 Classifications: {'peptide': 152} Link IDs: {'PCIS': 1, 'PTRANS': 7, 'TRANS': 143} Conformer: "B" Number of residues, atoms: 152, 1174 Classifications: {'peptide': 152} Link IDs: {'PCIS': 1, 'PTRANS': 7, 'TRANS': 143} bond proxies already assigned to first conformer: 1197 Chain: "E" Number of atoms: 964 Number of conformers: 1 Conformer: "" Number of residues, atoms: 125, 964 Classifications: {'peptide': 125} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 7, 'TRANS': 117} Chain: "F" Number of atoms: 805 Number of conformers: 1 Conformer: "" Number of residues, atoms: 110, 805 Classifications: {'peptide': 110} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 5, 'TRANS': 104} Chain: "H" Number of atoms: 964 Number of conformers: 1 Conformer: "" Number of residues, atoms: 125, 964 Classifications: {'peptide': 125} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 7, 'TRANS': 117} Chain: "L" Number of atoms: 805 Number of conformers: 1 Conformer: "" Number of residues, atoms: 110, 805 Classifications: {'peptide': 110} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 5, 'TRANS': 104} Residues with excluded nonbonded symmetry interactions: 5 residue: pdb=" N ASER A 466 " occ=0.15 ... (10 atoms not shown) pdb=" OG BSER A 466 " occ=0.85 residue: pdb=" N ASER A 474 " occ=0.58 ... (10 atoms not shown) pdb=" OG BSER A 474 " occ=0.42 residue: pdb=" N ASER A 502 " occ=0.52 ... (10 atoms not shown) pdb=" OG BSER A 502 " occ=0.48 residue: pdb=" N ASER B 474 " occ=0.58 ... (10 atoms not shown) pdb=" OG BSER B 474 " occ=0.42 residue: pdb=" N ASER B 502 " occ=0.52 ... (10 atoms not shown) pdb=" OG BSER B 502 " occ=0.48 Time building chain proxies: 2.12, per 1000 atoms: 0.36 Number of scatterers: 5916 At special positions: 0 Unit cell: (96.85, 79.95, 84.5, 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 18 16.00 O 1174 8.00 N 993 7.00 C 3731 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=4, symmetry=0 Simple disulfide: pdb=" SG CYS E 22 " - pdb=" SG CYS E 96 " distance=2.18 Simple disulfide: pdb=" SG CYS F 22 " - pdb=" SG CYS F 90 " distance=2.03 Simple disulfide: pdb=" SG CYS H 22 " - pdb=" SG CYS H 96 " distance=2.03 Simple disulfide: pdb=" SG CYS L 22 " - pdb=" SG CYS L 90 " 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: 0.48 Conformation dependent library (CDL) restraints added in 484.7 milliseconds Enol-peptide restraints added in 476.8 nanoseconds 1554 Ramachandran restraints generated. 777 Oldfield, 0 Emsley, 777 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1402 Finding SS restraints... Secondary structure from input PDB file: 11 helices and 12 sheets defined 6.2% alpha, 24.9% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.22 Creating SS restraints... Processing helix chain 'A' and resid 501 through 503 No H-bonds generated for 'chain 'A' and resid 501 through 503' Processing helix chain 'B' and resid 501 through 503 No H-bonds generated for 'chain 'B' and resid 501 through 503' Processing helix chain 'B' and resid 504 through 507 Processing helix chain 'E' and resid 62 through 65 Processing helix chain 'E' and resid 87 through 91 removed outlier: 3.564A pdb=" N THR E 91 " --> pdb=" O SER E 88 " (cutoff:3.500A) Processing helix chain 'F' and resid 31 through 35 removed outlier: 3.973A pdb=" N VAL F 35 " --> pdb=" O TYR F 32 " (cutoff:3.500A) Processing helix chain 'F' and resid 81 through 85 Processing helix chain 'H' and resid 62 through 65 Processing helix chain 'H' and resid 87 through 91 removed outlier: 3.537A pdb=" N THR H 91 " --> pdb=" O SER H 88 " (cutoff:3.500A) Processing helix chain 'L' and resid 31 through 35 removed outlier: 3.514A pdb=" N LEU L 34 " --> pdb=" O SER L 31 " (cutoff:3.500A) removed outlier: 4.043A pdb=" N VAL L 35 " --> pdb=" O TYR L 32 " (cutoff:3.500A) No H-bonds generated for 'chain 'L' and resid 31 through 35' Processing helix chain 'L' and resid 81 through 85 Processing sheet with id=AA1, first strand: chain 'A' and resid 453 through 454 Processing sheet with id=AA2, first strand: chain 'A' and resid 459 through 473 removed outlier: 4.126A pdb=" N SER A 472 " --> pdb=" O HIS A 479 " (cutoff:3.500A) removed outlier: 5.430A pdb=" N HIS A 479 " --> pdb=" O SER A 472 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'A' and resid 479 through 484 current: chain 'A' and resid 496 through 499 WARNING: can't find start of bonding for strands! previous: chain 'A' and resid 496 through 499 current: chain 'A' and resid 523 through 538 removed outlier: 4.522A pdb=" N PHE A 536 " --> pdb=" O GLY A 545 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'A' and resid 544 through 545 current: chain 'A' and resid 568 through 573 Processing sheet with id=AA3, first strand: chain 'B' and resid 453 through 454 Processing sheet with id=AA4, first strand: chain 'B' and resid 459 through 473 removed outlier: 4.113A pdb=" N SER B 472 " --> pdb=" O HIS B 479 " (cutoff:3.500A) removed outlier: 5.415A pdb=" N HIS B 479 " --> pdb=" O SER B 472 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'B' and resid 479 through 484 current: chain 'B' and resid 497 through 499 WARNING: can't find start of bonding for strands! previous: chain 'B' and resid 497 through 499 current: chain 'B' and resid 523 through 529 WARNING: can't find start of bonding for strands! previous: chain 'B' and resid 523 through 529 current: chain 'B' and resid 568 through 573 Processing sheet with id=AA5, first strand: chain 'E' and resid 3 through 6 removed outlier: 3.599A pdb=" N THR E 78 " --> pdb=" O ASP E 73 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'E' and resid 10 through 12 WARNING: can't find start of bonding for strands! previous: chain 'E' and resid 10 through 12 current: chain 'E' and resid 45 through 51 WARNING: can't find start of bonding for strands! previous: chain 'E' and resid 59 through 60 current: chain 'E' and resid 112 through 115 Processing sheet with id=AA7, first strand: chain 'F' and resid 9 through 12 WARNING: can't find start of bonding for strands! previous: chain 'F' and resid 9 through 12 current: chain 'F' and resid 47 through 50 WARNING: can't find start of bonding for strands! previous: chain 'F' and resid 47 through 50 current: chain 'F' and resid 99 through 101 No H-bonds generated for sheet with id=AA7 Processing sheet with id=AA8, first strand: chain 'F' and resid 17 through 23 Processing sheet with id=AA9, first strand: chain 'H' and resid 3 through 6 Processing sheet with id=AB1, first strand: chain 'H' and resid 10 through 12 WARNING: can't find start of bonding for strands! previous: chain 'H' and resid 10 through 12 current: chain 'H' and resid 45 through 51 WARNING: can't find start of bonding for strands! previous: chain 'H' and resid 59 through 60 current: chain 'H' and resid 112 through 115 Processing sheet with id=AB2, first strand: chain 'L' and resid 9 through 12 WARNING: can't find start of bonding for strands! previous: chain 'L' and resid 9 through 12 current: chain 'L' and resid 47 through 50 WARNING: can't find start of bonding for strands! previous: chain 'L' and resid 47 through 50 current: chain 'L' and resid 99 through 101 No H-bonds generated for sheet with id=AB2 Processing sheet with id=AB3, first strand: chain 'L' and resid 18 through 23 removed outlier: 3.626A pdb=" N SER L 74 " --> pdb=" O SER L 67 " (cutoff:3.500A) 83 hydrogen bonds defined for protein. 183 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: 0.90 Time building geometry restraints manager: 0.70 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.18 - 1.31: 967 1.31 - 1.43: 1775 1.43 - 1.56: 3307 1.56 - 1.69: 0 1.69 - 1.81: 26 Bond restraints: 6075 Sorted by residual: bond pdb=" C SER B 466 " pdb=" N ALA B 467 " ideal model delta sigma weight residual 1.330 1.204 0.126 1.32e-02 5.74e+03 9.06e+01 bond pdb=" C ASN E 110 " pdb=" N ARG E 111 " ideal model delta sigma weight residual 1.331 1.409 -0.078 1.23e-02 6.61e+03 4.04e+01 bond pdb=" C ASP L 28 " pdb=" O ASP L 28 " ideal model delta sigma weight residual 1.235 1.181 0.055 1.26e-02 6.30e+03 1.89e+01 bond pdb=" C ASP F 28 " pdb=" O ASP F 28 " ideal model delta sigma weight residual 1.236 1.193 0.042 1.35e-02 5.49e+03 9.86e+00 bond pdb=" CA SER L 27 " pdb=" CB SER L 27 " ideal model delta sigma weight residual 1.530 1.493 0.037 1.57e-02 4.06e+03 5.53e+00 ... (remaining 6070 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.96: 8183 1.96 - 3.93: 96 3.93 - 5.89: 25 5.89 - 7.85: 1 7.85 - 9.82: 2 Bond angle restraints: 8307 Sorted by residual: angle pdb=" N SER L 27 " pdb=" CA SER L 27 " pdb=" C SER L 27 " ideal model delta sigma weight residual 110.24 100.85 9.39 1.47e+00 4.63e-01 4.08e+01 angle pdb=" CA ASP L 28 " pdb=" CB ASP L 28 " pdb=" CG ASP L 28 " ideal model delta sigma weight residual 112.60 118.17 -5.57 1.00e+00 1.00e+00 3.10e+01 angle pdb=" C SER B 466 " pdb=" N ALA B 467 " pdb=" CA ALA B 467 " ideal model delta sigma weight residual 120.87 113.57 7.30 1.42e+00 4.96e-01 2.64e+01 angle pdb=" N ASP L 28 " pdb=" CA ASP L 28 " pdb=" C ASP L 28 " ideal model delta sigma weight residual 110.80 100.98 9.82 2.13e+00 2.20e-01 2.12e+01 angle pdb=" CA PRO B 465 " pdb=" C PRO B 465 " pdb=" N SER B 466 " ideal model delta sigma weight residual 115.81 120.95 -5.14 1.22e+00 6.72e-01 1.77e+01 ... (remaining 8302 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 15.56: 3048 15.56 - 31.11: 310 31.11 - 46.67: 121 46.67 - 62.22: 32 62.22 - 77.78: 10 Dihedral angle restraints: 3521 sinusoidal: 1301 harmonic: 2220 Sorted by residual: dihedral pdb=" CD ARG H 111 " pdb=" NE ARG H 111 " pdb=" CZ ARG H 111 " pdb=" NH1 ARG H 111 " ideal model delta sinusoidal sigma weight residual 0.00 46.53 -46.53 1 1.00e+01 1.00e-02 3.00e+01 dihedral pdb=" CB CYS E 22 " pdb=" SG CYS E 22 " pdb=" SG CYS E 96 " pdb=" CB CYS E 96 " ideal model delta sinusoidal sigma weight residual 93.00 49.37 43.63 1 1.00e+01 1.00e-02 2.65e+01 dihedral pdb=" CB CYS H 22 " pdb=" SG CYS H 22 " pdb=" SG CYS H 96 " pdb=" CB CYS H 96 " ideal model delta sinusoidal sigma weight residual 93.00 52.40 40.60 1 1.00e+01 1.00e-02 2.31e+01 ... (remaining 3518 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.040: 663 0.040 - 0.079: 166 0.079 - 0.118: 71 0.118 - 0.158: 12 0.158 - 0.197: 1 Chirality restraints: 913 Sorted by residual: chirality pdb=" CA ASP L 28 " pdb=" N ASP L 28 " pdb=" C ASP L 28 " pdb=" CB ASP L 28 " both_signs ideal model delta sigma weight residual False 2.51 2.71 -0.20 2.00e-01 2.50e+01 9.75e-01 chirality pdb=" CA SER L 26 " pdb=" N SER L 26 " pdb=" C SER L 26 " pdb=" CB SER L 26 " both_signs ideal model delta sigma weight residual False 2.51 2.36 0.15 2.00e-01 2.50e+01 5.77e-01 chirality pdb=" CB ILE A 534 " pdb=" CA ILE A 534 " pdb=" CG1 ILE A 534 " pdb=" CG2 ILE A 534 " both_signs ideal model delta sigma weight residual False 2.64 2.50 0.14 2.00e-01 2.50e+01 5.08e-01 ... (remaining 910 not shown) Planarity restraints: 1068 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CD ARG H 111 " 0.785 9.50e-02 1.11e+02 3.52e-01 7.53e+01 pdb=" NE ARG H 111 " -0.048 2.00e-02 2.50e+03 pdb=" CZ ARG H 111 " -0.006 2.00e-02 2.50e+03 pdb=" NH1 ARG H 111 " -0.003 2.00e-02 2.50e+03 pdb=" NH2 ARG H 111 " 0.022 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ASP L 28 " -0.020 2.00e-02 2.50e+03 4.25e-02 1.80e+01 pdb=" C ASP L 28 " 0.073 2.00e-02 2.50e+03 pdb=" O ASP L 28 " -0.028 2.00e-02 2.50e+03 pdb=" N VAL L 29 " -0.025 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ASP F 28 " 0.015 2.00e-02 2.50e+03 3.14e-02 9.87e+00 pdb=" C ASP F 28 " -0.054 2.00e-02 2.50e+03 pdb=" O ASP F 28 " 0.020 2.00e-02 2.50e+03 pdb=" N VAL F 29 " 0.019 2.00e-02 2.50e+03 ... (remaining 1065 not shown) Histogram of nonbonded interaction distances: 2.34 - 2.85: 2151 2.85 - 3.36: 4845 3.36 - 3.87: 10771 3.87 - 4.39: 12457 4.39 - 4.90: 20176 Nonbonded interactions: 50400 Sorted by model distance: nonbonded pdb=" OD2 ASP H 73 " pdb=" OG1 THR H 76 " model vdw 2.337 3.040 nonbonded pdb=" N ASP A 506 " pdb=" OD1 ASP A 506 " model vdw 2.356 3.120 nonbonded pdb=" O ASER A 466 " pdb=" OG ASER A 466 " model vdw 2.359 3.040 nonbonded pdb=" NH1 ARG L 56 " pdb=" O PHE L 64 " model vdw 2.389 3.120 nonbonded pdb=" NH1 ARG F 56 " pdb=" O PHE F 64 " model vdw 2.394 3.120 ... (remaining 50395 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 Found NCS groups: ncs_group { reference = (chain 'A' and (resid 446 through 465 or resid 467 through 473 or resid 475 thro \ ugh 501 or resid 503 through 597)) selection = (chain 'B' and (resid 446 through 465 or resid 467 through 473 or resid 475 thro \ ugh 501 or resid 503 through 597)) } ncs_group { reference = chain 'E' selection = chain 'H' } ncs_group { reference = chain 'F' selection = chain 'L' } 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=0.15 max=1.00 mean=0.99 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 7.340 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.000 Extract box with map and model: 0.150 Check model and map are aligned: 0.010 Set scattering table: 0.040 Process input model: 7.990 Find NCS groups from input model: 0.100 Set up NCS constraints: 0.030 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:10.110 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 25.770 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7986 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.150 6079 Z= 0.236 Angle : 0.584 9.816 8315 Z= 0.347 Chirality : 0.042 0.197 913 Planarity : 0.012 0.352 1068 Dihedral : 15.652 77.780 2107 Min Nonbonded Distance : 2.337 Molprobity Statistics. All-atom Clashscore : 5.61 Ramachandran Plot: Outliers : 0.26 % Allowed : 3.54 % Favored : 96.19 % Rotamer: Outliers : 0.94 % Allowed : 21.28 % Favored : 77.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.00 % 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 aren not related in a simple way. whole: 1.41 (0.32), residues: 777 helix: None (None), residues: 0 sheet: 1.80 (0.29), residues: 341 loop : 0.26 (0.33), residues: 436 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG H 111 TYR 0.010 0.001 TYR B 548 PHE 0.006 0.001 PHE F 93 TRP 0.010 0.001 TRP B 505 HIS 0.002 0.001 HIS B 516 Details of bonding type rmsd covalent geometry : bond 0.00341 ( 6075) covalent geometry : angle 0.58141 ( 8307) SS BOND : bond 0.07493 ( 4) SS BOND : angle 1.81856 ( 8) hydrogen bonds : bond 0.22819 ( 83) hydrogen bonds : angle 8.24473 ( 183) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1554 Ramachandran restraints generated. 777 Oldfield, 0 Emsley, 777 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1554 Ramachandran restraints generated. 777 Oldfield, 0 Emsley, 777 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 192 residues out of total 629 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 186 time to evaluate : 0.207 Fit side-chains REVERT: A 538 GLN cc_start: 0.8492 (tt0) cc_final: 0.8282 (tt0) REVERT: B 572 ILE cc_start: 0.8278 (pt) cc_final: 0.8022 (mp) REVERT: F 106 LYS cc_start: 0.8153 (tttm) cc_final: 0.7914 (tttm) outliers start: 6 outliers final: 0 residues processed: 189 average time/residue: 0.4152 time to fit residues: 83.2892 Evaluate side-chains 164 residues out of total 629 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 164 time to evaluate : 0.222 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 76 random chunks: chunk 49 optimal weight: 4.9990 chunk 53 optimal weight: 3.9990 chunk 5 optimal weight: 0.9990 chunk 33 optimal weight: 0.9980 chunk 65 optimal weight: 0.7980 chunk 62 optimal weight: 1.9990 chunk 51 optimal weight: 0.9990 chunk 38 optimal weight: 2.9990 chunk 61 optimal weight: 0.9980 chunk 45 optimal weight: 0.6980 chunk 74 optimal weight: 0.9990 overall best weight: 0.8982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 520 HIS A 595 ASN B 520 HIS B 527 GLN E 59 ASN E 62 GLN F 6 GLN F 40 GLN L 40 GLN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3536 r_free = 0.3536 target = 0.118346 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3236 r_free = 0.3236 target = 0.098432 restraints weight = 38879.517| |-----------------------------------------------------------------------------| r_work (start): 0.3214 rms_B_bonded: 3.75 r_work: 0.3027 rms_B_bonded: 3.93 restraints_weight: 0.5000 r_work (final): 0.3027 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3021 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3021 r_free = 0.3021 target_work(ls_wunit_k1) = 0.084 | | occupancies: max = 1.00 min = 0.15 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3021 r_free = 0.3021 target_work(ls_wunit_k1) = 0.084 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 1 | |-----------------------------------------------------------------------------| r_final: 0.3021 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8111 moved from start: 0.1676 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.038 6079 Z= 0.238 Angle : 0.619 5.870 8315 Z= 0.334 Chirality : 0.046 0.196 913 Planarity : 0.005 0.036 1068 Dihedral : 5.584 39.247 844 Min Nonbonded Distance : 2.470 Molprobity Statistics. All-atom Clashscore : 3.88 Ramachandran Plot: Outliers : 0.26 % Allowed : 3.81 % Favored : 95.93 % Rotamer: Outliers : 3.60 % Allowed : 22.22 % Favored : 74.18 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.00 % 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 aren not related in a simple way. whole: 0.99 (0.31), residues: 777 helix: -5.62 (0.22), residues: 12 sheet: 1.75 (0.28), residues: 323 loop : 0.03 (0.32), residues: 442 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG E 111 TYR 0.017 0.003 TYR B 548 PHE 0.013 0.002 PHE A 536 TRP 0.014 0.002 TRP A 461 HIS 0.005 0.001 HIS A 516 Details of bonding type rmsd covalent geometry : bond 0.00570 ( 6075) covalent geometry : angle 0.61919 ( 8307) SS BOND : bond 0.00575 ( 4) SS BOND : angle 0.72437 ( 8) hydrogen bonds : bond 0.03881 ( 83) hydrogen bonds : angle 5.93536 ( 183) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1554 Ramachandran restraints generated. 777 Oldfield, 0 Emsley, 777 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1554 Ramachandran restraints generated. 777 Oldfield, 0 Emsley, 777 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 206 residues out of total 629 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 183 time to evaluate : 0.202 Fit side-chains REVERT: A 534 ILE cc_start: 0.8574 (OUTLIER) cc_final: 0.8367 (tp) REVERT: E 85 SER cc_start: 0.8225 (t) cc_final: 0.7950 (t) outliers start: 23 outliers final: 9 residues processed: 187 average time/residue: 0.4250 time to fit residues: 83.9774 Evaluate side-chains 187 residues out of total 629 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 177 time to evaluate : 0.216 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 534 ILE Chi-restraints excluded: chain B residue 542 THR Chi-restraints excluded: chain B residue 553 THR Chi-restraints excluded: chain E residue 71 THR Chi-restraints excluded: chain F residue 5 THR Chi-restraints excluded: chain F residue 69 SER Chi-restraints excluded: chain H residue 7 SER Chi-restraints excluded: chain H residue 85 SER Chi-restraints excluded: chain H residue 87 ARG Chi-restraints excluded: chain L residue 47 LYS Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 76 random chunks: chunk 75 optimal weight: 1.9990 chunk 31 optimal weight: 3.9990 chunk 0 optimal weight: 0.9990 chunk 46 optimal weight: 0.5980 chunk 17 optimal weight: 0.9980 chunk 3 optimal weight: 0.9990 chunk 56 optimal weight: 0.6980 chunk 52 optimal weight: 1.9990 chunk 72 optimal weight: 2.9990 chunk 12 optimal weight: 0.6980 chunk 6 optimal weight: 0.9980 overall best weight: 0.7980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 527 GLN B 527 GLN B 539 GLN B 595 ASN E 103 ASN L 40 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3574 r_free = 0.3574 target = 0.120521 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3270 r_free = 0.3270 target = 0.100068 restraints weight = 37908.348| |-----------------------------------------------------------------------------| r_work (start): 0.3237 rms_B_bonded: 3.61 r_work: 0.3052 rms_B_bonded: 3.86 restraints_weight: 0.5000 r_work (final): 0.3052 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3049 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3049 r_free = 0.3049 target_work(ls_wunit_k1) = 0.085 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 1 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3049 r_free = 0.3049 target_work(ls_wunit_k1) = 0.085 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 1 | |-----------------------------------------------------------------------------| r_final: 0.3049 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8105 moved from start: 0.1917 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.037 6079 Z= 0.213 Angle : 0.590 5.433 8315 Z= 0.318 Chirality : 0.046 0.191 913 Planarity : 0.005 0.039 1068 Dihedral : 5.548 41.859 844 Min Nonbonded Distance : 2.530 Molprobity Statistics. All-atom Clashscore : 4.06 Ramachandran Plot: Outliers : 0.26 % Allowed : 3.28 % Favored : 96.46 % Rotamer: Outliers : 3.44 % Allowed : 23.47 % Favored : 73.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.00 % 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 aren not related in a simple way. whole: 0.71 (0.31), residues: 777 helix: -5.46 (0.31), residues: 12 sheet: 1.37 (0.27), residues: 333 loop : -0.04 (0.32), residues: 432 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG E 111 TYR 0.014 0.002 TYR L 38 PHE 0.011 0.002 PHE A 536 TRP 0.015 0.002 TRP A 461 HIS 0.005 0.001 HIS A 516 Details of bonding type rmsd covalent geometry : bond 0.00510 ( 6075) covalent geometry : angle 0.59017 ( 8307) SS BOND : bond 0.00203 ( 4) SS BOND : angle 0.66344 ( 8) hydrogen bonds : bond 0.03306 ( 83) hydrogen bonds : angle 5.66665 ( 183) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1554 Ramachandran restraints generated. 777 Oldfield, 0 Emsley, 777 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1554 Ramachandran restraints generated. 777 Oldfield, 0 Emsley, 777 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 205 residues out of total 629 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 183 time to evaluate : 0.259 Fit side-chains REVERT: A 534 ILE cc_start: 0.8570 (OUTLIER) cc_final: 0.8319 (tp) outliers start: 22 outliers final: 15 residues processed: 189 average time/residue: 0.4479 time to fit residues: 89.7162 Evaluate side-chains 201 residues out of total 629 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 185 time to evaluate : 0.230 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 534 ILE Chi-restraints excluded: chain B residue 452 THR Chi-restraints excluded: chain B residue 542 THR Chi-restraints excluded: chain B residue 553 THR Chi-restraints excluded: chain E residue 71 THR Chi-restraints excluded: chain F residue 11 SER Chi-restraints excluded: chain F residue 69 SER Chi-restraints excluded: chain H residue 2 VAL Chi-restraints excluded: chain H residue 7 SER Chi-restraints excluded: chain H residue 71 THR Chi-restraints excluded: chain H residue 77 SER Chi-restraints excluded: chain H residue 85 SER Chi-restraints excluded: chain H residue 87 ARG Chi-restraints excluded: chain H residue 125 SER Chi-restraints excluded: chain L residue 47 LYS Chi-restraints excluded: chain L residue 108 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 76 random chunks: chunk 28 optimal weight: 0.9980 chunk 64 optimal weight: 0.6980 chunk 52 optimal weight: 1.9990 chunk 6 optimal weight: 0.9990 chunk 36 optimal weight: 0.9980 chunk 0 optimal weight: 0.9990 chunk 9 optimal weight: 0.8980 chunk 54 optimal weight: 3.9990 chunk 8 optimal weight: 0.4980 chunk 48 optimal weight: 0.1980 chunk 67 optimal weight: 2.9990 overall best weight: 0.6580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 453 ASN B 527 GLN B 595 ASN F 6 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3573 r_free = 0.3573 target = 0.119177 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3265 r_free = 0.3265 target = 0.098872 restraints weight = 36039.534| |-----------------------------------------------------------------------------| r_work (start): 0.3244 rms_B_bonded: 3.55 r_work: 0.3053 rms_B_bonded: 3.91 restraints_weight: 0.5000 r_work (final): 0.3053 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3050 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3050 r_free = 0.3050 target_work(ls_wunit_k1) = 0.085 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 1 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3050 r_free = 0.3050 target_work(ls_wunit_k1) = 0.085 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 1 | |-----------------------------------------------------------------------------| r_final: 0.3050 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8102 moved from start: 0.2021 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.031 6079 Z= 0.183 Angle : 0.567 5.628 8315 Z= 0.305 Chirality : 0.045 0.188 913 Planarity : 0.004 0.039 1068 Dihedral : 5.435 40.740 844 Min Nonbonded Distance : 2.567 Molprobity Statistics. All-atom Clashscore : 3.54 Ramachandran Plot: Outliers : 0.26 % Allowed : 3.15 % Favored : 96.59 % Rotamer: Outliers : 3.91 % Allowed : 22.69 % Favored : 73.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.00 % 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 aren not related in a simple way. whole: 0.65 (0.31), residues: 777 helix: -5.36 (0.37), residues: 12 sheet: 1.32 (0.27), residues: 331 loop : -0.07 (0.32), residues: 434 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG E 111 TYR 0.014 0.002 TYR A 550 PHE 0.010 0.002 PHE A 536 TRP 0.013 0.002 TRP A 461 HIS 0.004 0.001 HIS A 516 Details of bonding type rmsd covalent geometry : bond 0.00433 ( 6075) covalent geometry : angle 0.56677 ( 8307) SS BOND : bond 0.00186 ( 4) SS BOND : angle 0.60380 ( 8) hydrogen bonds : bond 0.02931 ( 83) hydrogen bonds : angle 5.50005 ( 183) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1554 Ramachandran restraints generated. 777 Oldfield, 0 Emsley, 777 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1554 Ramachandran restraints generated. 777 Oldfield, 0 Emsley, 777 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 211 residues out of total 629 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 186 time to evaluate : 0.222 Fit side-chains REVERT: A 534 ILE cc_start: 0.8544 (OUTLIER) cc_final: 0.8330 (tp) REVERT: B 455 ARG cc_start: 0.8398 (mtm-85) cc_final: 0.8101 (mtt180) REVERT: H 65 GLN cc_start: 0.7650 (OUTLIER) cc_final: 0.7342 (mt0) outliers start: 25 outliers final: 19 residues processed: 194 average time/residue: 0.4350 time to fit residues: 89.3700 Evaluate side-chains 206 residues out of total 629 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 185 time to evaluate : 0.247 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 472 SER Chi-restraints excluded: chain A residue 534 ILE Chi-restraints excluded: chain A residue 553 THR Chi-restraints excluded: chain A residue 567 LYS Chi-restraints excluded: chain B residue 452 THR Chi-restraints excluded: chain B residue 542 THR Chi-restraints excluded: chain B residue 553 THR Chi-restraints excluded: chain E residue 71 THR Chi-restraints excluded: chain E residue 108 GLU Chi-restraints excluded: chain F residue 11 SER Chi-restraints excluded: chain F residue 69 SER Chi-restraints excluded: chain H residue 7 SER Chi-restraints excluded: chain H residue 65 GLN Chi-restraints excluded: chain H residue 71 THR Chi-restraints excluded: chain H residue 77 SER Chi-restraints excluded: chain H residue 85 SER Chi-restraints excluded: chain H residue 87 ARG Chi-restraints excluded: chain H residue 125 SER Chi-restraints excluded: chain L residue 29 VAL Chi-restraints excluded: chain L residue 47 LYS Chi-restraints excluded: chain L residue 108 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 76 random chunks: chunk 62 optimal weight: 1.9990 chunk 61 optimal weight: 0.6980 chunk 42 optimal weight: 2.9990 chunk 66 optimal weight: 0.9980 chunk 75 optimal weight: 0.7980 chunk 23 optimal weight: 0.9990 chunk 41 optimal weight: 0.0980 chunk 30 optimal weight: 1.9990 chunk 7 optimal weight: 0.9990 chunk 72 optimal weight: 0.8980 chunk 6 optimal weight: 0.6980 overall best weight: 0.6380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 453 ASN A 527 GLN B 453 ASN B 527 GLN B 595 ASN H 39 GLN L 40 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3574 r_free = 0.3574 target = 0.119196 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3261 r_free = 0.3261 target = 0.098593 restraints weight = 40408.763| |-----------------------------------------------------------------------------| r_work (start): 0.3240 rms_B_bonded: 3.71 r_work: 0.3040 rms_B_bonded: 4.09 restraints_weight: 0.5000 r_work (final): 0.3040 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3039 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3039 r_free = 0.3039 target_work(ls_wunit_k1) = 0.085 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 1 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3039 r_free = 0.3039 target_work(ls_wunit_k1) = 0.085 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 1 | |-----------------------------------------------------------------------------| r_final: 0.3039 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8115 moved from start: 0.2108 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.031 6079 Z= 0.178 Angle : 0.562 5.568 8315 Z= 0.301 Chirality : 0.045 0.215 913 Planarity : 0.004 0.040 1068 Dihedral : 5.397 40.688 844 Min Nonbonded Distance : 2.553 Molprobity Statistics. All-atom Clashscore : 3.71 Ramachandran Plot: Outliers : 0.26 % Allowed : 3.02 % Favored : 96.72 % Rotamer: Outliers : 4.23 % Allowed : 22.54 % Favored : 73.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.00 % 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 aren not related in a simple way. whole: 0.63 (0.31), residues: 777 helix: -5.14 (0.52), residues: 12 sheet: 1.26 (0.27), residues: 331 loop : -0.05 (0.32), residues: 434 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG E 111 TYR 0.015 0.002 TYR A 550 PHE 0.011 0.002 PHE F 93 TRP 0.013 0.002 TRP A 461 HIS 0.004 0.001 HIS A 516 Details of bonding type rmsd covalent geometry : bond 0.00421 ( 6075) covalent geometry : angle 0.56178 ( 8307) SS BOND : bond 0.00175 ( 4) SS BOND : angle 0.55473 ( 8) hydrogen bonds : bond 0.02844 ( 83) hydrogen bonds : angle 5.41686 ( 183) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1554 Ramachandran restraints generated. 777 Oldfield, 0 Emsley, 777 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1554 Ramachandran restraints generated. 777 Oldfield, 0 Emsley, 777 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 216 residues out of total 629 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 189 time to evaluate : 0.243 Fit side-chains REVERT: A 534 ILE cc_start: 0.8544 (OUTLIER) cc_final: 0.8334 (tp) REVERT: H 65 GLN cc_start: 0.7640 (OUTLIER) cc_final: 0.7343 (mt0) outliers start: 27 outliers final: 20 residues processed: 195 average time/residue: 0.4494 time to fit residues: 92.6929 Evaluate side-chains 210 residues out of total 629 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 188 time to evaluate : 0.223 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 534 ILE Chi-restraints excluded: chain A residue 553 THR Chi-restraints excluded: chain B residue 452 THR Chi-restraints excluded: chain B residue 501 SER Chi-restraints excluded: chain B residue 542 THR Chi-restraints excluded: chain B residue 552 THR Chi-restraints excluded: chain B residue 553 THR Chi-restraints excluded: chain B residue 576 THR Chi-restraints excluded: chain E residue 71 THR Chi-restraints excluded: chain F residue 11 SER Chi-restraints excluded: chain F residue 67 SER Chi-restraints excluded: chain H residue 2 VAL Chi-restraints excluded: chain H residue 7 SER Chi-restraints excluded: chain H residue 65 GLN Chi-restraints excluded: chain H residue 71 THR Chi-restraints excluded: chain H residue 77 SER Chi-restraints excluded: chain H residue 85 SER Chi-restraints excluded: chain H residue 87 ARG Chi-restraints excluded: chain H residue 125 SER Chi-restraints excluded: chain L residue 29 VAL Chi-restraints excluded: chain L residue 47 LYS Chi-restraints excluded: chain L residue 108 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 76 random chunks: chunk 34 optimal weight: 1.9990 chunk 42 optimal weight: 2.9990 chunk 25 optimal weight: 0.9990 chunk 6 optimal weight: 0.9990 chunk 14 optimal weight: 0.6980 chunk 59 optimal weight: 0.4980 chunk 47 optimal weight: 1.9990 chunk 50 optimal weight: 0.5980 chunk 66 optimal weight: 0.8980 chunk 73 optimal weight: 0.7980 chunk 35 optimal weight: 0.2980 overall best weight: 0.5780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 453 ASN A 527 GLN B 527 GLN B 551 ASN B 595 ASN F 6 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3578 r_free = 0.3578 target = 0.119406 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3266 r_free = 0.3266 target = 0.098875 restraints weight = 38895.410| |-----------------------------------------------------------------------------| r_work (start): 0.3244 rms_B_bonded: 3.68 r_work: 0.3047 rms_B_bonded: 4.05 restraints_weight: 0.5000 r_work (final): 0.3047 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3048 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3048 r_free = 0.3048 target_work(ls_wunit_k1) = 0.085 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 1 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3048 r_free = 0.3048 target_work(ls_wunit_k1) = 0.085 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 1 | |-----------------------------------------------------------------------------| r_final: 0.3048 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8106 moved from start: 0.2117 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.029 6079 Z= 0.165 Angle : 0.552 5.609 8315 Z= 0.295 Chirality : 0.044 0.203 913 Planarity : 0.004 0.039 1068 Dihedral : 5.319 40.109 844 Min Nonbonded Distance : 2.546 Molprobity Statistics. All-atom Clashscore : 3.80 Ramachandran Plot: Outliers : 0.26 % Allowed : 3.81 % Favored : 95.93 % Rotamer: Outliers : 3.91 % Allowed : 23.32 % Favored : 72.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.00 % 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 aren not related in a simple way. whole: 0.62 (0.31), residues: 777 helix: -5.09 (0.54), residues: 12 sheet: 1.24 (0.27), residues: 331 loop : -0.05 (0.32), residues: 434 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG E 111 TYR 0.011 0.002 TYR H 95 PHE 0.010 0.001 PHE F 93 TRP 0.012 0.002 TRP A 461 HIS 0.003 0.001 HIS A 516 Details of bonding type rmsd covalent geometry : bond 0.00389 ( 6075) covalent geometry : angle 0.55235 ( 8307) SS BOND : bond 0.00163 ( 4) SS BOND : angle 0.52429 ( 8) hydrogen bonds : bond 0.02746 ( 83) hydrogen bonds : angle 5.33284 ( 183) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1554 Ramachandran restraints generated. 777 Oldfield, 0 Emsley, 777 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1554 Ramachandran restraints generated. 777 Oldfield, 0 Emsley, 777 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 214 residues out of total 629 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 189 time to evaluate : 0.222 Fit side-chains REVERT: A 534 ILE cc_start: 0.8544 (OUTLIER) cc_final: 0.8327 (tp) REVERT: H 65 GLN cc_start: 0.7622 (OUTLIER) cc_final: 0.7325 (mt0) outliers start: 25 outliers final: 21 residues processed: 195 average time/residue: 0.4538 time to fit residues: 93.5594 Evaluate side-chains 209 residues out of total 629 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 186 time to evaluate : 0.215 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 472 SER Chi-restraints excluded: chain A residue 534 ILE Chi-restraints excluded: chain A residue 553 THR Chi-restraints excluded: chain B residue 452 THR Chi-restraints excluded: chain B residue 542 THR Chi-restraints excluded: chain B residue 552 THR Chi-restraints excluded: chain B residue 553 THR Chi-restraints excluded: chain B residue 576 THR Chi-restraints excluded: chain E residue 71 THR Chi-restraints excluded: chain F residue 11 SER Chi-restraints excluded: chain F residue 67 SER Chi-restraints excluded: chain H residue 2 VAL Chi-restraints excluded: chain H residue 7 SER Chi-restraints excluded: chain H residue 25 SER Chi-restraints excluded: chain H residue 65 GLN Chi-restraints excluded: chain H residue 71 THR Chi-restraints excluded: chain H residue 77 SER Chi-restraints excluded: chain H residue 85 SER Chi-restraints excluded: chain H residue 87 ARG Chi-restraints excluded: chain H residue 125 SER Chi-restraints excluded: chain L residue 29 VAL Chi-restraints excluded: chain L residue 47 LYS Chi-restraints excluded: chain L residue 108 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 76 random chunks: chunk 18 optimal weight: 1.9990 chunk 23 optimal weight: 0.6980 chunk 17 optimal weight: 0.5980 chunk 1 optimal weight: 0.4980 chunk 12 optimal weight: 0.5980 chunk 70 optimal weight: 2.9990 chunk 47 optimal weight: 1.9990 chunk 34 optimal weight: 1.9990 chunk 39 optimal weight: 0.7980 chunk 5 optimal weight: 0.7980 chunk 20 optimal weight: 0.7980 overall best weight: 0.6380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 453 ASN A 527 GLN B 453 ASN B 527 GLN B 595 ASN F 6 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3574 r_free = 0.3574 target = 0.119791 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3269 r_free = 0.3269 target = 0.099772 restraints weight = 34805.351| |-----------------------------------------------------------------------------| r_work (start): 0.3243 rms_B_bonded: 3.44 r_work: 0.3059 rms_B_bonded: 3.82 restraints_weight: 0.5000 r_work (final): 0.3059 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3059 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3059 r_free = 0.3059 target_work(ls_wunit_k1) = 0.086 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 1 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3059 r_free = 0.3059 target_work(ls_wunit_k1) = 0.086 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 1 | |-----------------------------------------------------------------------------| r_final: 0.3059 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8094 moved from start: 0.2195 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.031 6079 Z= 0.178 Angle : 0.564 5.624 8315 Z= 0.302 Chirality : 0.045 0.199 913 Planarity : 0.004 0.040 1068 Dihedral : 5.379 40.534 844 Min Nonbonded Distance : 2.539 Molprobity Statistics. All-atom Clashscore : 3.97 Ramachandran Plot: Outliers : 0.13 % Allowed : 4.07 % Favored : 95.80 % Rotamer: Outliers : 4.38 % Allowed : 23.16 % Favored : 72.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.00 % 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 aren not related in a simple way. whole: 0.59 (0.31), residues: 777 helix: -5.00 (0.60), residues: 12 sheet: 1.22 (0.27), residues: 331 loop : -0.06 (0.32), residues: 434 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG E 111 TYR 0.012 0.002 TYR F 32 PHE 0.011 0.002 PHE F 93 TRP 0.012 0.002 TRP A 483 HIS 0.003 0.001 HIS A 516 Details of bonding type rmsd covalent geometry : bond 0.00422 ( 6075) covalent geometry : angle 0.56416 ( 8307) SS BOND : bond 0.00163 ( 4) SS BOND : angle 0.54554 ( 8) hydrogen bonds : bond 0.02751 ( 83) hydrogen bonds : angle 5.38579 ( 183) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1554 Ramachandran restraints generated. 777 Oldfield, 0 Emsley, 777 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1554 Ramachandran restraints generated. 777 Oldfield, 0 Emsley, 777 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 214 residues out of total 629 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 186 time to evaluate : 0.234 Fit side-chains REVERT: A 534 ILE cc_start: 0.8550 (OUTLIER) cc_final: 0.8349 (tp) REVERT: H 65 GLN cc_start: 0.7596 (OUTLIER) cc_final: 0.7301 (mt0) outliers start: 28 outliers final: 24 residues processed: 193 average time/residue: 0.4457 time to fit residues: 90.8285 Evaluate side-chains 212 residues out of total 629 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 186 time to evaluate : 0.230 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 472 SER Chi-restraints excluded: chain A residue 534 ILE Chi-restraints excluded: chain A residue 553 THR Chi-restraints excluded: chain B residue 452 THR Chi-restraints excluded: chain B residue 486 GLU Chi-restraints excluded: chain B residue 501 SER Chi-restraints excluded: chain B residue 542 THR Chi-restraints excluded: chain B residue 552 THR Chi-restraints excluded: chain B residue 553 THR Chi-restraints excluded: chain B residue 576 THR Chi-restraints excluded: chain E residue 71 THR Chi-restraints excluded: chain E residue 125 SER Chi-restraints excluded: chain F residue 11 SER Chi-restraints excluded: chain F residue 67 SER Chi-restraints excluded: chain H residue 2 VAL Chi-restraints excluded: chain H residue 7 SER Chi-restraints excluded: chain H residue 25 SER Chi-restraints excluded: chain H residue 62 GLN Chi-restraints excluded: chain H residue 65 GLN Chi-restraints excluded: chain H residue 71 THR Chi-restraints excluded: chain H residue 77 SER Chi-restraints excluded: chain H residue 85 SER Chi-restraints excluded: chain H residue 87 ARG Chi-restraints excluded: chain H residue 125 SER Chi-restraints excluded: chain L residue 47 LYS Chi-restraints excluded: chain L residue 108 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 76 random chunks: chunk 1 optimal weight: 0.6980 chunk 32 optimal weight: 2.9990 chunk 65 optimal weight: 0.0060 chunk 8 optimal weight: 2.9990 chunk 55 optimal weight: 0.8980 chunk 37 optimal weight: 0.9980 chunk 56 optimal weight: 0.9990 chunk 46 optimal weight: 0.0170 chunk 10 optimal weight: 0.0980 chunk 18 optimal weight: 0.9980 chunk 11 optimal weight: 1.9990 overall best weight: 0.3434 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 453 ASN A 527 GLN B 527 GLN H 39 GLN L 40 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3573 r_free = 0.3573 target = 0.117914 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.3268 r_free = 0.3268 target = 0.097639 restraints weight = 35557.883| |-----------------------------------------------------------------------------| r_work (start): 0.3266 rms_B_bonded: 3.51 r_work: 0.3085 rms_B_bonded: 3.85 restraints_weight: 0.5000 r_work (final): 0.3085 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3084 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3084 r_free = 0.3084 target_work(ls_wunit_k1) = 0.087 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 1 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3084 r_free = 0.3084 target_work(ls_wunit_k1) = 0.087 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 1 | |-----------------------------------------------------------------------------| r_final: 0.3084 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8067 moved from start: 0.2134 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.021 6079 Z= 0.116 Angle : 0.514 5.648 8315 Z= 0.273 Chirality : 0.043 0.162 913 Planarity : 0.004 0.038 1068 Dihedral : 4.972 37.554 844 Min Nonbonded Distance : 2.533 Molprobity Statistics. All-atom Clashscore : 3.71 Ramachandran Plot: Outliers : 0.13 % Allowed : 3.67 % Favored : 96.19 % Rotamer: Outliers : 3.13 % Allowed : 24.10 % Favored : 72.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.00 % 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 aren not related in a simple way. whole: 0.70 (0.31), residues: 777 helix: -4.90 (0.68), residues: 12 sheet: 1.31 (0.27), residues: 331 loop : -0.00 (0.32), residues: 434 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG H 111 TYR 0.012 0.001 TYR F 32 PHE 0.009 0.001 PHE F 93 TRP 0.012 0.001 TRP A 483 HIS 0.002 0.001 HIS A 516 Details of bonding type rmsd covalent geometry : bond 0.00268 ( 6075) covalent geometry : angle 0.51387 ( 8307) SS BOND : bond 0.00150 ( 4) SS BOND : angle 0.41625 ( 8) hydrogen bonds : bond 0.02496 ( 83) hydrogen bonds : angle 4.95886 ( 183) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1554 Ramachandran restraints generated. 777 Oldfield, 0 Emsley, 777 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1554 Ramachandran restraints generated. 777 Oldfield, 0 Emsley, 777 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 204 residues out of total 629 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 184 time to evaluate : 0.296 Fit side-chains REVERT: A 534 ILE cc_start: 0.8550 (OUTLIER) cc_final: 0.8315 (tp) outliers start: 20 outliers final: 17 residues processed: 191 average time/residue: 0.4433 time to fit residues: 89.5276 Evaluate side-chains 201 residues out of total 629 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 183 time to evaluate : 0.138 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 472 SER Chi-restraints excluded: chain A residue 534 ILE Chi-restraints excluded: chain A residue 553 THR Chi-restraints excluded: chain B residue 452 THR Chi-restraints excluded: chain B residue 486 GLU Chi-restraints excluded: chain B residue 552 THR Chi-restraints excluded: chain B residue 553 THR Chi-restraints excluded: chain F residue 29 VAL Chi-restraints excluded: chain F residue 67 SER Chi-restraints excluded: chain H residue 2 VAL Chi-restraints excluded: chain H residue 7 SER Chi-restraints excluded: chain H residue 23 LYS Chi-restraints excluded: chain H residue 25 SER Chi-restraints excluded: chain H residue 77 SER Chi-restraints excluded: chain H residue 85 SER Chi-restraints excluded: chain H residue 87 ARG Chi-restraints excluded: chain H residue 125 SER Chi-restraints excluded: chain L residue 108 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 76 random chunks: chunk 55 optimal weight: 0.8980 chunk 75 optimal weight: 1.9990 chunk 11 optimal weight: 0.5980 chunk 41 optimal weight: 1.9990 chunk 22 optimal weight: 1.9990 chunk 42 optimal weight: 2.9990 chunk 59 optimal weight: 0.5980 chunk 44 optimal weight: 0.0670 chunk 62 optimal weight: 0.6980 chunk 23 optimal weight: 0.9990 chunk 66 optimal weight: 2.9990 overall best weight: 0.5718 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 527 GLN B 527 GLN F 6 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3577 r_free = 0.3577 target = 0.120023 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.3269 r_free = 0.3269 target = 0.099782 restraints weight = 38265.958| |-----------------------------------------------------------------------------| r_work (start): 0.3245 rms_B_bonded: 3.64 r_work: 0.3051 rms_B_bonded: 4.01 restraints_weight: 0.5000 r_work (final): 0.3051 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3050 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3050 r_free = 0.3050 target_work(ls_wunit_k1) = 0.085 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 1 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3050 r_free = 0.3050 target_work(ls_wunit_k1) = 0.085 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 1 | |-----------------------------------------------------------------------------| r_final: 0.3050 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8099 moved from start: 0.2186 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.029 6079 Z= 0.164 Angle : 0.556 5.819 8315 Z= 0.295 Chirality : 0.044 0.186 913 Planarity : 0.004 0.040 1068 Dihedral : 5.196 39.408 844 Min Nonbonded Distance : 2.525 Molprobity Statistics. All-atom Clashscore : 4.31 Ramachandran Plot: Outliers : 0.13 % Allowed : 3.67 % Favored : 96.19 % Rotamer: Outliers : 3.60 % Allowed : 23.32 % Favored : 73.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.00 % 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 aren not related in a simple way. whole: 0.65 (0.31), residues: 777 helix: -4.89 (0.69), residues: 12 sheet: 1.25 (0.27), residues: 331 loop : -0.01 (0.32), residues: 434 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG B 455 TYR 0.014 0.002 TYR A 550 PHE 0.010 0.001 PHE F 93 TRP 0.012 0.002 TRP A 461 HIS 0.003 0.001 HIS A 516 Details of bonding type rmsd covalent geometry : bond 0.00387 ( 6075) covalent geometry : angle 0.55575 ( 8307) SS BOND : bond 0.00132 ( 4) SS BOND : angle 0.48470 ( 8) hydrogen bonds : bond 0.02653 ( 83) hydrogen bonds : angle 5.18110 ( 183) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1554 Ramachandran restraints generated. 777 Oldfield, 0 Emsley, 777 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1554 Ramachandran restraints generated. 777 Oldfield, 0 Emsley, 777 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 197 residues out of total 629 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 174 time to evaluate : 0.242 Fit side-chains REVERT: A 534 ILE cc_start: 0.8552 (OUTLIER) cc_final: 0.8348 (tp) outliers start: 23 outliers final: 21 residues processed: 183 average time/residue: 0.4751 time to fit residues: 91.8365 Evaluate side-chains 194 residues out of total 629 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 172 time to evaluate : 0.216 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 472 SER Chi-restraints excluded: chain A residue 534 ILE Chi-restraints excluded: chain A residue 553 THR Chi-restraints excluded: chain B residue 452 THR Chi-restraints excluded: chain B residue 486 GLU Chi-restraints excluded: chain B residue 501 SER Chi-restraints excluded: chain B residue 552 THR Chi-restraints excluded: chain B residue 553 THR Chi-restraints excluded: chain E residue 125 SER Chi-restraints excluded: chain F residue 29 VAL Chi-restraints excluded: chain F residue 67 SER Chi-restraints excluded: chain H residue 2 VAL Chi-restraints excluded: chain H residue 7 SER Chi-restraints excluded: chain H residue 23 LYS Chi-restraints excluded: chain H residue 25 SER Chi-restraints excluded: chain H residue 62 GLN Chi-restraints excluded: chain H residue 77 SER Chi-restraints excluded: chain H residue 85 SER Chi-restraints excluded: chain H residue 87 ARG Chi-restraints excluded: chain H residue 125 SER Chi-restraints excluded: chain L residue 29 VAL Chi-restraints excluded: chain L residue 108 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 76 random chunks: chunk 10 optimal weight: 0.6980 chunk 29 optimal weight: 1.9990 chunk 45 optimal weight: 0.8980 chunk 32 optimal weight: 2.9990 chunk 39 optimal weight: 0.9990 chunk 73 optimal weight: 1.9990 chunk 70 optimal weight: 0.0270 chunk 51 optimal weight: 0.0060 chunk 4 optimal weight: 0.6980 chunk 43 optimal weight: 1.9990 chunk 17 optimal weight: 0.5980 overall best weight: 0.4054 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 527 GLN B 527 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3571 r_free = 0.3571 target = 0.117801 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3270 r_free = 0.3270 target = 0.097695 restraints weight = 33979.688| |-----------------------------------------------------------------------------| r_work (start): 0.3268 rms_B_bonded: 3.43 r_work: 0.3089 rms_B_bonded: 3.77 restraints_weight: 0.5000 r_work (final): 0.3089 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3088 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3088 r_free = 0.3088 target_work(ls_wunit_k1) = 0.087 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 1 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3088 r_free = 0.3088 target_work(ls_wunit_k1) = 0.087 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 1 | |-----------------------------------------------------------------------------| r_final: 0.3088 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8065 moved from start: 0.2210 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.022 6079 Z= 0.130 Angle : 0.533 5.832 8315 Z= 0.282 Chirality : 0.043 0.178 913 Planarity : 0.004 0.039 1068 Dihedral : 5.010 37.951 844 Min Nonbonded Distance : 2.525 Molprobity Statistics. All-atom Clashscore : 4.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.67 % Favored : 96.33 % Rotamer: Outliers : 3.44 % Allowed : 23.63 % Favored : 72.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.00 % 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 aren not related in a simple way. whole: 0.66 (0.31), residues: 777 helix: -4.87 (0.70), residues: 12 sheet: 1.21 (0.27), residues: 333 loop : 0.03 (0.32), residues: 432 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG B 455 TYR 0.010 0.002 TYR F 32 PHE 0.009 0.001 PHE F 93 TRP 0.011 0.001 TRP A 483 HIS 0.003 0.001 HIS A 516 Details of bonding type rmsd covalent geometry : bond 0.00303 ( 6075) covalent geometry : angle 0.53323 ( 8307) SS BOND : bond 0.00136 ( 4) SS BOND : angle 0.40826 ( 8) hydrogen bonds : bond 0.02558 ( 83) hydrogen bonds : angle 4.96732 ( 183) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1554 Ramachandran restraints generated. 777 Oldfield, 0 Emsley, 777 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1554 Ramachandran restraints generated. 777 Oldfield, 0 Emsley, 777 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 193 residues out of total 629 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 171 time to evaluate : 0.232 Fit side-chains REVERT: A 534 ILE cc_start: 0.8548 (OUTLIER) cc_final: 0.8304 (tp) outliers start: 22 outliers final: 21 residues processed: 179 average time/residue: 0.4434 time to fit residues: 83.9032 Evaluate side-chains 193 residues out of total 629 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 171 time to evaluate : 0.223 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 472 SER Chi-restraints excluded: chain A residue 534 ILE Chi-restraints excluded: chain A residue 553 THR Chi-restraints excluded: chain B residue 452 THR Chi-restraints excluded: chain B residue 486 GLU Chi-restraints excluded: chain B residue 501 SER Chi-restraints excluded: chain B residue 552 THR Chi-restraints excluded: chain B residue 553 THR Chi-restraints excluded: chain E residue 125 SER Chi-restraints excluded: chain F residue 29 VAL Chi-restraints excluded: chain F residue 67 SER Chi-restraints excluded: chain H residue 2 VAL Chi-restraints excluded: chain H residue 7 SER Chi-restraints excluded: chain H residue 23 LYS Chi-restraints excluded: chain H residue 25 SER Chi-restraints excluded: chain H residue 62 GLN Chi-restraints excluded: chain H residue 85 SER Chi-restraints excluded: chain H residue 87 ARG Chi-restraints excluded: chain H residue 125 SER Chi-restraints excluded: chain L residue 29 VAL Chi-restraints excluded: chain L residue 47 LYS Chi-restraints excluded: chain L residue 108 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 76 random chunks: chunk 73 optimal weight: 1.9990 chunk 65 optimal weight: 0.0070 chunk 36 optimal weight: 0.1980 chunk 47 optimal weight: 0.9990 chunk 12 optimal weight: 0.5980 chunk 24 optimal weight: 1.9990 chunk 13 optimal weight: 1.9990 chunk 67 optimal weight: 0.9990 chunk 59 optimal weight: 0.0670 chunk 58 optimal weight: 0.0470 chunk 19 optimal weight: 0.6980 overall best weight: 0.1834 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 527 GLN B 527 GLN H 39 GLN L 40 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3617 r_free = 0.3617 target = 0.122728 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3318 r_free = 0.3318 target = 0.102675 restraints weight = 36001.709| |-----------------------------------------------------------------------------| r_work (start): 0.3295 rms_B_bonded: 3.56 r_work: 0.3107 rms_B_bonded: 4.00 restraints_weight: 0.5000 r_work (final): 0.3107 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3107 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3107 r_free = 0.3107 target_work(ls_wunit_k1) = 0.088 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 1 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3107 r_free = 0.3107 target_work(ls_wunit_k1) = 0.088 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 1 | |-----------------------------------------------------------------------------| r_final: 0.3107 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8044 moved from start: 0.2186 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.019 6079 Z= 0.092 Angle : 0.498 6.828 8315 Z= 0.260 Chirality : 0.042 0.152 913 Planarity : 0.004 0.037 1068 Dihedral : 4.611 34.289 844 Min Nonbonded Distance : 2.529 Molprobity Statistics. All-atom Clashscore : 3.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.67 % Favored : 96.33 % Rotamer: Outliers : 2.82 % Allowed : 24.41 % Favored : 72.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.00 % 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 aren not related in a simple way. whole: 0.75 (0.31), residues: 777 helix: -4.81 (0.73), residues: 12 sheet: 1.27 (0.27), residues: 335 loop : 0.07 (0.32), residues: 430 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG B 455 TYR 0.012 0.001 TYR A 550 PHE 0.008 0.001 PHE F 93 TRP 0.009 0.001 TRP A 483 HIS 0.002 0.000 HIS A 516 Details of bonding type rmsd covalent geometry : bond 0.00209 ( 6075) covalent geometry : angle 0.49857 ( 8307) SS BOND : bond 0.00177 ( 4) SS BOND : angle 0.35074 ( 8) hydrogen bonds : bond 0.02345 ( 83) hydrogen bonds : angle 4.54202 ( 183) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2876.08 seconds wall clock time: 49 minutes 46.78 seconds (2986.78 seconds total)