Starting phenix.real_space_refine on Mon Dec 30 16:45:12 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7oxr_13104/12_2024/7oxr_13104.cif Found real_map, /net/cci-nas-00/data/ceres_data/7oxr_13104/12_2024/7oxr_13104.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.3 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/7oxr_13104/12_2024/7oxr_13104.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7oxr_13104/12_2024/7oxr_13104.map" model { file = "/net/cci-nas-00/data/ceres_data/7oxr_13104/12_2024/7oxr_13104.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7oxr_13104/12_2024/7oxr_13104.cif" } resolution = 3.3 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } 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= 0.005 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 60 5.16 5 C 8670 2.51 5 N 2270 2.21 5 O 2670 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 70 residue(s): 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5532/modules/chem_data/mon_lib" Total number of atoms: 13670 Number of models: 1 Model: "" Number of chains: 10 Chain: "A" Number of atoms: 1367 Number of conformers: 1 Conformer: "" Number of residues, atoms: 170, 1367 Classifications: {'peptide': 170} Link IDs: {'PTRANS': 8, 'TRANS': 161} Chain breaks: 1 Chain: "B" Number of atoms: 1367 Number of conformers: 1 Conformer: "" Number of residues, atoms: 170, 1367 Classifications: {'peptide': 170} Link IDs: {'PTRANS': 8, 'TRANS': 161} Chain breaks: 1 Chain: "C" Number of atoms: 1367 Number of conformers: 1 Conformer: "" Number of residues, atoms: 170, 1367 Classifications: {'peptide': 170} Link IDs: {'PTRANS': 8, 'TRANS': 161} Chain breaks: 1 Chain: "D" Number of atoms: 1367 Number of conformers: 1 Conformer: "" Number of residues, atoms: 170, 1367 Classifications: {'peptide': 170} Link IDs: {'PTRANS': 8, 'TRANS': 161} Chain breaks: 1 Chain: "E" Number of atoms: 1367 Number of conformers: 1 Conformer: "" Number of residues, atoms: 170, 1367 Classifications: {'peptide': 170} Link IDs: {'PTRANS': 8, 'TRANS': 161} Chain breaks: 1 Chain: "F" Number of atoms: 1367 Number of conformers: 1 Conformer: "" Number of residues, atoms: 170, 1367 Classifications: {'peptide': 170} Link IDs: {'PTRANS': 8, 'TRANS': 161} Chain breaks: 1 Chain: "G" Number of atoms: 1367 Number of conformers: 1 Conformer: "" Number of residues, atoms: 170, 1367 Classifications: {'peptide': 170} Link IDs: {'PTRANS': 8, 'TRANS': 161} Chain breaks: 1 Chain: "H" Number of atoms: 1367 Number of conformers: 1 Conformer: "" Number of residues, atoms: 170, 1367 Classifications: {'peptide': 170} Link IDs: {'PTRANS': 8, 'TRANS': 161} Chain breaks: 1 Chain: "I" Number of atoms: 1367 Number of conformers: 1 Conformer: "" Number of residues, atoms: 170, 1367 Classifications: {'peptide': 170} Link IDs: {'PTRANS': 8, 'TRANS': 161} Chain breaks: 1 Chain: "J" Number of atoms: 1367 Number of conformers: 1 Conformer: "" Number of residues, atoms: 170, 1367 Classifications: {'peptide': 170} Link IDs: {'PTRANS': 8, 'TRANS': 161} Chain breaks: 1 Time building chain proxies: 8.82, per 1000 atoms: 0.65 Number of scatterers: 13670 At special positions: 0 Unit cell: (150.592, 157.248, 49.088, 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 60 16.00 O 2670 8.00 N 2270 7.00 C 8670 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=10, symmetry=0 Simple disulfide: pdb=" SG CYS A 113 " - pdb=" SG CYS A 159 " distance=2.03 Simple disulfide: pdb=" SG CYS B 113 " - pdb=" SG CYS B 159 " distance=2.03 Simple disulfide: pdb=" SG CYS C 113 " - pdb=" SG CYS C 159 " distance=2.03 Simple disulfide: pdb=" SG CYS D 113 " - pdb=" SG CYS D 159 " distance=2.03 Simple disulfide: pdb=" SG CYS E 113 " - pdb=" SG CYS E 159 " distance=2.03 Simple disulfide: pdb=" SG CYS F 113 " - pdb=" SG CYS F 159 " distance=2.03 Simple disulfide: pdb=" SG CYS G 113 " - pdb=" SG CYS G 159 " distance=2.03 Simple disulfide: pdb=" SG CYS H 113 " - pdb=" SG CYS H 159 " distance=2.03 Simple disulfide: pdb=" SG CYS I 113 " - pdb=" SG CYS I 159 " distance=2.03 Simple disulfide: pdb=" SG CYS J 113 " - pdb=" SG CYS J 159 " 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: 3.07 Conformation dependent library (CDL) restraints added in 1.8 seconds 3320 Ramachandran restraints generated. 1660 Oldfield, 0 Emsley, 1660 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3260 Finding SS restraints... Secondary structure from input PDB file: 30 helices and 10 sheets defined 12.9% alpha, 15.9% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.12 Creating SS restraints... Processing helix chain 'A' and resid 56 through 58 No H-bonds generated for 'chain 'A' and resid 56 through 58' Processing helix chain 'A' and resid 167 through 175 Processing helix chain 'A' and resid 177 through 186 Processing helix chain 'B' and resid 56 through 58 No H-bonds generated for 'chain 'B' and resid 56 through 58' Processing helix chain 'B' and resid 167 through 175 Processing helix chain 'B' and resid 177 through 186 Processing helix chain 'C' and resid 56 through 58 No H-bonds generated for 'chain 'C' and resid 56 through 58' Processing helix chain 'C' and resid 167 through 175 Processing helix chain 'C' and resid 177 through 186 Processing helix chain 'D' and resid 56 through 58 No H-bonds generated for 'chain 'D' and resid 56 through 58' Processing helix chain 'D' and resid 167 through 175 Processing helix chain 'D' and resid 177 through 186 Processing helix chain 'E' and resid 56 through 58 No H-bonds generated for 'chain 'E' and resid 56 through 58' Processing helix chain 'E' and resid 167 through 175 Processing helix chain 'E' and resid 177 through 186 Processing helix chain 'F' and resid 56 through 58 No H-bonds generated for 'chain 'F' and resid 56 through 58' Processing helix chain 'F' and resid 167 through 175 Processing helix chain 'F' and resid 177 through 186 Processing helix chain 'G' and resid 56 through 58 No H-bonds generated for 'chain 'G' and resid 56 through 58' Processing helix chain 'G' and resid 167 through 175 Processing helix chain 'G' and resid 177 through 186 Processing helix chain 'H' and resid 56 through 58 No H-bonds generated for 'chain 'H' and resid 56 through 58' Processing helix chain 'H' and resid 167 through 175 Processing helix chain 'H' and resid 177 through 186 Processing helix chain 'I' and resid 56 through 58 No H-bonds generated for 'chain 'I' and resid 56 through 58' Processing helix chain 'I' and resid 167 through 175 Processing helix chain 'I' and resid 177 through 186 Processing helix chain 'J' and resid 56 through 58 No H-bonds generated for 'chain 'J' and resid 56 through 58' Processing helix chain 'J' and resid 167 through 175 Processing helix chain 'J' and resid 177 through 186 Processing sheet with id=AA1, first strand: chain 'A' and resid 51 through 54 WARNING: can't find start of bonding for strands! previous: chain 'A' and resid 51 through 54 current: chain 'A' and resid 68 through 77 WARNING: can't find start of bonding for strands! previous: chain 'A' and resid 95 through 98 current: chain 'A' and resid 148 through 160 Processing sheet with id=AA2, first strand: chain 'B' and resid 51 through 54 WARNING: can't find start of bonding for strands! previous: chain 'B' and resid 51 through 54 current: chain 'B' and resid 68 through 77 WARNING: can't find start of bonding for strands! previous: chain 'B' and resid 95 through 98 current: chain 'B' and resid 148 through 160 Processing sheet with id=AA3, first strand: chain 'C' and resid 51 through 54 WARNING: can't find start of bonding for strands! previous: chain 'C' and resid 51 through 54 current: chain 'C' and resid 68 through 77 WARNING: can't find start of bonding for strands! previous: chain 'C' and resid 95 through 98 current: chain 'C' and resid 148 through 160 Processing sheet with id=AA4, first strand: chain 'D' and resid 51 through 54 WARNING: can't find start of bonding for strands! previous: chain 'D' and resid 51 through 54 current: chain 'D' and resid 68 through 77 WARNING: can't find start of bonding for strands! previous: chain 'D' and resid 95 through 98 current: chain 'D' and resid 148 through 160 Processing sheet with id=AA5, first strand: chain 'E' and resid 51 through 54 WARNING: can't find start of bonding for strands! previous: chain 'E' and resid 51 through 54 current: chain 'E' and resid 68 through 77 WARNING: can't find start of bonding for strands! previous: chain 'E' and resid 95 through 98 current: chain 'E' and resid 148 through 160 Processing sheet with id=AA6, first strand: chain 'F' and resid 51 through 54 WARNING: can't find start of bonding for strands! previous: chain 'F' and resid 51 through 54 current: chain 'F' and resid 68 through 77 WARNING: can't find start of bonding for strands! previous: chain 'F' and resid 95 through 98 current: chain 'F' and resid 148 through 160 Processing sheet with id=AA7, first strand: chain 'G' and resid 51 through 54 WARNING: can't find start of bonding for strands! previous: chain 'G' and resid 51 through 54 current: chain 'G' and resid 68 through 77 WARNING: can't find start of bonding for strands! previous: chain 'G' and resid 95 through 98 current: chain 'G' and resid 148 through 160 Processing sheet with id=AA8, first strand: chain 'H' and resid 51 through 54 WARNING: can't find start of bonding for strands! previous: chain 'H' and resid 51 through 54 current: chain 'H' and resid 68 through 77 WARNING: can't find start of bonding for strands! previous: chain 'H' and resid 95 through 98 current: chain 'H' and resid 148 through 160 Processing sheet with id=AA9, first strand: chain 'I' and resid 51 through 54 WARNING: can't find start of bonding for strands! previous: chain 'I' and resid 51 through 54 current: chain 'I' and resid 68 through 77 WARNING: can't find start of bonding for strands! previous: chain 'I' and resid 95 through 98 current: chain 'I' and resid 148 through 160 Processing sheet with id=AB1, first strand: chain 'J' and resid 51 through 54 WARNING: can't find start of bonding for strands! previous: chain 'J' and resid 51 through 54 current: chain 'J' and resid 68 through 77 WARNING: can't find start of bonding for strands! previous: chain 'J' and resid 95 through 98 current: chain 'J' and resid 148 through 160 150 hydrogen bonds defined for protein. 420 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: 3.23 Time building geometry restraints manager: 3.57 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.34: 4510 1.34 - 1.46: 2585 1.46 - 1.57: 6705 1.57 - 1.69: 0 1.69 - 1.80: 100 Bond restraints: 13900 Sorted by residual: bond pdb=" CB PRO J 78 " pdb=" CG PRO J 78 " ideal model delta sigma weight residual 1.492 1.556 -0.064 5.00e-02 4.00e+02 1.63e+00 bond pdb=" CB PRO E 78 " pdb=" CG PRO E 78 " ideal model delta sigma weight residual 1.492 1.556 -0.064 5.00e-02 4.00e+02 1.63e+00 bond pdb=" CB PRO B 78 " pdb=" CG PRO B 78 " ideal model delta sigma weight residual 1.492 1.556 -0.064 5.00e-02 4.00e+02 1.62e+00 bond pdb=" CB PRO I 78 " pdb=" CG PRO I 78 " ideal model delta sigma weight residual 1.492 1.555 -0.063 5.00e-02 4.00e+02 1.60e+00 bond pdb=" CB PRO H 78 " pdb=" CG PRO H 78 " ideal model delta sigma weight residual 1.492 1.555 -0.063 5.00e-02 4.00e+02 1.60e+00 ... (remaining 13895 not shown) Histogram of bond angle deviations from ideal: 0.00 - 0.98: 17514 0.98 - 1.95: 1035 1.95 - 2.93: 161 2.93 - 3.91: 50 3.91 - 4.88: 50 Bond angle restraints: 18810 Sorted by residual: angle pdb=" CA VAL D 64 " pdb=" C VAL D 64 " pdb=" N GLN D 65 " ideal model delta sigma weight residual 116.60 119.95 -3.35 1.45e+00 4.76e-01 5.35e+00 angle pdb=" CA VAL I 64 " pdb=" C VAL I 64 " pdb=" N GLN I 65 " ideal model delta sigma weight residual 116.60 119.95 -3.35 1.45e+00 4.76e-01 5.32e+00 angle pdb=" CA VAL E 64 " pdb=" C VAL E 64 " pdb=" N GLN E 65 " ideal model delta sigma weight residual 116.60 119.94 -3.34 1.45e+00 4.76e-01 5.32e+00 angle pdb=" CA VAL G 64 " pdb=" C VAL G 64 " pdb=" N GLN G 65 " ideal model delta sigma weight residual 116.60 119.94 -3.34 1.45e+00 4.76e-01 5.31e+00 angle pdb=" CA VAL H 64 " pdb=" C VAL H 64 " pdb=" N GLN H 65 " ideal model delta sigma weight residual 116.60 119.94 -3.34 1.45e+00 4.76e-01 5.31e+00 ... (remaining 18805 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.97: 7670 17.97 - 35.94: 732 35.94 - 53.91: 98 53.91 - 71.88: 30 71.88 - 89.86: 60 Dihedral angle restraints: 8590 sinusoidal: 3600 harmonic: 4990 Sorted by residual: dihedral pdb=" CB GLU A 184 " pdb=" CG GLU A 184 " pdb=" CD GLU A 184 " pdb=" OE1 GLU A 184 " ideal model delta sinusoidal sigma weight residual 0.00 79.73 -79.73 1 3.00e+01 1.11e-03 8.77e+00 dihedral pdb=" CB GLU E 184 " pdb=" CG GLU E 184 " pdb=" CD GLU E 184 " pdb=" OE1 GLU E 184 " ideal model delta sinusoidal sigma weight residual 0.00 79.71 -79.71 1 3.00e+01 1.11e-03 8.76e+00 dihedral pdb=" CB GLU D 184 " pdb=" CG GLU D 184 " pdb=" CD GLU D 184 " pdb=" OE1 GLU D 184 " ideal model delta sinusoidal sigma weight residual 0.00 79.69 -79.69 1 3.00e+01 1.11e-03 8.76e+00 ... (remaining 8587 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.024: 1156 0.024 - 0.048: 515 0.048 - 0.071: 271 0.071 - 0.095: 95 0.095 - 0.119: 153 Chirality restraints: 2190 Sorted by residual: chirality pdb=" CA ILE C 219 " pdb=" N ILE C 219 " pdb=" C ILE C 219 " pdb=" CB ILE C 219 " both_signs ideal model delta sigma weight residual False 2.43 2.55 -0.12 2.00e-01 2.50e+01 3.52e-01 chirality pdb=" CA ILE G 219 " pdb=" N ILE G 219 " pdb=" C ILE G 219 " pdb=" CB ILE G 219 " both_signs ideal model delta sigma weight residual False 2.43 2.55 -0.12 2.00e-01 2.50e+01 3.47e-01 chirality pdb=" CA ILE B 219 " pdb=" N ILE B 219 " pdb=" C ILE B 219 " pdb=" CB ILE B 219 " both_signs ideal model delta sigma weight residual False 2.43 2.55 -0.12 2.00e-01 2.50e+01 3.46e-01 ... (remaining 2187 not shown) Planarity restraints: 2420 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C SER H 167 " -0.049 5.00e-02 4.00e+02 7.51e-02 9.03e+00 pdb=" N PRO H 168 " 0.130 5.00e-02 4.00e+02 pdb=" CA PRO H 168 " -0.039 5.00e-02 4.00e+02 pdb=" CD PRO H 168 " -0.041 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C SER C 167 " 0.049 5.00e-02 4.00e+02 7.51e-02 9.03e+00 pdb=" N PRO C 168 " -0.130 5.00e-02 4.00e+02 pdb=" CA PRO C 168 " 0.039 5.00e-02 4.00e+02 pdb=" CD PRO C 168 " 0.041 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C SER G 167 " 0.049 5.00e-02 4.00e+02 7.51e-02 9.02e+00 pdb=" N PRO G 168 " -0.130 5.00e-02 4.00e+02 pdb=" CA PRO G 168 " 0.039 5.00e-02 4.00e+02 pdb=" CD PRO G 168 " 0.041 5.00e-02 4.00e+02 ... (remaining 2417 not shown) Histogram of nonbonded interaction distances: 2.00 - 2.58: 61 2.58 - 3.16: 10589 3.16 - 3.74: 19984 3.74 - 4.32: 29423 4.32 - 4.90: 50855 Nonbonded interactions: 110912 Sorted by model distance: nonbonded pdb=" OH TYR I 182 " pdb=" ND2 ASN J 121 " model vdw 1.998 3.120 nonbonded pdb=" O PRO D 78 " pdb=" NH1 ARG D 98 " model vdw 2.307 3.120 nonbonded pdb=" O PRO I 78 " pdb=" NH1 ARG I 98 " model vdw 2.308 3.120 nonbonded pdb=" O PRO F 78 " pdb=" NH1 ARG F 98 " model vdw 2.308 3.120 nonbonded pdb=" O PRO H 78 " pdb=" NH1 ARG H 98 " model vdw 2.308 3.120 ... (remaining 110907 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' selection = chain 'B' selection = chain 'C' selection = chain 'D' selection = chain 'E' selection = chain 'F' selection = chain 'G' selection = chain 'H' selection = chain 'I' selection = chain 'J' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as 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: 10.810 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: 0.020 Extract box with map and model: 0.580 Check model and map are aligned: 0.120 Set scattering table: 0.130 Process input model: 30.740 Find NCS groups from input model: 0.470 Set up NCS constraints: 0.070 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:4.050 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 46.990 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8336 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.064 13900 Z= 0.212 Angle : 0.581 4.882 18810 Z= 0.332 Chirality : 0.043 0.119 2190 Planarity : 0.007 0.075 2420 Dihedral : 16.460 89.855 5300 Min Nonbonded Distance : 1.998 Molprobity Statistics. All-atom Clashscore : 8.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.41 % Favored : 97.59 % Rotamer: Outliers : 0.00 % Allowed : 0.50 % Favored : 99.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.36 (0.19), residues: 1660 helix: -0.87 (0.38), residues: 150 sheet: -0.76 (0.18), residues: 730 loop : -0.90 (0.20), residues: 780 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.002 TRP J 186 HIS 0.001 0.001 HIS F 221 PHE 0.007 0.001 PHE E 70 TYR 0.012 0.002 TYR I 182 ARG 0.010 0.001 ARG G 229 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3320 Ramachandran restraints generated. 1660 Oldfield, 0 Emsley, 1660 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3320 Ramachandran restraints generated. 1660 Oldfield, 0 Emsley, 1660 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 465 residues out of total 1610 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 465 time to evaluate : 1.993 Fit side-chains REVERT: C 106 ASP cc_start: 0.7820 (m-30) cc_final: 0.7577 (m-30) REVERT: C 108 ASN cc_start: 0.8111 (t0) cc_final: 0.7821 (t0) REVERT: C 148 GLU cc_start: 0.7961 (pt0) cc_final: 0.7758 (pt0) REVERT: E 52 VAL cc_start: 0.9206 (t) cc_final: 0.9000 (t) REVERT: F 103 TYR cc_start: 0.8637 (m-80) cc_final: 0.8140 (m-80) REVERT: F 215 GLN cc_start: 0.7493 (tt0) cc_final: 0.7013 (tt0) REVERT: G 148 GLU cc_start: 0.7976 (pt0) cc_final: 0.7724 (pt0) REVERT: H 103 TYR cc_start: 0.8645 (m-80) cc_final: 0.8137 (m-80) REVERT: H 106 ASP cc_start: 0.7904 (m-30) cc_final: 0.7664 (m-30) REVERT: H 108 ASN cc_start: 0.8133 (t0) cc_final: 0.7838 (t0) REVERT: H 215 GLN cc_start: 0.7508 (tt0) cc_final: 0.7189 (tt0) outliers start: 0 outliers final: 0 residues processed: 465 average time/residue: 0.3286 time to fit residues: 211.6195 Evaluate side-chains 370 residues out of total 1610 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 370 time to evaluate : 1.763 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 170 random chunks: chunk 143 optimal weight: 2.9990 chunk 128 optimal weight: 1.9990 chunk 71 optimal weight: 0.0980 chunk 44 optimal weight: 1.9990 chunk 86 optimal weight: 1.9990 chunk 68 optimal weight: 2.9990 chunk 133 optimal weight: 1.9990 chunk 51 optimal weight: 2.9990 chunk 81 optimal weight: 0.4980 chunk 99 optimal weight: 1.9990 chunk 154 optimal weight: 1.9990 overall best weight: 1.3186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 114 GLN B 173 GLN B 215 GLN C 121 ASN C 215 GLN D 114 GLN D 121 ASN E 114 GLN E 121 ASN E 215 GLN F 110 GLN F 114 GLN F 121 ASN G 114 GLN G 121 ASN G 173 GLN G 215 GLN H 121 ASN I 114 GLN I 121 ASN I 215 GLN J 100 ASN J 215 GLN Total number of N/Q/H flips: 23 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8591 moved from start: 0.2850 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.038 13900 Z= 0.417 Angle : 0.610 6.033 18810 Z= 0.310 Chirality : 0.047 0.129 2190 Planarity : 0.005 0.066 2420 Dihedral : 4.938 14.246 1800 Min Nonbonded Distance : 2.355 Molprobity Statistics. All-atom Clashscore : 5.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.47 % Favored : 97.53 % Rotamer: Outliers : 1.93 % Allowed : 12.80 % Favored : 85.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.04 (0.20), residues: 1660 helix: -0.20 (0.40), residues: 170 sheet: -0.46 (0.20), residues: 660 loop : -0.90 (0.20), residues: 830 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.002 TRP C 186 HIS 0.004 0.002 HIS A 221 PHE 0.013 0.002 PHE I 58 TYR 0.019 0.003 TYR F 182 ARG 0.004 0.001 ARG F 229 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3320 Ramachandran restraints generated. 1660 Oldfield, 0 Emsley, 1660 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3320 Ramachandran restraints generated. 1660 Oldfield, 0 Emsley, 1660 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 399 residues out of total 1610 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 368 time to evaluate : 1.607 Fit side-chains REVERT: A 227 LYS cc_start: 0.8625 (ttpt) cc_final: 0.8403 (ttpt) REVERT: B 98 ARG cc_start: 0.8776 (tpp-160) cc_final: 0.8571 (tpp-160) REVERT: B 199 GLU cc_start: 0.8011 (tt0) cc_final: 0.7680 (tt0) REVERT: B 201 SER cc_start: 0.8716 (m) cc_final: 0.8202 (m) REVERT: D 98 ARG cc_start: 0.8751 (tpp-160) cc_final: 0.8535 (tpp-160) REVERT: E 98 ARG cc_start: 0.8734 (tpp-160) cc_final: 0.8396 (tpp-160) REVERT: E 227 LYS cc_start: 0.8627 (ttmm) cc_final: 0.8351 (ttpt) REVERT: F 199 GLU cc_start: 0.7999 (tt0) cc_final: 0.7689 (tt0) REVERT: F 201 SER cc_start: 0.8773 (m) cc_final: 0.8334 (m) REVERT: G 98 ARG cc_start: 0.8772 (tpp-160) cc_final: 0.8555 (tpp-160) REVERT: G 148 GLU cc_start: 0.8043 (pt0) cc_final: 0.7781 (pt0) REVERT: G 199 GLU cc_start: 0.8016 (tt0) cc_final: 0.7677 (tt0) REVERT: G 201 SER cc_start: 0.8710 (m) cc_final: 0.8188 (m) REVERT: I 98 ARG cc_start: 0.8753 (tpp-160) cc_final: 0.8504 (tpp-160) REVERT: J 193 GLU cc_start: 0.7832 (mt-10) cc_final: 0.7576 (mt-10) outliers start: 31 outliers final: 8 residues processed: 391 average time/residue: 0.3030 time to fit residues: 163.7498 Evaluate side-chains 355 residues out of total 1610 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 347 time to evaluate : 1.625 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 211 THR Chi-restraints excluded: chain B residue 68 THR Chi-restraints excluded: chain B residue 230 MET Chi-restraints excluded: chain C residue 230 MET Chi-restraints excluded: chain E residue 62 ASN Chi-restraints excluded: chain G residue 68 THR Chi-restraints excluded: chain I residue 87 ILE Chi-restraints excluded: chain I residue 230 MET Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 170 random chunks: chunk 85 optimal weight: 2.9990 chunk 47 optimal weight: 3.9990 chunk 128 optimal weight: 0.9990 chunk 105 optimal weight: 0.0010 chunk 42 optimal weight: 0.9990 chunk 154 optimal weight: 0.6980 chunk 167 optimal weight: 1.9990 chunk 137 optimal weight: 1.9990 chunk 153 optimal weight: 0.9980 chunk 52 optimal weight: 1.9990 chunk 124 optimal weight: 2.9990 overall best weight: 0.7390 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 72 GLN A 100 ASN A 173 GLN B 114 GLN B 173 GLN B 215 GLN C 215 GLN D 215 GLN E 110 GLN E 215 GLN F 110 GLN G 215 GLN H 215 GLN I 215 GLN J 72 GLN J 100 ASN J 173 GLN Total number of N/Q/H flips: 17 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8574 moved from start: 0.3201 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.026 13900 Z= 0.247 Angle : 0.491 5.667 18810 Z= 0.253 Chirality : 0.045 0.131 2190 Planarity : 0.005 0.057 2420 Dihedral : 4.556 14.065 1800 Min Nonbonded Distance : 2.286 Molprobity Statistics. All-atom Clashscore : 4.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.41 % Favored : 97.59 % Rotamer: Outliers : 2.30 % Allowed : 14.16 % Favored : 83.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.76 (0.21), residues: 1660 helix: 0.55 (0.43), residues: 170 sheet: -0.30 (0.19), residues: 790 loop : -0.87 (0.23), residues: 700 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.002 TRP B 186 HIS 0.003 0.001 HIS G 221 PHE 0.009 0.001 PHE B 58 TYR 0.010 0.002 TYR A 103 ARG 0.005 0.000 ARG H 229 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3320 Ramachandran restraints generated. 1660 Oldfield, 0 Emsley, 1660 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3320 Ramachandran restraints generated. 1660 Oldfield, 0 Emsley, 1660 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 391 residues out of total 1610 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 354 time to evaluate : 1.954 Fit side-chains REVERT: B 199 GLU cc_start: 0.7919 (tt0) cc_final: 0.7585 (tt0) REVERT: B 201 SER cc_start: 0.8762 (m) cc_final: 0.8298 (m) REVERT: C 98 ARG cc_start: 0.8756 (tpp-160) cc_final: 0.8554 (mmt180) REVERT: E 227 LYS cc_start: 0.8673 (ttmm) cc_final: 0.8281 (ttpt) REVERT: F 199 GLU cc_start: 0.7867 (tt0) cc_final: 0.7534 (tt0) REVERT: F 201 SER cc_start: 0.8819 (m) cc_final: 0.8349 (m) REVERT: H 98 ARG cc_start: 0.8707 (tpp-160) cc_final: 0.8363 (mmt180) REVERT: H 199 GLU cc_start: 0.7862 (tt0) cc_final: 0.7657 (tm-30) REVERT: J 193 GLU cc_start: 0.7862 (mt-10) cc_final: 0.7527 (mt-10) outliers start: 37 outliers final: 19 residues processed: 373 average time/residue: 0.3257 time to fit residues: 165.3640 Evaluate side-chains 375 residues out of total 1610 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 356 time to evaluate : 1.943 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 75 LYS Chi-restraints excluded: chain A residue 87 ILE Chi-restraints excluded: chain A residue 211 THR Chi-restraints excluded: chain B residue 163 THR Chi-restraints excluded: chain B residue 230 MET Chi-restraints excluded: chain C residue 68 THR Chi-restraints excluded: chain C residue 77 ILE Chi-restraints excluded: chain C residue 205 ILE Chi-restraints excluded: chain D residue 68 THR Chi-restraints excluded: chain D residue 77 ILE Chi-restraints excluded: chain E residue 77 ILE Chi-restraints excluded: chain F residue 62 ASN Chi-restraints excluded: chain F residue 68 THR Chi-restraints excluded: chain F residue 77 ILE Chi-restraints excluded: chain G residue 77 ILE Chi-restraints excluded: chain H residue 68 THR Chi-restraints excluded: chain H residue 77 ILE Chi-restraints excluded: chain I residue 77 ILE Chi-restraints excluded: chain J residue 211 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 170 random chunks: chunk 152 optimal weight: 1.9990 chunk 116 optimal weight: 0.4980 chunk 80 optimal weight: 0.7980 chunk 17 optimal weight: 2.9990 chunk 73 optimal weight: 3.9990 chunk 103 optimal weight: 0.5980 chunk 155 optimal weight: 2.9990 chunk 164 optimal weight: 1.9990 chunk 81 optimal weight: 0.9990 chunk 147 optimal weight: 0.9980 chunk 44 optimal weight: 0.8980 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 100 ASN A 110 GLN A 215 GLN B 85 GLN B 169 GLN B 173 GLN C 100 ASN C 114 GLN C 215 GLN D 215 GLN E 110 GLN F 110 GLN H 215 GLN I 114 GLN I 215 GLN J 100 ASN Total number of N/Q/H flips: 16 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8583 moved from start: 0.3480 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.027 13900 Z= 0.251 Angle : 0.492 5.152 18810 Z= 0.252 Chirality : 0.045 0.129 2190 Planarity : 0.005 0.052 2420 Dihedral : 4.496 13.489 1800 Min Nonbonded Distance : 2.339 Molprobity Statistics. All-atom Clashscore : 5.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.47 % Favored : 97.53 % Rotamer: Outliers : 2.98 % Allowed : 13.35 % Favored : 83.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.65 (0.21), residues: 1660 helix: 0.65 (0.44), residues: 170 sheet: -0.23 (0.19), residues: 790 loop : -0.81 (0.24), residues: 700 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.002 TRP E 186 HIS 0.003 0.001 HIS H 152 PHE 0.009 0.001 PHE G 58 TYR 0.013 0.002 TYR J 182 ARG 0.006 0.000 ARG C 229 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3320 Ramachandran restraints generated. 1660 Oldfield, 0 Emsley, 1660 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3320 Ramachandran restraints generated. 1660 Oldfield, 0 Emsley, 1660 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 395 residues out of total 1610 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 347 time to evaluate : 1.643 Fit side-chains REVERT: C 98 ARG cc_start: 0.8707 (tpp-160) cc_final: 0.8418 (mmt180) REVERT: E 227 LYS cc_start: 0.8664 (ttmm) cc_final: 0.8310 (ttpt) REVERT: E 230 MET cc_start: 0.3555 (tpt) cc_final: 0.3346 (tpt) REVERT: F 199 GLU cc_start: 0.7826 (tt0) cc_final: 0.7441 (tt0) REVERT: F 201 SER cc_start: 0.8824 (m) cc_final: 0.8401 (m) REVERT: G 148 GLU cc_start: 0.8110 (pt0) cc_final: 0.7791 (pt0) REVERT: G 199 GLU cc_start: 0.7926 (tt0) cc_final: 0.7607 (tt0) REVERT: G 201 SER cc_start: 0.8825 (m) cc_final: 0.8456 (m) REVERT: G 230 MET cc_start: 0.3288 (tpt) cc_final: 0.3082 (tpt) REVERT: H 98 ARG cc_start: 0.8710 (tpp-160) cc_final: 0.8287 (mmt180) REVERT: H 230 MET cc_start: 0.3627 (tpt) cc_final: 0.3341 (tpt) outliers start: 48 outliers final: 20 residues processed: 374 average time/residue: 0.3037 time to fit residues: 160.2340 Evaluate side-chains 357 residues out of total 1610 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 337 time to evaluate : 1.676 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 75 LYS Chi-restraints excluded: chain A residue 87 ILE Chi-restraints excluded: chain A residue 205 ILE Chi-restraints excluded: chain A residue 211 THR Chi-restraints excluded: chain B residue 62 ASN Chi-restraints excluded: chain B residue 205 ILE Chi-restraints excluded: chain B residue 230 MET Chi-restraints excluded: chain C residue 77 ILE Chi-restraints excluded: chain C residue 205 ILE Chi-restraints excluded: chain C residue 230 MET Chi-restraints excluded: chain D residue 68 THR Chi-restraints excluded: chain D residue 77 ILE Chi-restraints excluded: chain E residue 62 ASN Chi-restraints excluded: chain E residue 77 ILE Chi-restraints excluded: chain F residue 62 ASN Chi-restraints excluded: chain F residue 68 THR Chi-restraints excluded: chain F residue 205 ILE Chi-restraints excluded: chain H residue 77 ILE Chi-restraints excluded: chain I residue 77 ILE Chi-restraints excluded: chain J residue 62 ASN Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 170 random chunks: chunk 136 optimal weight: 2.9990 chunk 93 optimal weight: 0.5980 chunk 2 optimal weight: 2.9990 chunk 122 optimal weight: 3.9990 chunk 67 optimal weight: 3.9990 chunk 140 optimal weight: 1.9990 chunk 113 optimal weight: 0.5980 chunk 0 optimal weight: 1.9990 chunk 83 optimal weight: 0.7980 chunk 147 optimal weight: 0.9980 chunk 41 optimal weight: 2.9990 overall best weight: 0.9982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 100 ASN A 110 GLN B 85 GLN B 173 GLN C 100 ASN C 215 GLN D 215 GLN E 110 GLN E 215 GLN F 110 GLN G 114 GLN H 100 ASN H 215 GLN I 215 GLN J 114 GLN Total number of N/Q/H flips: 15 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8602 moved from start: 0.3698 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.030 13900 Z= 0.309 Angle : 0.533 5.413 18810 Z= 0.272 Chirality : 0.046 0.130 2190 Planarity : 0.005 0.050 2420 Dihedral : 4.598 14.203 1800 Min Nonbonded Distance : 2.303 Molprobity Statistics. All-atom Clashscore : 4.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.41 % Favored : 97.59 % Rotamer: Outliers : 2.30 % Allowed : 15.40 % Favored : 82.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.58 (0.22), residues: 1660 helix: 0.60 (0.44), residues: 170 sheet: -0.10 (0.20), residues: 780 loop : -0.84 (0.23), residues: 710 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.002 TRP I 186 HIS 0.004 0.001 HIS F 152 PHE 0.009 0.001 PHE I 58 TYR 0.013 0.002 TYR A 103 ARG 0.006 0.001 ARG F 229 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3320 Ramachandran restraints generated. 1660 Oldfield, 0 Emsley, 1660 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3320 Ramachandran restraints generated. 1660 Oldfield, 0 Emsley, 1660 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 382 residues out of total 1610 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 345 time to evaluate : 1.612 Fit side-chains REVERT: C 98 ARG cc_start: 0.8735 (tpp-160) cc_final: 0.8363 (mmt180) REVERT: D 98 ARG cc_start: 0.8555 (tpp-160) cc_final: 0.8303 (mmt180) REVERT: E 227 LYS cc_start: 0.8655 (ttmm) cc_final: 0.8277 (ttpt) REVERT: G 148 GLU cc_start: 0.8129 (pt0) cc_final: 0.7782 (pt0) outliers start: 37 outliers final: 26 residues processed: 364 average time/residue: 0.2948 time to fit residues: 150.4887 Evaluate side-chains 364 residues out of total 1610 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 338 time to evaluate : 1.608 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 75 LYS Chi-restraints excluded: chain A residue 87 ILE Chi-restraints excluded: chain A residue 211 THR Chi-restraints excluded: chain A residue 230 MET Chi-restraints excluded: chain B residue 62 ASN Chi-restraints excluded: chain B residue 68 THR Chi-restraints excluded: chain B residue 163 THR Chi-restraints excluded: chain B residue 205 ILE Chi-restraints excluded: chain C residue 77 ILE Chi-restraints excluded: chain C residue 205 ILE Chi-restraints excluded: chain C residue 230 MET Chi-restraints excluded: chain D residue 77 ILE Chi-restraints excluded: chain E residue 62 ASN Chi-restraints excluded: chain E residue 77 ILE Chi-restraints excluded: chain E residue 87 ILE Chi-restraints excluded: chain F residue 68 THR Chi-restraints excluded: chain F residue 205 ILE Chi-restraints excluded: chain G residue 68 THR Chi-restraints excluded: chain G residue 87 ILE Chi-restraints excluded: chain G residue 205 ILE Chi-restraints excluded: chain H residue 77 ILE Chi-restraints excluded: chain H residue 201 SER Chi-restraints excluded: chain I residue 77 ILE Chi-restraints excluded: chain I residue 87 ILE Chi-restraints excluded: chain J residue 62 ASN Chi-restraints excluded: chain J residue 211 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 170 random chunks: chunk 55 optimal weight: 1.9990 chunk 147 optimal weight: 0.9980 chunk 32 optimal weight: 1.9990 chunk 96 optimal weight: 0.5980 chunk 40 optimal weight: 2.9990 chunk 164 optimal weight: 0.0470 chunk 136 optimal weight: 2.9990 chunk 76 optimal weight: 2.9990 chunk 13 optimal weight: 2.9990 chunk 54 optimal weight: 2.9990 chunk 86 optimal weight: 1.9990 overall best weight: 1.1282 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 85 GLN B 114 GLN B 173 GLN C 100 ASN C 215 GLN D 215 GLN E 110 GLN E 215 GLN H 100 ASN H 215 GLN I 215 GLN J 100 ASN Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8614 moved from start: 0.3867 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.032 13900 Z= 0.343 Angle : 0.553 8.652 18810 Z= 0.277 Chirality : 0.046 0.130 2190 Planarity : 0.005 0.050 2420 Dihedral : 4.703 17.033 1800 Min Nonbonded Distance : 2.475 Molprobity Statistics. All-atom Clashscore : 4.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.47 % Favored : 97.53 % Rotamer: Outliers : 2.55 % Allowed : 15.16 % Favored : 82.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.54 (0.22), residues: 1660 helix: 0.57 (0.43), residues: 170 sheet: -0.03 (0.20), residues: 780 loop : -0.86 (0.23), residues: 710 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.002 TRP D 186 HIS 0.004 0.002 HIS E 152 PHE 0.010 0.001 PHE G 58 TYR 0.015 0.002 TYR A 103 ARG 0.007 0.001 ARG F 229 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3320 Ramachandran restraints generated. 1660 Oldfield, 0 Emsley, 1660 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3320 Ramachandran restraints generated. 1660 Oldfield, 0 Emsley, 1660 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 384 residues out of total 1610 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 343 time to evaluate : 1.597 Fit side-chains REVERT: A 98 ARG cc_start: 0.8132 (tpp-160) cc_final: 0.7856 (mmt180) REVERT: B 121 ASN cc_start: 0.8872 (t0) cc_final: 0.8648 (t0) REVERT: E 199 GLU cc_start: 0.7805 (tt0) cc_final: 0.7557 (tt0) REVERT: E 201 SER cc_start: 0.8877 (m) cc_final: 0.8610 (p) REVERT: E 227 LYS cc_start: 0.8644 (ttmm) cc_final: 0.8267 (ttpt) REVERT: G 85 GLN cc_start: 0.8773 (mm-40) cc_final: 0.8550 (mm-40) REVERT: G 131 ARG cc_start: 0.8741 (ptt180) cc_final: 0.8520 (ptt180) REVERT: G 148 GLU cc_start: 0.8128 (pt0) cc_final: 0.7786 (pt0) REVERT: H 98 ARG cc_start: 0.8667 (tpp-160) cc_final: 0.8300 (mmt180) outliers start: 41 outliers final: 22 residues processed: 363 average time/residue: 0.2939 time to fit residues: 149.5034 Evaluate side-chains 358 residues out of total 1610 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 336 time to evaluate : 1.515 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 75 LYS Chi-restraints excluded: chain A residue 87 ILE Chi-restraints excluded: chain A residue 205 ILE Chi-restraints excluded: chain A residue 211 THR Chi-restraints excluded: chain B residue 62 ASN Chi-restraints excluded: chain B residue 68 THR Chi-restraints excluded: chain B residue 163 THR Chi-restraints excluded: chain B residue 205 ILE Chi-restraints excluded: chain C residue 205 ILE Chi-restraints excluded: chain D residue 77 ILE Chi-restraints excluded: chain E residue 62 ASN Chi-restraints excluded: chain E residue 77 ILE Chi-restraints excluded: chain F residue 68 THR Chi-restraints excluded: chain F residue 205 ILE Chi-restraints excluded: chain G residue 68 THR Chi-restraints excluded: chain G residue 87 ILE Chi-restraints excluded: chain G residue 205 ILE Chi-restraints excluded: chain H residue 201 SER Chi-restraints excluded: chain I residue 77 ILE Chi-restraints excluded: chain I residue 87 ILE Chi-restraints excluded: chain J residue 62 ASN Chi-restraints excluded: chain J residue 87 ILE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 170 random chunks: chunk 158 optimal weight: 0.9980 chunk 18 optimal weight: 0.9980 chunk 93 optimal weight: 0.9980 chunk 120 optimal weight: 0.9990 chunk 138 optimal weight: 2.9990 chunk 91 optimal weight: 2.9990 chunk 163 optimal weight: 0.6980 chunk 102 optimal weight: 2.9990 chunk 99 optimal weight: 1.9990 chunk 75 optimal weight: 1.9990 chunk 101 optimal weight: 0.1980 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 85 GLN B 114 GLN B 173 GLN C 100 ASN C 215 GLN D 215 GLN E 110 GLN E 215 GLN F 110 GLN H 100 ASN H 114 GLN H 215 GLN I 215 GLN Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8596 moved from start: 0.3943 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.031 13900 Z= 0.257 Angle : 0.537 10.033 18810 Z= 0.265 Chirality : 0.045 0.126 2190 Planarity : 0.004 0.049 2420 Dihedral : 4.512 20.713 1800 Min Nonbonded Distance : 2.562 Molprobity Statistics. All-atom Clashscore : 4.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.47 % Favored : 97.53 % Rotamer: Outliers : 2.05 % Allowed : 16.02 % Favored : 81.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.53 (0.22), residues: 1660 helix: 0.72 (0.44), residues: 170 sheet: -0.09 (0.20), residues: 790 loop : -0.80 (0.24), residues: 700 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.002 TRP I 186 HIS 0.003 0.001 HIS F 152 PHE 0.008 0.001 PHE B 58 TYR 0.015 0.002 TYR A 103 ARG 0.005 0.000 ARG H 191 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3320 Ramachandran restraints generated. 1660 Oldfield, 0 Emsley, 1660 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3320 Ramachandran restraints generated. 1660 Oldfield, 0 Emsley, 1660 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 379 residues out of total 1610 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 346 time to evaluate : 1.703 Fit side-chains REVERT: A 98 ARG cc_start: 0.8013 (tpp-160) cc_final: 0.7692 (mmt180) REVERT: C 98 ARG cc_start: 0.8673 (tpp-160) cc_final: 0.8347 (mmt180) REVERT: D 98 ARG cc_start: 0.8518 (tpp-160) cc_final: 0.8287 (mmt180) REVERT: E 199 GLU cc_start: 0.7750 (tt0) cc_final: 0.7509 (tt0) REVERT: E 201 SER cc_start: 0.8872 (m) cc_final: 0.8623 (p) REVERT: E 227 LYS cc_start: 0.8650 (ttmm) cc_final: 0.8268 (ttpt) REVERT: H 98 ARG cc_start: 0.8645 (tpp-160) cc_final: 0.8413 (mmt-90) REVERT: I 98 ARG cc_start: 0.8493 (tpp-160) cc_final: 0.8229 (mmt180) outliers start: 33 outliers final: 22 residues processed: 365 average time/residue: 0.2998 time to fit residues: 153.3749 Evaluate side-chains 356 residues out of total 1610 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 334 time to evaluate : 1.763 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 75 LYS Chi-restraints excluded: chain A residue 87 ILE Chi-restraints excluded: chain A residue 205 ILE Chi-restraints excluded: chain A residue 211 THR Chi-restraints excluded: chain B residue 68 THR Chi-restraints excluded: chain B residue 163 THR Chi-restraints excluded: chain C residue 205 ILE Chi-restraints excluded: chain D residue 77 ILE Chi-restraints excluded: chain D residue 211 THR Chi-restraints excluded: chain E residue 62 ASN Chi-restraints excluded: chain E residue 77 ILE Chi-restraints excluded: chain E residue 87 ILE Chi-restraints excluded: chain F residue 62 ASN Chi-restraints excluded: chain F residue 68 THR Chi-restraints excluded: chain F residue 205 ILE Chi-restraints excluded: chain G residue 68 THR Chi-restraints excluded: chain G residue 87 ILE Chi-restraints excluded: chain H residue 201 SER Chi-restraints excluded: chain I residue 77 ILE Chi-restraints excluded: chain I residue 87 ILE Chi-restraints excluded: chain J residue 62 ASN Chi-restraints excluded: chain J residue 77 ILE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 170 random chunks: chunk 65 optimal weight: 0.5980 chunk 97 optimal weight: 0.7980 chunk 49 optimal weight: 1.9990 chunk 32 optimal weight: 0.0040 chunk 31 optimal weight: 0.8980 chunk 104 optimal weight: 2.9990 chunk 111 optimal weight: 3.9990 chunk 81 optimal weight: 3.9990 chunk 15 optimal weight: 0.9990 chunk 128 optimal weight: 0.8980 chunk 149 optimal weight: 1.9990 overall best weight: 0.6392 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 110 GLN B 114 GLN B 173 GLN C 100 ASN C 215 GLN D 114 GLN D 215 GLN E 110 GLN E 215 GLN F 110 GLN I 215 GLN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8587 moved from start: 0.3996 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 13900 Z= 0.222 Angle : 0.518 10.387 18810 Z= 0.257 Chirality : 0.044 0.125 2190 Planarity : 0.004 0.048 2420 Dihedral : 4.404 19.817 1800 Min Nonbonded Distance : 2.584 Molprobity Statistics. All-atom Clashscore : 4.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.47 % Favored : 97.53 % Rotamer: Outliers : 1.74 % Allowed : 16.96 % Favored : 81.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.47 (0.22), residues: 1660 helix: 0.77 (0.44), residues: 170 sheet: -0.06 (0.20), residues: 790 loop : -0.76 (0.24), residues: 700 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.002 TRP I 186 HIS 0.002 0.001 HIS F 152 PHE 0.007 0.001 PHE G 58 TYR 0.012 0.001 TYR A 103 ARG 0.005 0.000 ARG H 191 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3320 Ramachandran restraints generated. 1660 Oldfield, 0 Emsley, 1660 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3320 Ramachandran restraints generated. 1660 Oldfield, 0 Emsley, 1660 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 373 residues out of total 1610 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 345 time to evaluate : 1.625 Fit side-chains REVERT: A 85 GLN cc_start: 0.8657 (mm-40) cc_final: 0.8298 (mt0) REVERT: A 98 ARG cc_start: 0.7976 (tpp-160) cc_final: 0.7687 (mmt180) REVERT: B 85 GLN cc_start: 0.8760 (mm-40) cc_final: 0.8526 (mm-40) REVERT: C 98 ARG cc_start: 0.8636 (tpp-160) cc_final: 0.8419 (mmt-90) REVERT: D 98 ARG cc_start: 0.8477 (tpp-160) cc_final: 0.8222 (mmt180) REVERT: D 199 GLU cc_start: 0.7658 (tt0) cc_final: 0.7117 (tm-30) REVERT: D 201 SER cc_start: 0.8938 (m) cc_final: 0.8593 (p) REVERT: E 199 GLU cc_start: 0.7730 (tt0) cc_final: 0.7474 (tt0) REVERT: E 201 SER cc_start: 0.8897 (m) cc_final: 0.8597 (p) REVERT: E 227 LYS cc_start: 0.8653 (ttmm) cc_final: 0.8278 (ttpt) REVERT: I 98 ARG cc_start: 0.8474 (tpp-160) cc_final: 0.8179 (mmt180) REVERT: J 229 ARG cc_start: 0.8511 (mtm110) cc_final: 0.8277 (mtm110) outliers start: 28 outliers final: 22 residues processed: 362 average time/residue: 0.2890 time to fit residues: 147.3088 Evaluate side-chains 364 residues out of total 1610 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 342 time to evaluate : 1.520 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 75 LYS Chi-restraints excluded: chain A residue 87 ILE Chi-restraints excluded: chain A residue 205 ILE Chi-restraints excluded: chain A residue 211 THR Chi-restraints excluded: chain B residue 68 THR Chi-restraints excluded: chain B residue 163 THR Chi-restraints excluded: chain B residue 205 ILE Chi-restraints excluded: chain D residue 77 ILE Chi-restraints excluded: chain D residue 211 THR Chi-restraints excluded: chain E residue 62 ASN Chi-restraints excluded: chain E residue 77 ILE Chi-restraints excluded: chain E residue 87 ILE Chi-restraints excluded: chain F residue 68 THR Chi-restraints excluded: chain F residue 205 ILE Chi-restraints excluded: chain G residue 68 THR Chi-restraints excluded: chain G residue 87 ILE Chi-restraints excluded: chain H residue 87 ILE Chi-restraints excluded: chain H residue 201 SER Chi-restraints excluded: chain I residue 77 ILE Chi-restraints excluded: chain I residue 87 ILE Chi-restraints excluded: chain I residue 211 THR Chi-restraints excluded: chain J residue 77 ILE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 170 random chunks: chunk 156 optimal weight: 6.9990 chunk 143 optimal weight: 2.9990 chunk 152 optimal weight: 2.9990 chunk 91 optimal weight: 2.9990 chunk 66 optimal weight: 1.9990 chunk 119 optimal weight: 2.9990 chunk 46 optimal weight: 0.9990 chunk 137 optimal weight: 0.9980 chunk 144 optimal weight: 2.9990 chunk 100 optimal weight: 1.9990 chunk 161 optimal weight: 0.9980 overall best weight: 1.3986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 110 GLN B 173 GLN C 100 ASN C 114 GLN C 215 GLN D 215 GLN E 110 GLN E 215 GLN F 110 GLN H 215 GLN I 215 GLN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8627 moved from start: 0.4106 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.035 13900 Z= 0.412 Angle : 0.612 10.926 18810 Z= 0.298 Chirality : 0.047 0.130 2190 Planarity : 0.005 0.048 2420 Dihedral : 4.801 19.131 1800 Min Nonbonded Distance : 2.583 Molprobity Statistics. All-atom Clashscore : 4.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.47 % Favored : 97.53 % Rotamer: Outliers : 1.99 % Allowed : 17.02 % Favored : 80.99 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.49 (0.22), residues: 1660 helix: 0.44 (0.43), residues: 170 sheet: 0.07 (0.20), residues: 780 loop : -0.86 (0.23), residues: 710 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.002 TRP D 186 HIS 0.005 0.002 HIS E 152 PHE 0.011 0.002 PHE D 58 TYR 0.017 0.002 TYR E 103 ARG 0.004 0.001 ARG H 191 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3320 Ramachandran restraints generated. 1660 Oldfield, 0 Emsley, 1660 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3320 Ramachandran restraints generated. 1660 Oldfield, 0 Emsley, 1660 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 367 residues out of total 1610 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 335 time to evaluate : 1.690 Fit side-chains REVERT: A 98 ARG cc_start: 0.8206 (tpp-160) cc_final: 0.7933 (mmt180) REVERT: D 199 GLU cc_start: 0.7645 (tt0) cc_final: 0.7380 (tt0) REVERT: D 201 SER cc_start: 0.8932 (m) cc_final: 0.8723 (p) REVERT: E 199 GLU cc_start: 0.7723 (tt0) cc_final: 0.7488 (tt0) REVERT: E 201 SER cc_start: 0.8935 (m) cc_final: 0.8622 (p) REVERT: E 227 LYS cc_start: 0.8642 (ttmm) cc_final: 0.8275 (ttpt) REVERT: H 98 ARG cc_start: 0.8499 (mmt-90) cc_final: 0.8260 (mmt180) REVERT: I 121 ASN cc_start: 0.8907 (t0) cc_final: 0.8630 (t0) outliers start: 32 outliers final: 24 residues processed: 353 average time/residue: 0.2863 time to fit residues: 142.0633 Evaluate side-chains 346 residues out of total 1610 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 322 time to evaluate : 1.492 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 75 LYS Chi-restraints excluded: chain A residue 87 ILE Chi-restraints excluded: chain A residue 205 ILE Chi-restraints excluded: chain A residue 211 THR Chi-restraints excluded: chain B residue 68 THR Chi-restraints excluded: chain B residue 163 THR Chi-restraints excluded: chain B residue 205 ILE Chi-restraints excluded: chain D residue 211 THR Chi-restraints excluded: chain E residue 62 ASN Chi-restraints excluded: chain E residue 77 ILE Chi-restraints excluded: chain E residue 87 ILE Chi-restraints excluded: chain F residue 68 THR Chi-restraints excluded: chain F residue 205 ILE Chi-restraints excluded: chain F residue 212 GLU Chi-restraints excluded: chain G residue 68 THR Chi-restraints excluded: chain G residue 87 ILE Chi-restraints excluded: chain G residue 205 ILE Chi-restraints excluded: chain G residue 212 GLU Chi-restraints excluded: chain H residue 87 ILE Chi-restraints excluded: chain H residue 201 SER Chi-restraints excluded: chain I residue 87 ILE Chi-restraints excluded: chain I residue 211 THR Chi-restraints excluded: chain J residue 62 ASN Chi-restraints excluded: chain J residue 77 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 170 random chunks: chunk 98 optimal weight: 0.8980 chunk 76 optimal weight: 1.9990 chunk 112 optimal weight: 1.9990 chunk 169 optimal weight: 0.7980 chunk 155 optimal weight: 2.9990 chunk 134 optimal weight: 2.9990 chunk 14 optimal weight: 0.8980 chunk 104 optimal weight: 2.9990 chunk 82 optimal weight: 0.9990 chunk 107 optimal weight: 2.9990 chunk 143 optimal weight: 1.9990 overall best weight: 1.1184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 173 GLN C 100 ASN C 215 GLN D 215 GLN E 110 GLN E 215 GLN F 110 GLN H 215 GLN I 215 GLN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8617 moved from start: 0.4122 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.033 13900 Z= 0.343 Angle : 0.596 11.726 18810 Z= 0.289 Chirality : 0.046 0.126 2190 Planarity : 0.005 0.049 2420 Dihedral : 4.714 18.798 1800 Min Nonbonded Distance : 2.583 Molprobity Statistics. All-atom Clashscore : 4.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.59 % Favored : 97.41 % Rotamer: Outliers : 1.43 % Allowed : 17.64 % Favored : 80.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.51 (0.22), residues: 1660 helix: 0.52 (0.43), residues: 170 sheet: -0.04 (0.20), residues: 790 loop : -0.80 (0.24), residues: 700 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.002 TRP D 186 HIS 0.004 0.001 HIS F 152 PHE 0.010 0.001 PHE G 58 TYR 0.020 0.002 TYR E 103 ARG 0.004 0.001 ARG H 191 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3320 Ramachandran restraints generated. 1660 Oldfield, 0 Emsley, 1660 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3320 Ramachandran restraints generated. 1660 Oldfield, 0 Emsley, 1660 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 346 residues out of total 1610 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 323 time to evaluate : 1.711 Fit side-chains REVERT: C 98 ARG cc_start: 0.8744 (tpp-160) cc_final: 0.8469 (mmt-90) REVERT: D 199 GLU cc_start: 0.7617 (tt0) cc_final: 0.7336 (tt0) REVERT: D 201 SER cc_start: 0.8951 (m) cc_final: 0.8712 (p) REVERT: E 199 GLU cc_start: 0.7717 (tt0) cc_final: 0.7475 (tt0) REVERT: E 201 SER cc_start: 0.8948 (m) cc_final: 0.8634 (p) REVERT: E 227 LYS cc_start: 0.8653 (ttmm) cc_final: 0.8284 (ttpt) outliers start: 23 outliers final: 21 residues processed: 338 average time/residue: 0.2858 time to fit residues: 135.6811 Evaluate side-chains 347 residues out of total 1610 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 326 time to evaluate : 1.518 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 75 LYS Chi-restraints excluded: chain A residue 87 ILE Chi-restraints excluded: chain A residue 205 ILE Chi-restraints excluded: chain A residue 211 THR Chi-restraints excluded: chain B residue 68 THR Chi-restraints excluded: chain B residue 163 THR Chi-restraints excluded: chain B residue 205 ILE Chi-restraints excluded: chain D residue 211 THR Chi-restraints excluded: chain E residue 62 ASN Chi-restraints excluded: chain E residue 77 ILE Chi-restraints excluded: chain E residue 87 ILE Chi-restraints excluded: chain F residue 68 THR Chi-restraints excluded: chain F residue 205 ILE Chi-restraints excluded: chain G residue 68 THR Chi-restraints excluded: chain G residue 87 ILE Chi-restraints excluded: chain G residue 212 GLU Chi-restraints excluded: chain H residue 87 ILE Chi-restraints excluded: chain H residue 201 SER Chi-restraints excluded: chain I residue 87 ILE Chi-restraints excluded: chain I residue 211 THR Chi-restraints excluded: chain J residue 77 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 170 random chunks: chunk 41 optimal weight: 1.9990 chunk 124 optimal weight: 0.9980 chunk 19 optimal weight: 2.9990 chunk 37 optimal weight: 2.9990 chunk 135 optimal weight: 0.5980 chunk 56 optimal weight: 3.9990 chunk 138 optimal weight: 2.9990 chunk 17 optimal weight: 1.9990 chunk 24 optimal weight: 0.8980 chunk 118 optimal weight: 0.7980 chunk 7 optimal weight: 0.3980 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 110 GLN B 114 GLN B 173 GLN C 100 ASN C 114 GLN C 215 GLN D 215 GLN E 110 GLN E 215 GLN F 110 GLN H 215 GLN I 215 GLN Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3109 r_free = 0.3109 target = 0.109775 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.2740 r_free = 0.2740 target = 0.084296 restraints weight = 15529.203| |-----------------------------------------------------------------------------| r_work (start): 0.2771 rms_B_bonded: 2.10 r_work: 0.2621 rms_B_bonded: 2.42 restraints_weight: 0.5000 r_work: 0.2442 rms_B_bonded: 3.88 restraints_weight: 0.2500 r_work (final): 0.2442 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8818 moved from start: 0.4135 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.033 13900 Z= 0.250 Angle : 0.553 11.651 18810 Z= 0.269 Chirality : 0.045 0.124 2190 Planarity : 0.004 0.048 2420 Dihedral : 4.516 19.821 1800 Min Nonbonded Distance : 2.582 Molprobity Statistics. All-atom Clashscore : 4.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.59 % Favored : 97.41 % Rotamer: Outliers : 1.55 % Allowed : 17.76 % Favored : 80.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.43 (0.22), residues: 1660 helix: 0.75 (0.44), residues: 170 sheet: -0.01 (0.20), residues: 790 loop : -0.74 (0.24), residues: 700 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.002 TRP B 186 HIS 0.003 0.001 HIS F 152 PHE 0.008 0.001 PHE G 58 TYR 0.015 0.002 TYR E 103 ARG 0.004 0.000 ARG H 191 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3694.17 seconds wall clock time: 68 minutes 27.23 seconds (4107.23 seconds total)