Starting phenix.real_space_refine on Wed Jul 1 23:54:30 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/7yr6_34047/07_2026/7yr6_34047.cif Found real_map, /net/cci-nas-00/data/ceres_data/7yr6_34047/07_2026/7yr6_34047.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.8 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/7yr6_34047/07_2026/7yr6_34047.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7yr6_34047/07_2026/7yr6_34047.cif" restraint_files = "/net/cci-nas-00/data/ceres_data/7yr6_34047/07_2026/7yr6_34047.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/7yr6_34047/07_2026/7yr6_34047.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/7yr6_34047/07_2026/7yr6_34047.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7yr6_34047/07_2026/7yr6_34047.map" } resolution = 4.8 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= 0.004 sd= 0.039 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: 5 Type Number sf(0) Gaussians P 118 5.49 5 S 8 5.16 5 C 2197 2.51 5 N 797 2.21 5 O 1128 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 6 residue(s): 0.00s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 4248 Number of models: 1 Model: "" Number of chains: 5 Chain: "E" Number of atoms: 424 Number of conformers: 1 Conformer: "" Number of residues, atoms: 55, 424 Classifications: {'peptide': 55} Incomplete info: {'backbone_only': 1} Link IDs: {'PTRANS': 1, 'TRANS': 53} Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "D" Number of atoms: 426 Number of conformers: 1 Conformer: "" Number of residues, atoms: 55, 426 Classifications: {'peptide': 55} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 1, 'TRANS': 53} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 6 Chain: "C" Number of atoms: 425 Number of conformers: 1 Conformer: "" Number of residues, atoms: 55, 425 Classifications: {'peptide': 55} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 1, 'TRANS': 53} Unresolved non-hydrogen bonds: 7 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 6 Planarities with less than four sites: {'ASP:plan': 1} Unresolved non-hydrogen planarities: 3 Chain: "B" Number of atoms: 426 Number of conformers: 1 Conformer: "" Number of residues, atoms: 55, 426 Classifications: {'peptide': 55} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 1, 'TRANS': 53} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 6 Chain: "A" Number of atoms: 2547 Number of conformers: 1 Conformer: "" Number of residues, atoms: 118, 2547 Classifications: {'RNA': 118} Modifications used: {'rna2p_pur': 20, 'rna2p_pyr': 7, 'rna3p_pur': 52, 'rna3p_pyr': 39} Link IDs: {'rna2p': 26, 'rna3p': 91} Time building chain proxies: 1.06, per 1000 atoms: 0.25 Number of scatterers: 4248 At special positions: 0 Unit cell: (84.15, 91.8, 101.15, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 8 16.00 P 118 15.00 O 1128 8.00 N 797 7.00 C 2197 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 0.40 Conformation dependent library (CDL) restraints added in 74.2 milliseconds 424 Ramachandran restraints generated. 212 Oldfield, 0 Emsley, 212 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 398 Finding SS restraints... Secondary structure from input PDB file: 4 helices and 3 sheets defined 14.1% alpha, 14.1% beta 30 base pairs and 49 stacking pairs defined. Time for finding SS restraints: 0.53 Creating SS restraints... Processing helix chain 'E' and resid 48 through 55 Processing helix chain 'D' and resid 47 through 55 Processing helix chain 'C' and resid 46 through 54 Processing helix chain 'B' and resid 45 through 49 Processing sheet with id=AA1, first strand: chain 'E' and resid 2 through 7 removed outlier: 3.787A pdb=" N GLY D 33 " --> pdb=" O THR D 21 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'C' and resid 20 through 26 removed outlier: 5.104A pdb=" N VAL C 22 " --> pdb=" O GLY C 33 " (cutoff:3.500A) removed outlier: 6.340A pdb=" N GLY C 33 " --> pdb=" O VAL C 22 " (cutoff:3.500A) removed outlier: 3.774A pdb=" N VAL C 30 " --> pdb=" O ARG B 6 " (cutoff:3.500A) removed outlier: 3.565A pdb=" N ARG B 6 " --> pdb=" O VAL C 30 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 21 through 25 removed outlier: 3.744A pdb=" N THR B 21 " --> pdb=" O GLY B 33 " (cutoff:3.500A) removed outlier: 3.823A pdb=" N GLY B 33 " --> pdb=" O THR B 21 " (cutoff:3.500A) removed outlier: 5.288A pdb=" N ARG B 31 " --> pdb=" O LEU B 23 " (cutoff:3.500A) 28 hydrogen bonds defined for protein. 72 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 82 hydrogen bonds 160 hydrogen bond angles 0 basepair planarities 30 basepair parallelities 49 stacking parallelities Total time for adding SS restraints: 0.58 Time building geometry restraints manager: 0.48 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 672 1.33 - 1.45: 1678 1.45 - 1.57: 1962 1.57 - 1.69: 235 1.69 - 1.80: 16 Bond restraints: 4563 Sorted by residual: bond pdb=" O3' C A 15 " pdb=" P G A 16 " ideal model delta sigma weight residual 1.607 1.666 -0.059 1.50e-02 4.44e+03 1.54e+01 bond pdb=" O3' G A 57 " pdb=" P A A 58 " ideal model delta sigma weight residual 1.607 1.656 -0.049 1.50e-02 4.44e+03 1.05e+01 bond pdb=" O3' C A 61 " pdb=" P C A 62 " ideal model delta sigma weight residual 1.607 1.651 -0.044 1.50e-02 4.44e+03 8.77e+00 bond pdb=" N VAL D 40 " pdb=" CA VAL D 40 " ideal model delta sigma weight residual 1.458 1.494 -0.037 1.27e-02 6.20e+03 8.30e+00 bond pdb=" O3' A A 63 " pdb=" P U A 64 " ideal model delta sigma weight residual 1.607 1.641 -0.034 1.50e-02 4.44e+03 5.28e+00 ... (remaining 4558 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.00: 6451 2.00 - 4.01: 267 4.01 - 6.01: 29 6.01 - 8.01: 6 8.01 - 10.01: 3 Bond angle restraints: 6756 Sorted by residual: angle pdb=" O3' C A 61 " pdb=" C3' C A 61 " pdb=" C2' C A 61 " ideal model delta sigma weight residual 109.50 119.51 -10.01 1.50e+00 4.44e-01 4.46e+01 angle pdb=" N ILE D 47 " pdb=" CA ILE D 47 " pdb=" C ILE D 47 " ideal model delta sigma weight residual 113.71 109.21 4.50 9.50e-01 1.11e+00 2.25e+01 angle pdb=" C ILE E 47 " pdb=" N TYR E 48 " pdb=" CA TYR E 48 " ideal model delta sigma weight residual 121.54 130.25 -8.71 1.91e+00 2.74e-01 2.08e+01 angle pdb=" O3' G A 81 " pdb=" C3' G A 81 " pdb=" C2' G A 81 " ideal model delta sigma weight residual 109.50 115.96 -6.46 1.50e+00 4.44e-01 1.85e+01 angle pdb=" N LEU E 23 " pdb=" CA LEU E 23 " pdb=" C LEU E 23 " ideal model delta sigma weight residual 110.88 116.23 -5.35 1.28e+00 6.10e-01 1.75e+01 ... (remaining 6751 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.86: 2275 35.86 - 71.71: 171 71.71 - 107.57: 20 107.57 - 143.42: 3 143.42 - 179.28: 2 Dihedral angle restraints: 2471 sinusoidal: 1853 harmonic: 618 Sorted by residual: dihedral pdb=" O4' U A 60 " pdb=" C1' U A 60 " pdb=" N1 U A 60 " pdb=" C2 U A 60 " ideal model delta sinusoidal sigma weight residual 200.00 53.25 146.75 1 1.50e+01 4.44e-03 7.83e+01 dihedral pdb=" O4' G A 39 " pdb=" C1' G A 39 " pdb=" N9 G A 39 " pdb=" C4 G A 39 " ideal model delta sinusoidal sigma weight residual 68.00 153.16 -85.16 1 1.70e+01 3.46e-03 3.04e+01 dihedral pdb=" CA VAL D 18 " pdb=" C VAL D 18 " pdb=" N THR D 19 " pdb=" CA THR D 19 " ideal model delta harmonic sigma weight residual -180.00 -152.48 -27.52 0 5.00e+00 4.00e-02 3.03e+01 ... (remaining 2468 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.105: 822 0.105 - 0.210: 46 0.210 - 0.316: 6 0.316 - 0.421: 1 0.421 - 0.526: 1 Chirality restraints: 876 Sorted by residual: chirality pdb=" C3' C A 61 " pdb=" C4' C A 61 " pdb=" O3' C A 61 " pdb=" C2' C A 61 " both_signs ideal model delta sigma weight residual False -2.74 -2.22 -0.53 2.00e-01 2.50e+01 6.92e+00 chirality pdb=" CB ILE C 32 " pdb=" CA ILE C 32 " pdb=" CG1 ILE C 32 " pdb=" CG2 ILE C 32 " both_signs ideal model delta sigma weight residual False 2.64 2.30 0.35 2.00e-01 2.50e+01 3.06e+00 chirality pdb=" P G A 57 " pdb=" OP1 G A 57 " pdb=" OP2 G A 57 " pdb=" O5' G A 57 " both_signs ideal model delta sigma weight residual True 2.41 -2.72 -0.31 2.00e-01 2.50e+01 2.34e+00 ... (remaining 873 not shown) Planarity restraints: 413 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C1' G A 35 " -0.022 2.00e-02 2.50e+03 1.05e-02 3.31e+00 pdb=" N9 G A 35 " 0.027 2.00e-02 2.50e+03 pdb=" C8 G A 35 " 0.003 2.00e-02 2.50e+03 pdb=" N7 G A 35 " 0.001 2.00e-02 2.50e+03 pdb=" C5 G A 35 " -0.000 2.00e-02 2.50e+03 pdb=" C6 G A 35 " -0.005 2.00e-02 2.50e+03 pdb=" O6 G A 35 " -0.004 2.00e-02 2.50e+03 pdb=" N1 G A 35 " -0.003 2.00e-02 2.50e+03 pdb=" C2 G A 35 " -0.001 2.00e-02 2.50e+03 pdb=" N2 G A 35 " 0.006 2.00e-02 2.50e+03 pdb=" N3 G A 35 " -0.001 2.00e-02 2.50e+03 pdb=" C4 G A 35 " -0.001 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1' U A 91 " 0.021 2.00e-02 2.50e+03 1.08e-02 2.63e+00 pdb=" N1 U A 91 " -0.022 2.00e-02 2.50e+03 pdb=" C2 U A 91 " -0.003 2.00e-02 2.50e+03 pdb=" O2 U A 91 " -0.002 2.00e-02 2.50e+03 pdb=" N3 U A 91 " 0.002 2.00e-02 2.50e+03 pdb=" C4 U A 91 " -0.001 2.00e-02 2.50e+03 pdb=" O4 U A 91 " 0.009 2.00e-02 2.50e+03 pdb=" C5 U A 91 " -0.001 2.00e-02 2.50e+03 pdb=" C6 U A 91 " -0.004 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA TYR E 48 " -0.008 2.00e-02 2.50e+03 1.54e-02 2.37e+00 pdb=" C TYR E 48 " 0.027 2.00e-02 2.50e+03 pdb=" O TYR E 48 " -0.010 2.00e-02 2.50e+03 pdb=" N GLN E 49 " -0.009 2.00e-02 2.50e+03 ... (remaining 410 not shown) Histogram of nonbonded interaction distances: 2.29 - 2.81: 1060 2.81 - 3.33: 3678 3.33 - 3.86: 8638 3.86 - 4.38: 9229 4.38 - 4.90: 12472 Nonbonded interactions: 35077 Sorted by model distance: nonbonded pdb=" O2' G A 50 " pdb=" O4' G A 51 " model vdw 2.291 3.040 nonbonded pdb=" O2' A A 41 " pdb=" O5' G A 43 " model vdw 2.326 3.040 nonbonded pdb=" O GLU B 10 " pdb=" OG1 THR B 21 " model vdw 2.342 3.040 nonbonded pdb=" O VAL E 40 " pdb=" N1 G A 10 " model vdw 2.370 3.120 nonbonded pdb=" O VAL B 42 " pdb=" N2 G A 39 " model vdw 2.397 3.120 ... (remaining 35072 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 'B' and (resid 1 through 16 or (resid 17 and (name N or name CA or name C \ or name O or name CB )) or resid 18 through 22 or (resid 23 through 24 and (nam \ e N or name CA or name C or name O )) or resid 25 through 55)) selection = (chain 'C' and (resid 1 through 22 or (resid 23 through 24 and (name N or name C \ A or name C or name O )) or resid 25 or (resid 26 and (name N or name CA or name \ C or name O or name CB )) or resid 27 through 55)) selection = (chain 'D' and (resid 1 through 16 or (resid 17 and (name N or name CA or name C \ or name O or name CB )) or resid 18 through 22 or (resid 23 through 24 and (nam \ e N or name CA or name C or name O )) or resid 25 through 55)) selection = (chain 'E' and (resid 1 through 16 or (resid 17 and (name N or name CA or name C \ or name O or name CB )) or resid 18 through 25 or (resid 26 and (name N or name \ CA or name C or name O or name CB )) or resid 27 through 55)) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.730 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: 0.100 Check model and map are aligned: 0.010 Set scattering table: 0.010 Process input model: 5.670 Find NCS groups from input model: 0.060 Set up NCS constraints: 0.010 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.030 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 7.620 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7363 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 0.059 4563 Z= 0.257 Angle : 0.883 10.014 6756 Z= 0.497 Chirality : 0.055 0.526 876 Planarity : 0.004 0.028 413 Dihedral : 20.675 179.280 2073 Min Nonbonded Distance : 2.291 Molprobity Statistics. All-atom Clashscore : 7.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 15.09 % Favored : 84.91 % Rotamer: Outliers : 3.30 % Allowed : 12.09 % Favored : 84.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -5.39 (0.42), residues: 212 helix: -3.34 (0.76), residues: 24 sheet: -3.13 (0.95), residues: 29 loop : -4.07 (0.34), residues: 159 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG C 44 TYR 0.008 0.001 TYR B 48 HIS 0.004 0.001 HIS B 43 Details of bonding type rmsd/Z covalent geometry : bond 0.00424 / 0.26 ( 4563) covalent geometry : angle 0.88334 / 0.50 ( 6756) hydrogen bonds : bond 0.13349 / 9.96 ( 110) hydrogen bonds : angle 5.47836 / 3.83 ( 232) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 424 Ramachandran restraints generated. 212 Oldfield, 0 Emsley, 212 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 424 Ramachandran restraints generated. 212 Oldfield, 0 Emsley, 212 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 87 residues out of total 192 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 81 time to evaluate : 0.066 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: E 13 MET cc_start: 0.9402 (tmm) cc_final: 0.9171 (tmm) REVERT: E 46 GLU cc_start: 0.9307 (tp30) cc_final: 0.8712 (tp30) REVERT: E 47 ILE cc_start: 0.8852 (mt) cc_final: 0.8353 (mp) REVERT: C 43 HIS cc_start: 0.9032 (m-70) cc_final: 0.8789 (m90) outliers start: 6 outliers final: 3 residues processed: 84 average time/residue: 0.1020 time to fit residues: 9.9732 Evaluate side-chains 59 residues out of total 192 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 56 time to evaluate : 0.101 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 31 random chunks: chunk 27 optimal weight: 9.9990 chunk 12 optimal weight: 4.9990 chunk 24 optimal weight: 10.0000 chunk 28 optimal weight: 10.9990 chunk 13 optimal weight: 10.0000 chunk 1 optimal weight: 2.9990 chunk 8 optimal weight: 10.0000 chunk 30 optimal weight: 30.0000 chunk 16 optimal weight: 7.9990 chunk 15 optimal weight: 0.9990 chunk 29 optimal weight: 9.9990 overall best weight: 5.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** E 49 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 52 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 52 GLN ** C 43 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 35 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3412 r_free = 0.3412 target = 0.067250 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3104 r_free = 0.3104 target = 0.052697 restraints weight = 39347.442| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3144 r_free = 0.3144 target = 0.054262 restraints weight = 22821.023| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3169 r_free = 0.3169 target = 0.055262 restraints weight = 15478.704| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 46)----------------| | r_work = 0.3190 r_free = 0.3190 target = 0.056070 restraints weight = 11718.906| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3201 r_free = 0.3201 target = 0.056505 restraints weight = 9538.644| |-----------------------------------------------------------------------------| r_work (final): 0.3157 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7933 moved from start: 0.2895 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.038 4563 Z= 0.274 Angle : 0.764 6.779 6756 Z= 0.398 Chirality : 0.043 0.215 876 Planarity : 0.006 0.035 413 Dihedral : 21.247 172.757 1653 Min Nonbonded Distance : 2.491 Molprobity Statistics. All-atom Clashscore : 29.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 23.11 % Favored : 76.89 % Rotamer: Outliers : 0.55 % Allowed : 10.99 % Favored : 88.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -5.26 (0.46), residues: 212 helix: -2.47 (0.91), residues: 28 sheet: -2.96 (1.08), residues: 22 loop : -4.15 (0.38), residues: 162 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG D 31 TYR 0.006 0.002 TYR D 48 HIS 0.009 0.004 HIS B 43 Details of bonding type rmsd/Z covalent geometry : bond 0.00523 / 0.27 ( 4563) covalent geometry : angle 0.76422 / 0.40 ( 6756) hydrogen bonds : bond 0.09442 / 6.51 ( 110) hydrogen bonds : angle 4.86814 / 3.27 ( 232) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 424 Ramachandran restraints generated. 212 Oldfield, 0 Emsley, 212 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 424 Ramachandran restraints generated. 212 Oldfield, 0 Emsley, 212 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 57 residues out of total 192 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 56 time to evaluate : 0.104 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: E 13 MET cc_start: 0.9533 (tmm) cc_final: 0.9216 (tmm) REVERT: E 44 ARG cc_start: 0.8896 (mtp180) cc_final: 0.8329 (mtt-85) REVERT: E 47 ILE cc_start: 0.8842 (mt) cc_final: 0.8517 (mp) REVERT: C 2 LEU cc_start: 0.8199 (mm) cc_final: 0.7926 (mm) REVERT: B 1 MET cc_start: 0.7322 (mpp) cc_final: 0.6786 (mpp) outliers start: 1 outliers final: 1 residues processed: 56 average time/residue: 0.1108 time to fit residues: 7.2833 Evaluate side-chains 46 residues out of total 192 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 45 time to evaluate : 0.117 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 31 random chunks: chunk 18 optimal weight: 0.8980 chunk 22 optimal weight: 10.0000 chunk 2 optimal weight: 2.9990 chunk 4 optimal weight: 9.9990 chunk 19 optimal weight: 5.9990 chunk 12 optimal weight: 4.9990 chunk 27 optimal weight: 10.0000 chunk 24 optimal weight: 9.9990 chunk 30 optimal weight: 30.0000 chunk 11 optimal weight: 1.9990 chunk 23 optimal weight: 6.9990 overall best weight: 3.3788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** E 52 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 35 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3446 r_free = 0.3446 target = 0.068947 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3156 r_free = 0.3156 target = 0.054628 restraints weight = 40564.001| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3190 r_free = 0.3190 target = 0.056081 restraints weight = 23721.229| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3214 r_free = 0.3214 target = 0.057105 restraints weight = 16065.380| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3227 r_free = 0.3227 target = 0.057721 restraints weight = 12101.648| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 47)----------------| | r_work = 0.3240 r_free = 0.3240 target = 0.058270 restraints weight = 10005.564| |-----------------------------------------------------------------------------| r_work (final): 0.3191 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7901 moved from start: 0.3195 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.023 4563 Z= 0.178 Angle : 0.647 5.768 6756 Z= 0.340 Chirality : 0.039 0.171 876 Planarity : 0.004 0.035 413 Dihedral : 21.063 169.726 1653 Min Nonbonded Distance : 2.468 Molprobity Statistics. All-atom Clashscore : 21.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 18.87 % Favored : 81.13 % Rotamer: Outliers : 0.55 % Allowed : 10.44 % Favored : 89.01 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.47 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -4.87 (0.50), residues: 212 helix: -2.12 (0.92), residues: 28 sheet: -2.95 (1.06), residues: 22 loop : -3.83 (0.43), residues: 162 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG D 31 TYR 0.005 0.001 TYR E 48 HIS 0.006 0.002 HIS B 43 Details of bonding type rmsd/Z covalent geometry : bond 0.00341 / 0.18 ( 4563) covalent geometry : angle 0.64695 / 0.34 ( 6756) hydrogen bonds : bond 0.05913 / 4.13 ( 110) hydrogen bonds : angle 4.49594 / 3.06 ( 232) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 424 Ramachandran restraints generated. 212 Oldfield, 0 Emsley, 212 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 424 Ramachandran restraints generated. 212 Oldfield, 0 Emsley, 212 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 60 residues out of total 192 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 59 time to evaluate : 0.070 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: E 1 MET cc_start: 0.9429 (ptt) cc_final: 0.9204 (ptm) REVERT: E 13 MET cc_start: 0.9577 (tmm) cc_final: 0.9241 (tmm) REVERT: E 44 ARG cc_start: 0.8887 (mtp180) cc_final: 0.8362 (mtt-85) REVERT: E 47 ILE cc_start: 0.8745 (mt) cc_final: 0.8372 (mp) REVERT: B 1 MET cc_start: 0.7050 (mpp) cc_final: 0.6840 (mpp) REVERT: B 4 LEU cc_start: 0.8344 (OUTLIER) cc_final: 0.8068 (pp) outliers start: 1 outliers final: 0 residues processed: 59 average time/residue: 0.0875 time to fit residues: 5.9856 Evaluate side-chains 52 residues out of total 192 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 51 time to evaluate : 0.072 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 31 random chunks: chunk 13 optimal weight: 10.0000 chunk 17 optimal weight: 0.0040 chunk 10 optimal weight: 10.0000 chunk 7 optimal weight: 8.9990 chunk 1 optimal weight: 6.9990 chunk 26 optimal weight: 9.9990 chunk 28 optimal weight: 10.0000 chunk 0 optimal weight: 9.9990 chunk 8 optimal weight: 0.9980 chunk 19 optimal weight: 0.6980 chunk 12 optimal weight: 5.9990 overall best weight: 2.9396 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** E 52 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 35 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3446 r_free = 0.3446 target = 0.068618 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3142 r_free = 0.3142 target = 0.053890 restraints weight = 39958.482| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3181 r_free = 0.3181 target = 0.055482 restraints weight = 23487.229| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 46)----------------| | r_work = 0.3207 r_free = 0.3207 target = 0.056609 restraints weight = 15936.583| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 35)----------------| | r_work = 0.3223 r_free = 0.3223 target = 0.057277 restraints weight = 11997.020| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3230 r_free = 0.3230 target = 0.057588 restraints weight = 9819.974| |-----------------------------------------------------------------------------| r_work (final): 0.3188 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7886 moved from start: 0.3535 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.055 4563 Z= 0.169 Angle : 0.635 7.637 6756 Z= 0.332 Chirality : 0.038 0.170 876 Planarity : 0.004 0.037 413 Dihedral : 20.941 167.576 1653 Min Nonbonded Distance : 2.502 Molprobity Statistics. All-atom Clashscore : 22.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 21.23 % Favored : 78.77 % Rotamer: Outliers : 0.00 % Allowed : 10.44 % Favored : 89.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.47 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -4.77 (0.51), residues: 212 helix: -2.13 (0.85), residues: 28 sheet: -2.96 (1.04), residues: 22 loop : -3.73 (0.44), residues: 162 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.001 ARG E 6 TYR 0.010 0.001 TYR C 48 HIS 0.006 0.002 HIS B 43 Details of bonding type rmsd/Z covalent geometry : bond 0.00331 / 0.17 ( 4563) covalent geometry : angle 0.63495 / 0.33 ( 6756) hydrogen bonds : bond 0.05679 / 3.91 ( 110) hydrogen bonds : angle 4.30634 / 2.99 ( 232) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 424 Ramachandran restraints generated. 212 Oldfield, 0 Emsley, 212 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 424 Ramachandran restraints generated. 212 Oldfield, 0 Emsley, 212 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 58 residues out of total 192 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 58 time to evaluate : 0.073 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: E 1 MET cc_start: 0.9410 (ptt) cc_final: 0.9113 (ppp) REVERT: E 13 MET cc_start: 0.9531 (tmm) cc_final: 0.9162 (tmm) REVERT: E 44 ARG cc_start: 0.8780 (mtp180) cc_final: 0.8336 (mtt-85) REVERT: E 47 ILE cc_start: 0.8728 (mt) cc_final: 0.8401 (mp) REVERT: B 1 MET cc_start: 0.7211 (mpp) cc_final: 0.6978 (mpp) REVERT: B 4 LEU cc_start: 0.8314 (pp) cc_final: 0.8024 (pp) outliers start: 0 outliers final: 0 residues processed: 58 average time/residue: 0.0826 time to fit residues: 5.6055 Evaluate side-chains 51 residues out of total 192 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 51 time to evaluate : 0.063 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 31 random chunks: chunk 10 optimal weight: 20.0000 chunk 8 optimal weight: 6.9990 chunk 18 optimal weight: 6.9990 chunk 11 optimal weight: 0.5980 chunk 27 optimal weight: 10.0000 chunk 25 optimal weight: 10.0000 chunk 5 optimal weight: 0.5980 chunk 12 optimal weight: 1.9990 chunk 21 optimal weight: 10.0000 chunk 28 optimal weight: 10.0000 chunk 23 optimal weight: 9.9990 overall best weight: 3.4386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... E 49 GLN E 52 GLN ** B 35 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3424 r_free = 0.3424 target = 0.067775 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3121 r_free = 0.3121 target = 0.053088 restraints weight = 40316.509| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3162 r_free = 0.3162 target = 0.054716 restraints weight = 23434.226| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 45)----------------| | r_work = 0.3188 r_free = 0.3188 target = 0.055822 restraints weight = 15785.407| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3203 r_free = 0.3203 target = 0.056458 restraints weight = 11861.354| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 33)----------------| | r_work = 0.3215 r_free = 0.3215 target = 0.056946 restraints weight = 9762.549| |-----------------------------------------------------------------------------| r_work (final): 0.3169 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7917 moved from start: 0.3953 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.024 4563 Z= 0.183 Angle : 0.657 6.433 6756 Z= 0.343 Chirality : 0.039 0.172 876 Planarity : 0.004 0.036 413 Dihedral : 21.101 166.968 1653 Min Nonbonded Distance : 2.493 Molprobity Statistics. All-atom Clashscore : 24.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 19.81 % Favored : 80.19 % Rotamer: Outliers : 0.00 % Allowed : 5.49 % Favored : 94.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.47 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -4.67 (0.52), residues: 212 helix: -2.23 (0.85), residues: 28 sheet: -2.58 (1.15), residues: 22 loop : -3.68 (0.45), residues: 162 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG C 6 TYR 0.017 0.003 TYR B 48 HIS 0.009 0.003 HIS B 43 Details of bonding type rmsd/Z covalent geometry : bond 0.00353 / 0.18 ( 4563) covalent geometry : angle 0.65670 / 0.34 ( 6756) hydrogen bonds : bond 0.06279 / 4.36 ( 110) hydrogen bonds : angle 4.36473 / 3.03 ( 232) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 424 Ramachandran restraints generated. 212 Oldfield, 0 Emsley, 212 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 424 Ramachandran restraints generated. 212 Oldfield, 0 Emsley, 212 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 58 residues out of total 192 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 58 time to evaluate : 0.085 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: E 1 MET cc_start: 0.9344 (ptt) cc_final: 0.8917 (ptm) REVERT: E 2 LEU cc_start: 0.9280 (mt) cc_final: 0.9076 (mt) REVERT: E 13 MET cc_start: 0.9561 (tmm) cc_final: 0.9230 (tmm) REVERT: D 48 TYR cc_start: 0.9157 (t80) cc_final: 0.8876 (t80) REVERT: B 1 MET cc_start: 0.7318 (mpp) cc_final: 0.7098 (mpp) outliers start: 0 outliers final: 0 residues processed: 58 average time/residue: 0.1114 time to fit residues: 7.4924 Evaluate side-chains 48 residues out of total 192 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 48 time to evaluate : 0.099 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 31 random chunks: chunk 8 optimal weight: 2.9990 chunk 21 optimal weight: 10.0000 chunk 12 optimal weight: 7.9990 chunk 4 optimal weight: 3.9990 chunk 13 optimal weight: 0.6980 chunk 14 optimal weight: 0.9980 chunk 9 optimal weight: 3.9990 chunk 7 optimal weight: 0.9980 chunk 23 optimal weight: 10.0000 chunk 25 optimal weight: 10.0000 chunk 6 optimal weight: 20.0000 overall best weight: 1.9384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 35 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3466 r_free = 0.3466 target = 0.070229 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3166 r_free = 0.3166 target = 0.055148 restraints weight = 40146.591| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3207 r_free = 0.3207 target = 0.056839 restraints weight = 23221.152| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 46)----------------| | r_work = 0.3234 r_free = 0.3234 target = 0.058021 restraints weight = 15519.583| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3248 r_free = 0.3248 target = 0.058681 restraints weight = 11640.497| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3261 r_free = 0.3261 target = 0.059227 restraints weight = 9578.252| |-----------------------------------------------------------------------------| r_work (final): 0.3219 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7845 moved from start: 0.3970 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 4563 Z= 0.131 Angle : 0.606 6.150 6756 Z= 0.319 Chirality : 0.037 0.183 876 Planarity : 0.004 0.037 413 Dihedral : 20.762 166.175 1653 Min Nonbonded Distance : 2.436 Molprobity Statistics. All-atom Clashscore : 17.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 17.92 % Favored : 82.08 % Rotamer: Outliers : 0.00 % Allowed : 6.04 % Favored : 93.96 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.47 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -4.82 (0.51), residues: 212 helix: -3.09 (0.67), residues: 28 sheet: -2.47 (1.13), residues: 22 loop : -3.66 (0.45), residues: 162 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG E 6 TYR 0.008 0.001 TYR C 48 HIS 0.003 0.001 HIS B 43 Details of bonding type rmsd/Z covalent geometry : bond 0.00253 / 0.13 ( 4563) covalent geometry : angle 0.60561 / 0.32 ( 6756) hydrogen bonds : bond 0.04715 / 3.18 ( 110) hydrogen bonds : angle 4.38076 / 3.06 ( 232) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 424 Ramachandran restraints generated. 212 Oldfield, 0 Emsley, 212 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 424 Ramachandran restraints generated. 212 Oldfield, 0 Emsley, 212 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 60 residues out of total 192 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 60 time to evaluate : 0.100 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: E 1 MET cc_start: 0.9252 (ptt) cc_final: 0.8822 (ptm) REVERT: E 2 LEU cc_start: 0.9302 (mt) cc_final: 0.9098 (mt) REVERT: E 13 MET cc_start: 0.9565 (tmm) cc_final: 0.9285 (tmm) REVERT: D 48 TYR cc_start: 0.9293 (t80) cc_final: 0.9061 (t80) outliers start: 0 outliers final: 0 residues processed: 60 average time/residue: 0.1083 time to fit residues: 7.5535 Evaluate side-chains 50 residues out of total 192 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 50 time to evaluate : 0.097 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 31 random chunks: chunk 29 optimal weight: 10.0000 chunk 18 optimal weight: 2.9990 chunk 16 optimal weight: 8.9990 chunk 11 optimal weight: 0.5980 chunk 1 optimal weight: 9.9990 chunk 17 optimal weight: 8.9990 chunk 4 optimal weight: 5.9990 chunk 23 optimal weight: 10.0000 chunk 8 optimal weight: 7.9990 chunk 0 optimal weight: 2.9990 chunk 15 optimal weight: 7.9990 overall best weight: 4.1188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 35 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3404 r_free = 0.3404 target = 0.066522 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3084 r_free = 0.3084 target = 0.051589 restraints weight = 41310.227| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 49)----------------| | r_work = 0.3127 r_free = 0.3127 target = 0.053197 restraints weight = 23711.882| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3156 r_free = 0.3156 target = 0.054325 restraints weight = 15972.256| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 33)----------------| | r_work = 0.3175 r_free = 0.3175 target = 0.055107 restraints weight = 11910.294| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3184 r_free = 0.3184 target = 0.055489 restraints weight = 9637.786| |-----------------------------------------------------------------------------| r_work (final): 0.3140 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7944 moved from start: 0.4438 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 4563 Z= 0.217 Angle : 0.691 5.867 6756 Z= 0.363 Chirality : 0.040 0.208 876 Planarity : 0.005 0.028 413 Dihedral : 21.248 166.618 1653 Min Nonbonded Distance : 2.484 Molprobity Statistics. All-atom Clashscore : 27.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 22.17 % Favored : 77.83 % Rotamer: Outliers : 0.00 % Allowed : 6.59 % Favored : 93.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.47 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -5.01 (0.51), residues: 212 helix: -3.19 (0.64), residues: 28 sheet: -2.42 (1.11), residues: 22 loop : -3.84 (0.45), residues: 162 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG C 6 TYR 0.010 0.001 TYR C 48 HIS 0.007 0.003 HIS E 43 Details of bonding type rmsd/Z covalent geometry : bond 0.00415 / 0.22 ( 4563) covalent geometry : angle 0.69129 / 0.36 ( 6756) hydrogen bonds : bond 0.07286 / 5.08 ( 110) hydrogen bonds : angle 4.53697 / 3.16 ( 232) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 424 Ramachandran restraints generated. 212 Oldfield, 0 Emsley, 212 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 424 Ramachandran restraints generated. 212 Oldfield, 0 Emsley, 212 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 60 residues out of total 192 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 60 time to evaluate : 0.103 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: E 1 MET cc_start: 0.9227 (ptt) cc_final: 0.8895 (ptp) REVERT: E 2 LEU cc_start: 0.9290 (mt) cc_final: 0.9025 (mt) REVERT: E 13 MET cc_start: 0.9565 (tmm) cc_final: 0.9278 (tmm) REVERT: E 44 ARG cc_start: 0.8819 (mtp180) cc_final: 0.8373 (ttm-80) REVERT: D 48 TYR cc_start: 0.9261 (t80) cc_final: 0.9008 (t80) outliers start: 0 outliers final: 0 residues processed: 60 average time/residue: 0.1086 time to fit residues: 7.6026 Evaluate side-chains 49 residues out of total 192 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 49 time to evaluate : 0.100 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 31 random chunks: chunk 10 optimal weight: 20.0000 chunk 19 optimal weight: 5.9990 chunk 26 optimal weight: 9.9990 chunk 27 optimal weight: 9.9990 chunk 16 optimal weight: 2.9990 chunk 1 optimal weight: 6.9990 chunk 7 optimal weight: 9.9990 chunk 9 optimal weight: 0.9990 chunk 21 optimal weight: 10.0000 chunk 24 optimal weight: 8.9990 chunk 13 optimal weight: 7.9990 overall best weight: 4.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 35 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3367 r_free = 0.3367 target = 0.064736 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3041 r_free = 0.3041 target = 0.049814 restraints weight = 40096.417| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3084 r_free = 0.3084 target = 0.051440 restraints weight = 23029.173| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3111 r_free = 0.3111 target = 0.052520 restraints weight = 15414.778| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 39)----------------| | r_work = 0.3130 r_free = 0.3130 target = 0.053296 restraints weight = 11602.373| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 39)----------------| | r_work = 0.3142 r_free = 0.3142 target = 0.053799 restraints weight = 9446.446| |-----------------------------------------------------------------------------| r_work (final): 0.3100 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7986 moved from start: 0.4991 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.047 4563 Z= 0.248 Angle : 0.750 6.731 6756 Z= 0.393 Chirality : 0.043 0.277 876 Planarity : 0.006 0.055 413 Dihedral : 21.633 166.422 1653 Min Nonbonded Distance : 2.381 Molprobity Statistics. All-atom Clashscore : 31.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 23.11 % Favored : 76.89 % Rotamer: Outliers : 0.00 % Allowed : 2.75 % Favored : 97.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.47 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -5.23 (0.47), residues: 212 helix: -3.24 (0.66), residues: 28 sheet: -2.82 (1.31), residues: 12 loop : -3.97 (0.41), residues: 172 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG C 6 TYR 0.014 0.002 TYR C 48 HIS 0.008 0.003 HIS B 43 Details of bonding type rmsd/Z covalent geometry : bond 0.00479 / 0.25 ( 4563) covalent geometry : angle 0.75015 / 0.39 ( 6756) hydrogen bonds : bond 0.08321 / 5.74 ( 110) hydrogen bonds : angle 4.82324 / 3.18 ( 232) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 424 Ramachandran restraints generated. 212 Oldfield, 0 Emsley, 212 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 424 Ramachandran restraints generated. 212 Oldfield, 0 Emsley, 212 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 59 residues out of total 192 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 59 time to evaluate : 0.061 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: E 1 MET cc_start: 0.9171 (ptt) cc_final: 0.8810 (ptt) REVERT: E 2 LEU cc_start: 0.9291 (mt) cc_final: 0.9046 (mt) REVERT: E 44 ARG cc_start: 0.8953 (mtp180) cc_final: 0.8303 (mtt-85) REVERT: E 47 ILE cc_start: 0.8556 (mp) cc_final: 0.8144 (mp) outliers start: 0 outliers final: 0 residues processed: 59 average time/residue: 0.0989 time to fit residues: 6.8561 Evaluate side-chains 47 residues out of total 192 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 47 time to evaluate : 0.060 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 31 random chunks: chunk 20 optimal weight: 10.0000 chunk 24 optimal weight: 9.9990 chunk 6 optimal weight: 10.0000 chunk 12 optimal weight: 8.9990 chunk 13 optimal weight: 2.9990 chunk 30 optimal weight: 30.0000 chunk 19 optimal weight: 7.9990 chunk 3 optimal weight: 0.7980 chunk 26 optimal weight: 10.0000 chunk 25 optimal weight: 8.9990 chunk 23 optimal weight: 8.9990 overall best weight: 5.9588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 35 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3336 r_free = 0.3336 target = 0.063457 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3007 r_free = 0.3007 target = 0.048270 restraints weight = 41100.225| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 52)----------------| | r_work = 0.3049 r_free = 0.3049 target = 0.049887 restraints weight = 23453.886| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3074 r_free = 0.3074 target = 0.050911 restraints weight = 15738.477| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 45)----------------| | r_work = 0.3093 r_free = 0.3093 target = 0.051701 restraints weight = 11859.119| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3103 r_free = 0.3103 target = 0.052132 restraints weight = 9646.079| |-----------------------------------------------------------------------------| r_work (final): 0.3064 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8041 moved from start: 0.5418 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.052 4563 Z= 0.293 Angle : 0.825 6.072 6756 Z= 0.432 Chirality : 0.047 0.317 876 Planarity : 0.007 0.083 413 Dihedral : 21.997 166.655 1653 Min Nonbonded Distance : 2.360 Molprobity Statistics. All-atom Clashscore : 37.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 23.58 % Favored : 76.42 % Rotamer: Outliers : 0.00 % Allowed : 2.75 % Favored : 97.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.47 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -5.38 (0.46), residues: 212 helix: -3.52 (0.62), residues: 28 sheet: -2.70 (1.34), residues: 12 loop : -4.06 (0.40), residues: 172 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG C 6 TYR 0.015 0.002 TYR C 48 HIS 0.010 0.003 HIS B 43 Details of bonding type rmsd/Z covalent geometry : bond 0.00567 / 0.29 ( 4563) covalent geometry : angle 0.82461 / 0.43 ( 6756) hydrogen bonds : bond 0.09562 / 6.64 ( 110) hydrogen bonds : angle 4.91494 / 3.26 ( 232) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 424 Ramachandran restraints generated. 212 Oldfield, 0 Emsley, 212 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 424 Ramachandran restraints generated. 212 Oldfield, 0 Emsley, 212 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 54 residues out of total 192 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 54 time to evaluate : 0.102 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: E 1 MET cc_start: 0.9185 (ptt) cc_final: 0.8859 (ptt) REVERT: E 2 LEU cc_start: 0.9311 (mt) cc_final: 0.9015 (mt) REVERT: E 44 ARG cc_start: 0.9054 (mtp180) cc_final: 0.8640 (ttm-80) REVERT: D 48 TYR cc_start: 0.9375 (t80) cc_final: 0.9113 (t80) REVERT: C 31 ARG cc_start: 0.9106 (mtm180) cc_final: 0.8699 (ttt180) REVERT: B 4 LEU cc_start: 0.7929 (pp) cc_final: 0.7719 (pp) outliers start: 0 outliers final: 0 residues processed: 54 average time/residue: 0.1132 time to fit residues: 7.1052 Evaluate side-chains 45 residues out of total 192 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 45 time to evaluate : 0.100 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 31 random chunks: chunk 11 optimal weight: 0.9980 chunk 0 optimal weight: 10.0000 chunk 4 optimal weight: 6.9990 chunk 8 optimal weight: 6.9990 chunk 22 optimal weight: 10.0000 chunk 26 optimal weight: 10.0000 chunk 6 optimal weight: 4.9990 chunk 29 optimal weight: 10.0000 chunk 14 optimal weight: 4.9990 chunk 12 optimal weight: 5.9990 chunk 20 optimal weight: 8.9990 overall best weight: 4.7988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** C 49 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 35 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3360 r_free = 0.3360 target = 0.064642 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.3046 r_free = 0.3046 target = 0.049881 restraints weight = 41658.560| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3086 r_free = 0.3086 target = 0.051441 restraints weight = 24294.676| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 42)----------------| | r_work = 0.3111 r_free = 0.3111 target = 0.052485 restraints weight = 16525.818| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.3126 r_free = 0.3126 target = 0.053112 restraints weight = 12581.029| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 47)----------------| | r_work = 0.3139 r_free = 0.3139 target = 0.053647 restraints weight = 10425.186| |-----------------------------------------------------------------------------| r_work (final): 0.3092 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8023 moved from start: 0.5482 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.056 4563 Z= 0.240 Angle : 0.759 5.900 6756 Z= 0.397 Chirality : 0.043 0.253 876 Planarity : 0.005 0.048 413 Dihedral : 21.856 165.495 1653 Min Nonbonded Distance : 2.390 Molprobity Statistics. All-atom Clashscore : 30.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 23.58 % Favored : 76.42 % Rotamer: Outliers : 0.00 % Allowed : 0.55 % Favored : 99.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.47 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -5.24 (0.48), residues: 212 helix: -3.40 (0.66), residues: 28 sheet: -2.83 (1.28), residues: 12 loop : -3.94 (0.42), residues: 172 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG C 50 TYR 0.012 0.002 TYR C 48 HIS 0.008 0.003 HIS B 43 Details of bonding type rmsd/Z covalent geometry : bond 0.00465 / 0.24 ( 4563) covalent geometry : angle 0.75897 / 0.40 ( 6756) hydrogen bonds : bond 0.07967 / 5.46 ( 110) hydrogen bonds : angle 4.83243 / 3.17 ( 232) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 424 Ramachandran restraints generated. 212 Oldfield, 0 Emsley, 212 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 424 Ramachandran restraints generated. 212 Oldfield, 0 Emsley, 212 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 55 residues out of total 192 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 55 time to evaluate : 0.061 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: E 1 MET cc_start: 0.9151 (ptt) cc_final: 0.8852 (ptt) REVERT: E 2 LEU cc_start: 0.9274 (mt) cc_final: 0.8997 (mt) REVERT: E 38 LYS cc_start: 0.8903 (mmtm) cc_final: 0.8628 (mmmt) REVERT: E 44 ARG cc_start: 0.9048 (mtp180) cc_final: 0.8763 (ttm-80) REVERT: E 47 ILE cc_start: 0.8717 (mp) cc_final: 0.8343 (mp) REVERT: E 50 ARG cc_start: 0.9505 (pmt170) cc_final: 0.9193 (pmt170) REVERT: D 48 TYR cc_start: 0.9374 (t80) cc_final: 0.9093 (t80) REVERT: C 31 ARG cc_start: 0.9110 (mtm180) cc_final: 0.8618 (ttt180) REVERT: B 4 LEU cc_start: 0.7913 (pp) cc_final: 0.7609 (pp) outliers start: 0 outliers final: 0 residues processed: 55 average time/residue: 0.0901 time to fit residues: 5.6957 Evaluate side-chains 44 residues out of total 192 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 44 time to evaluate : 0.060 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 31 random chunks: chunk 28 optimal weight: 10.0000 chunk 1 optimal weight: 5.9990 chunk 2 optimal weight: 10.0000 chunk 14 optimal weight: 10.0000 chunk 4 optimal weight: 6.9990 chunk 17 optimal weight: 9.9990 chunk 16 optimal weight: 4.9990 chunk 5 optimal weight: 4.9990 chunk 23 optimal weight: 10.0000 chunk 30 optimal weight: 30.0000 chunk 19 optimal weight: 7.9990 overall best weight: 6.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** C 49 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 35 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3319 r_free = 0.3319 target = 0.062753 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.2989 r_free = 0.2989 target = 0.047559 restraints weight = 38102.412| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3032 r_free = 0.3032 target = 0.049191 restraints weight = 21672.270| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 41)----------------| | r_work = 0.3060 r_free = 0.3060 target = 0.050301 restraints weight = 14526.972| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 47)----------------| | r_work = 0.3079 r_free = 0.3079 target = 0.051079 restraints weight = 11004.553| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 38)----------------| | r_work = 0.3091 r_free = 0.3091 target = 0.051573 restraints weight = 8908.721| |-----------------------------------------------------------------------------| r_work (final): 0.3050 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8041 moved from start: 0.5971 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.057 4563 Z= 0.303 Angle : 0.845 6.511 6756 Z= 0.439 Chirality : 0.047 0.294 876 Planarity : 0.006 0.046 413 Dihedral : 22.242 165.675 1653 Min Nonbonded Distance : 2.401 Molprobity Statistics. All-atom Clashscore : 39.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 25.47 % Favored : 74.53 % Rotamer: Outliers : 0.00 % Allowed : 2.20 % Favored : 97.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.47 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -5.39 (0.47), residues: 212 helix: -3.46 (0.66), residues: 28 sheet: -2.84 (1.30), residues: 12 loop : -4.07 (0.41), residues: 172 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.017 0.001 ARG C 50 TYR 0.012 0.002 TYR C 48 HIS 0.010 0.003 HIS B 43 Details of bonding type rmsd/Z covalent geometry : bond 0.00589 / 0.30 ( 4563) covalent geometry : angle 0.84514 / 0.44 ( 6756) hydrogen bonds : bond 0.09861 / 6.84 ( 110) hydrogen bonds : angle 5.12569 / 3.35 ( 232) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 857.22 seconds wall clock time: 15 minutes 28.41 seconds (928.41 seconds total)