Starting phenix.real_space_refine on Wed Jun 4 23:14:54 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9cqo_45817/06_2025/9cqo_45817.cif Found real_map, /net/cci-nas-00/data/ceres_data/9cqo_45817/06_2025/9cqo_45817.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.01 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9cqo_45817/06_2025/9cqo_45817.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9cqo_45817/06_2025/9cqo_45817.map" model { file = "/net/cci-nas-00/data/ceres_data/9cqo_45817/06_2025/9cqo_45817.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9cqo_45817/06_2025/9cqo_45817.cif" } resolution = 3.01 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= 0.018 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 Fe 4 7.16 5 S 12 5.16 5 C 2900 2.51 5 N 760 2.21 5 O 794 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 11 residue(s): 0.01s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/chem_data/mon_lib" Total number of atoms: 4470 Number of models: 1 Model: "" Number of chains: 8 Chain: "A" Number of atoms: 1058 Number of conformers: 1 Conformer: "" Number of residues, atoms: 140, 1058 Classifications: {'peptide': 140} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 7, 'TRANS': 132} Chain: "B" Number of atoms: 1091 Number of conformers: 1 Conformer: "" Number of residues, atoms: 143, 1091 Classifications: {'peptide': 143} Link IDs: {'PTRANS': 7, 'TRANS': 135} Chain: "C" Number of atoms: 1058 Number of conformers: 1 Conformer: "" Number of residues, atoms: 140, 1058 Classifications: {'peptide': 140} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 7, 'TRANS': 132} Chain: "D" Number of atoms: 1091 Number of conformers: 1 Conformer: "" Number of residues, atoms: 143, 1091 Classifications: {'peptide': 143} Link IDs: {'PTRANS': 7, 'TRANS': 135} Chain: "A" Number of atoms: 43 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 43 Unusual residues: {'HEM': 1} Classifications: {'undetermined': 1} Chain: "B" Number of atoms: 43 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 43 Unusual residues: {'HEM': 1} Classifications: {'undetermined': 1} Chain: "C" Number of atoms: 43 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 43 Unusual residues: {'HEM': 1} Classifications: {'undetermined': 1} Chain: "D" Number of atoms: 43 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 43 Unusual residues: {'HEM': 1} Classifications: {'undetermined': 1} Time building chain proxies: 4.11, per 1000 atoms: 0.92 Number of scatterers: 4470 At special positions: 0 Unit cell: (76.44, 72.765, 66.15, 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) Fe 4 26.01 S 12 16.00 O 794 8.00 N 760 7.00 C 2900 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=4, symmetry=0 Number of additional bonds: simple=4, symmetry=0 Coordination: Other bonds: Time building additional restraints: 1.26 Conformation dependent library (CDL) restraints added in 553.0 milliseconds 1116 Ramachandran restraints generated. 558 Oldfield, 0 Emsley, 558 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1052 Finding SS restraints... Secondary structure from input PDB file: 39 helices and 0 sheets defined 89.0% alpha, 0.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.43 Creating SS restraints... Processing helix chain 'A' and resid 3 through 18 Processing helix chain 'A' and resid 20 through 36 Processing helix chain 'A' and resid 37 through 43 Processing helix chain 'A' and resid 52 through 72 Processing helix chain 'A' and resid 75 through 80 Processing helix chain 'A' and resid 80 through 89 Processing helix chain 'A' and resid 94 through 113 removed outlier: 3.607A pdb=" N PHE A 98 " --> pdb=" O ASP A 94 " (cutoff:3.500A) Processing helix chain 'A' and resid 118 through 138 Processing helix chain 'B' and resid 4 through 17 removed outlier: 3.766A pdb=" N LYS B 17 " --> pdb=" O ALA B 13 " (cutoff:3.500A) Processing helix chain 'B' and resid 19 through 35 removed outlier: 4.182A pdb=" N GLY B 25 " --> pdb=" O ASP B 21 " (cutoff:3.500A) Processing helix chain 'B' and resid 36 through 46 removed outlier: 4.057A pdb=" N GLU B 43 " --> pdb=" O ARG B 40 " (cutoff:3.500A) removed outlier: 5.392A pdb=" N SER B 44 " --> pdb=" O PHE B 41 " (cutoff:3.500A) removed outlier: 3.939A pdb=" N GLY B 46 " --> pdb=" O GLU B 43 " (cutoff:3.500A) Processing helix chain 'B' and resid 50 through 56 Processing helix chain 'B' and resid 57 through 76 Processing helix chain 'B' and resid 77 through 79 No H-bonds generated for 'chain 'B' and resid 77 through 79' Processing helix chain 'B' and resid 80 through 85 Processing helix chain 'B' and resid 85 through 95 Processing helix chain 'B' and resid 99 through 119 removed outlier: 4.015A pdb=" N PHE B 103 " --> pdb=" O ASP B 99 " (cutoff:3.500A) removed outlier: 3.571A pdb=" N ARG B 104 " --> pdb=" O PRO B 100 " (cutoff:3.500A) Processing helix chain 'B' and resid 120 through 122 No H-bonds generated for 'chain 'B' and resid 120 through 122' Processing helix chain 'B' and resid 123 through 143 Processing helix chain 'C' and resid 3 through 18 Processing helix chain 'C' and resid 20 through 36 Processing helix chain 'C' and resid 37 through 43 Processing helix chain 'C' and resid 52 through 72 Processing helix chain 'C' and resid 75 through 80 Processing helix chain 'C' and resid 80 through 90 Processing helix chain 'C' and resid 94 through 113 removed outlier: 3.690A pdb=" N PHE C 98 " --> pdb=" O ASP C 94 " (cutoff:3.500A) Processing helix chain 'C' and resid 118 through 137 Processing helix chain 'D' and resid 4 through 17 removed outlier: 3.657A pdb=" N LYS D 17 " --> pdb=" O ALA D 13 " (cutoff:3.500A) Processing helix chain 'D' and resid 19 through 35 removed outlier: 3.905A pdb=" N GLY D 25 " --> pdb=" O ASP D 21 " (cutoff:3.500A) Processing helix chain 'D' and resid 36 through 41 Processing helix chain 'D' and resid 42 through 46 removed outlier: 3.568A pdb=" N GLY D 46 " --> pdb=" O GLU D 43 " (cutoff:3.500A) Processing helix chain 'D' and resid 50 through 56 Processing helix chain 'D' and resid 57 through 76 Processing helix chain 'D' and resid 77 through 79 No H-bonds generated for 'chain 'D' and resid 77 through 79' Processing helix chain 'D' and resid 80 through 85 Processing helix chain 'D' and resid 85 through 95 Processing helix chain 'D' and resid 99 through 119 removed outlier: 3.990A pdb=" N PHE D 103 " --> pdb=" O ASP D 99 " (cutoff:3.500A) removed outlier: 3.580A pdb=" N ARG D 104 " --> pdb=" O PRO D 100 " (cutoff:3.500A) Processing helix chain 'D' and resid 120 through 122 No H-bonds generated for 'chain 'D' and resid 120 through 122' Processing helix chain 'D' and resid 123 through 143 343 hydrogen bonds defined for protein. 978 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: 1.29 Time building geometry restraints manager: 1.50 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.38: 1647 1.38 - 1.55: 2921 1.55 - 1.72: 8 1.72 - 1.89: 18 1.89 - 2.06: 16 Bond restraints: 4610 Sorted by residual: bond pdb=" N PHE D 42 " pdb=" CA PHE D 42 " ideal model delta sigma weight residual 1.456 1.494 -0.038 1.18e-02 7.18e+03 1.03e+01 bond pdb=" N GLU D 43 " pdb=" CA GLU D 43 " ideal model delta sigma weight residual 1.459 1.496 -0.037 1.21e-02 6.83e+03 9.34e+00 bond pdb=" N VAL D 11 " pdb=" CA VAL D 11 " ideal model delta sigma weight residual 1.461 1.496 -0.035 1.17e-02 7.31e+03 8.83e+00 bond pdb=" N HIS C 89 " pdb=" CA HIS C 89 " ideal model delta sigma weight residual 1.459 1.494 -0.035 1.23e-02 6.61e+03 8.15e+00 bond pdb=" N VAL B 133 " pdb=" CA VAL B 133 " ideal model delta sigma weight residual 1.461 1.494 -0.034 1.19e-02 7.06e+03 8.10e+00 ... (remaining 4605 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.22: 5772 1.22 - 2.43: 338 2.43 - 3.65: 161 3.65 - 4.87: 43 4.87 - 6.09: 16 Bond angle restraints: 6330 Sorted by residual: angle pdb=" N HIS C 89 " pdb=" CA HIS C 89 " pdb=" C HIS C 89 " ideal model delta sigma weight residual 111.36 116.19 -4.83 1.09e+00 8.42e-01 1.96e+01 angle pdb=" O LEU A 113 " pdb=" C LEU A 113 " pdb=" N PRO A 114 " ideal model delta sigma weight residual 121.37 117.45 3.92 9.00e-01 1.23e+00 1.90e+01 angle pdb=" O LEU C 113 " pdb=" C LEU C 113 " pdb=" N PRO C 114 " ideal model delta sigma weight residual 121.37 117.52 3.85 9.00e-01 1.23e+00 1.83e+01 angle pdb=" CA HIS C 87 " pdb=" C HIS C 87 " pdb=" O HIS C 87 " ideal model delta sigma weight residual 120.82 116.46 4.36 1.05e+00 9.07e-01 1.72e+01 angle pdb=" CA THR C 118 " pdb=" C THR C 118 " pdb=" N PRO C 119 " ideal model delta sigma weight residual 117.48 122.07 -4.59 1.15e+00 7.56e-01 1.59e+01 ... (remaining 6325 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.73: 2368 17.73 - 35.46: 166 35.46 - 53.19: 56 53.19 - 70.93: 15 70.93 - 88.66: 9 Dihedral angle restraints: 2614 sinusoidal: 990 harmonic: 1624 Sorted by residual: dihedral pdb=" C2D HEM B 201 " pdb=" C3D HEM B 201 " pdb=" CAD HEM B 201 " pdb=" CBD HEM B 201 " ideal model delta sinusoidal sigma weight residual -0.00 -83.44 83.44 2 2.00e+01 2.50e-03 1.18e+01 dihedral pdb=" C2D HEM D 201 " pdb=" C3D HEM D 201 " pdb=" CAD HEM D 201 " pdb=" CBD HEM D 201 " ideal model delta sinusoidal sigma weight residual 0.00 -75.84 75.84 2 2.00e+01 2.50e-03 1.13e+01 dihedral pdb=" C2D HEM C 201 " pdb=" C3D HEM C 201 " pdb=" CAD HEM C 201 " pdb=" CBD HEM C 201 " ideal model delta sinusoidal sigma weight residual -180.00 -107.83 -72.17 2 2.00e+01 2.50e-03 1.09e+01 ... (remaining 2611 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.055: 564 0.055 - 0.110: 99 0.110 - 0.164: 20 0.164 - 0.219: 6 0.219 - 0.274: 3 Chirality restraints: 692 Sorted by residual: chirality pdb=" CB VAL B 134 " pdb=" CA VAL B 134 " pdb=" CG1 VAL B 134 " pdb=" CG2 VAL B 134 " both_signs ideal model delta sigma weight residual False -2.63 -2.36 -0.27 2.00e-01 2.50e+01 1.87e+00 chirality pdb=" CB VAL D 134 " pdb=" CA VAL D 134 " pdb=" CG1 VAL D 134 " pdb=" CG2 VAL D 134 " both_signs ideal model delta sigma weight residual False -2.63 -2.36 -0.27 2.00e-01 2.50e+01 1.76e+00 chirality pdb=" CA HIS C 89 " pdb=" N HIS C 89 " pdb=" C HIS C 89 " pdb=" CB HIS C 89 " both_signs ideal model delta sigma weight residual False 2.51 2.25 0.26 2.00e-01 2.50e+01 1.73e+00 ... (remaining 689 not shown) Planarity restraints: 790 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C SER A 3 " 0.036 5.00e-02 4.00e+02 5.52e-02 4.87e+00 pdb=" N PRO A 4 " -0.095 5.00e-02 4.00e+02 pdb=" CA PRO A 4 " 0.028 5.00e-02 4.00e+02 pdb=" CD PRO A 4 " 0.031 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA LEU A 113 " 0.011 2.00e-02 2.50e+03 2.06e-02 4.25e+00 pdb=" C LEU A 113 " -0.036 2.00e-02 2.50e+03 pdb=" O LEU A 113 " 0.013 2.00e-02 2.50e+03 pdb=" N PRO A 114 " 0.012 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C THR B 123 " 0.030 5.00e-02 4.00e+02 4.55e-02 3.31e+00 pdb=" N PRO B 124 " -0.079 5.00e-02 4.00e+02 pdb=" CA PRO B 124 " 0.024 5.00e-02 4.00e+02 pdb=" CD PRO B 124 " 0.025 5.00e-02 4.00e+02 ... (remaining 787 not shown) Histogram of nonbonded interaction distances: 2.22 - 2.75: 599 2.75 - 3.29: 4268 3.29 - 3.83: 7836 3.83 - 4.36: 8979 4.36 - 4.90: 15757 Nonbonded interactions: 37439 Sorted by model distance: nonbonded pdb=" OE1 GLU A 27 " pdb=" NE2 HIS A 112 " model vdw 2.218 3.120 nonbonded pdb=" OE1 GLU C 27 " pdb=" NE2 HIS C 112 " model vdw 2.223 3.120 nonbonded pdb=" OE1 GLU D 26 " pdb=" NE2 HIS D 117 " model vdw 2.266 3.120 nonbonded pdb=" O PRO A 77 " pdb=" OH TYR A 140 " model vdw 2.287 3.040 nonbonded pdb=" O SER A 133 " pdb=" OG1 THR A 137 " model vdw 2.305 3.040 ... (remaining 37434 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: 0.01 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'C' } ncs_group { reference = chain 'B' selection = chain 'D' } 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: 45.230 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.190 Check model and map are aligned: 0.030 Set scattering table: 0.050 Process input model: 16.550 Find NCS groups from input model: 0.170 Set up NCS constraints: 0.020 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:3.070 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 65.320 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8054 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 : 0.007 0.225 4614 Z= 0.339 Angle : 0.837 6.087 6330 Z= 0.564 Chirality : 0.050 0.274 692 Planarity : 0.006 0.055 790 Dihedral : 15.651 88.657 1562 Min Nonbonded Distance : 2.218 Molprobity Statistics. All-atom Clashscore : 5.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.08 % Favored : 98.92 % Rotamer: Outliers : 2.86 % Allowed : 10.79 % Favored : 86.34 % 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: 3.00 (0.36), residues: 558 helix: 2.39 (0.25), residues: 434 sheet: None (None), residues: 0 loop : 0.58 (0.62), residues: 124 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP D 15 HIS 0.005 0.001 HIS C 87 PHE 0.013 0.002 PHE D 42 TYR 0.006 0.001 TYR B 35 ARG 0.008 0.001 ARG A 92 Details of bonding type rmsd hydrogen bonds : bond 0.11535 ( 343) hydrogen bonds : angle 4.90656 ( 978) covalent geometry : bond 0.00512 ( 4610) covalent geometry : angle 0.83665 ( 6330) Misc. bond : bond 0.17153 ( 4) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1116 Ramachandran restraints generated. 558 Oldfield, 0 Emsley, 558 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1116 Ramachandran restraints generated. 558 Oldfield, 0 Emsley, 558 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 61 residues out of total 454 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 48 time to evaluate : 0.502 Fit side-chains revert: symmetry clash REVERT: A 60 LYS cc_start: 0.7942 (tptp) cc_final: 0.7455 (ttmm) REVERT: A 61 LYS cc_start: 0.8204 (mtpp) cc_final: 0.7676 (mtpt) REVERT: A 92 ARG cc_start: 0.8636 (mtt-85) cc_final: 0.7604 (mtm-85) REVERT: B 52 ASP cc_start: 0.8214 (m-30) cc_final: 0.8006 (m-30) REVERT: B 65 LYS cc_start: 0.8388 (ttmt) cc_final: 0.8160 (tttt) outliers start: 13 outliers final: 4 residues processed: 58 average time/residue: 0.2608 time to fit residues: 18.1731 Evaluate side-chains 46 residues out of total 454 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 42 time to evaluate : 0.433 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 85 ASP Chi-restraints excluded: chain B residue 134 VAL Chi-restraints excluded: chain C residue 34 LEU Chi-restraints excluded: chain D residue 43 GLU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 56 random chunks: chunk 47 optimal weight: 3.9990 chunk 42 optimal weight: 0.0470 chunk 23 optimal weight: 0.4980 chunk 14 optimal weight: 1.9990 chunk 28 optimal weight: 2.9990 chunk 22 optimal weight: 1.9990 chunk 43 optimal weight: 2.9990 chunk 16 optimal weight: 2.9990 chunk 26 optimal weight: 0.6980 chunk 32 optimal weight: 1.9990 chunk 50 optimal weight: 0.9990 overall best weight: 0.8482 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 131 GLN C 89 HIS D 39 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3628 r_free = 0.3628 target = 0.154863 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3350 r_free = 0.3350 target = 0.129123 restraints weight = 4202.894| |-----------------------------------------------------------------------------| r_work (start): 0.3342 rms_B_bonded: 1.31 r_work: 0.3191 rms_B_bonded: 2.37 restraints_weight: 0.5000 r_work: 0.3030 rms_B_bonded: 3.89 restraints_weight: 0.2500 r_work (final): 0.3030 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7994 moved from start: 0.1033 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.114 4614 Z= 0.165 Angle : 0.605 5.361 6330 Z= 0.285 Chirality : 0.041 0.128 692 Planarity : 0.006 0.048 790 Dihedral : 10.228 85.074 624 Min Nonbonded Distance : 2.490 Molprobity Statistics. All-atom Clashscore : 4.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.08 % Favored : 98.92 % Rotamer: Outliers : 3.08 % Allowed : 9.25 % Favored : 87.67 % 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: 2.80 (0.36), residues: 558 helix: 2.25 (0.25), residues: 434 sheet: None (None), residues: 0 loop : 0.54 (0.61), residues: 124 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP C 14 HIS 0.005 0.001 HIS C 87 PHE 0.013 0.002 PHE D 85 TYR 0.008 0.001 TYR A 42 ARG 0.006 0.001 ARG A 92 Details of bonding type rmsd hydrogen bonds : bond 0.04168 ( 343) hydrogen bonds : angle 4.18022 ( 978) covalent geometry : bond 0.00440 ( 4610) covalent geometry : angle 0.60539 ( 6330) Misc. bond : bond 0.10215 ( 4) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1116 Ramachandran restraints generated. 558 Oldfield, 0 Emsley, 558 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1116 Ramachandran restraints generated. 558 Oldfield, 0 Emsley, 558 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 60 residues out of total 454 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 46 time to evaluate : 0.907 Fit side-chains revert: symmetry clash REVERT: A 60 LYS cc_start: 0.7905 (tptp) cc_final: 0.7301 (ttmm) REVERT: A 61 LYS cc_start: 0.7933 (mtpp) cc_final: 0.7346 (mtpt) REVERT: A 92 ARG cc_start: 0.8747 (mtt-85) cc_final: 0.7718 (mtm-85) REVERT: B 65 LYS cc_start: 0.8319 (ttmt) cc_final: 0.7820 (tttm) REVERT: C 76 MET cc_start: 0.7179 (OUTLIER) cc_final: 0.6867 (mtt) REVERT: D 120 LYS cc_start: 0.7542 (mmtp) cc_final: 0.7164 (mmmt) outliers start: 14 outliers final: 9 residues processed: 54 average time/residue: 0.3128 time to fit residues: 20.9261 Evaluate side-chains 54 residues out of total 454 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 44 time to evaluate : 0.503 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 34 LEU Chi-restraints excluded: chain A residue 76 MET Chi-restraints excluded: chain A residue 85 ASP Chi-restraints excluded: chain B residue 134 VAL Chi-restraints excluded: chain C residue 34 LEU Chi-restraints excluded: chain C residue 76 MET Chi-restraints excluded: chain D residue 43 GLU Chi-restraints excluded: chain D residue 78 LEU Chi-restraints excluded: chain D residue 89 SER Chi-restraints excluded: chain D residue 141 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 56 random chunks: chunk 8 optimal weight: 0.7980 chunk 5 optimal weight: 0.5980 chunk 12 optimal weight: 0.5980 chunk 2 optimal weight: 0.8980 chunk 22 optimal weight: 0.0870 chunk 42 optimal weight: 0.5980 chunk 15 optimal weight: 0.9990 chunk 55 optimal weight: 0.8980 chunk 28 optimal weight: 2.9990 chunk 31 optimal weight: 0.7980 chunk 43 optimal weight: 0.8980 overall best weight: 0.5358 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 89 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3676 r_free = 0.3676 target = 0.159579 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3440 r_free = 0.3440 target = 0.137192 restraints weight = 4150.392| |-----------------------------------------------------------------------------| r_work (start): 0.3441 rms_B_bonded: 0.99 r_work: 0.3249 rms_B_bonded: 2.41 restraints_weight: 0.5000 r_work: 0.3098 rms_B_bonded: 4.03 restraints_weight: 0.2500 r_work (final): 0.3098 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8084 moved from start: 0.1201 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.119 4614 Z= 0.127 Angle : 0.562 5.593 6330 Z= 0.257 Chirality : 0.038 0.122 692 Planarity : 0.005 0.046 790 Dihedral : 9.920 83.434 624 Min Nonbonded Distance : 2.518 Molprobity Statistics. All-atom Clashscore : 3.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.08 % Favored : 98.92 % Rotamer: Outliers : 3.08 % Allowed : 7.71 % Favored : 89.21 % 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: 2.97 (0.36), residues: 558 helix: 2.38 (0.25), residues: 436 sheet: None (None), residues: 0 loop : 0.54 (0.60), residues: 122 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 14 HIS 0.003 0.001 HIS D 116 PHE 0.008 0.001 PHE D 85 TYR 0.005 0.001 TYR A 42 ARG 0.004 0.001 ARG A 92 Details of bonding type rmsd hydrogen bonds : bond 0.03396 ( 343) hydrogen bonds : angle 3.96947 ( 978) covalent geometry : bond 0.00341 ( 4610) covalent geometry : angle 0.56222 ( 6330) Misc. bond : bond 0.08606 ( 4) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1116 Ramachandran restraints generated. 558 Oldfield, 0 Emsley, 558 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1116 Ramachandran restraints generated. 558 Oldfield, 0 Emsley, 558 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 60 residues out of total 454 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 46 time to evaluate : 0.548 Fit side-chains revert: symmetry clash REVERT: A 60 LYS cc_start: 0.8082 (tptp) cc_final: 0.7593 (ttmm) REVERT: A 61 LYS cc_start: 0.8057 (mtpp) cc_final: 0.7572 (mtpt) REVERT: A 76 MET cc_start: 0.7369 (OUTLIER) cc_final: 0.6575 (mmt) REVERT: A 92 ARG cc_start: 0.8699 (mtt-85) cc_final: 0.7844 (mtm-85) REVERT: B 14 LEU cc_start: 0.8071 (OUTLIER) cc_final: 0.7791 (tp) REVERT: B 66 LYS cc_start: 0.8405 (mmmm) cc_final: 0.7832 (mtpt) REVERT: C 76 MET cc_start: 0.7217 (OUTLIER) cc_final: 0.6794 (mtt) REVERT: D 120 LYS cc_start: 0.7556 (mmtp) cc_final: 0.7229 (mmmt) outliers start: 14 outliers final: 9 residues processed: 53 average time/residue: 0.3005 time to fit residues: 19.5938 Evaluate side-chains 53 residues out of total 454 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 41 time to evaluate : 0.719 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 3 SER Chi-restraints excluded: chain A residue 34 LEU Chi-restraints excluded: chain A residue 76 MET Chi-restraints excluded: chain A residue 86 LEU Chi-restraints excluded: chain B residue 14 LEU Chi-restraints excluded: chain B residue 134 VAL Chi-restraints excluded: chain C residue 34 LEU Chi-restraints excluded: chain C residue 76 MET Chi-restraints excluded: chain C residue 89 HIS Chi-restraints excluded: chain D residue 43 GLU Chi-restraints excluded: chain D residue 78 LEU Chi-restraints excluded: chain D residue 141 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 56 random chunks: chunk 39 optimal weight: 0.5980 chunk 36 optimal weight: 7.9990 chunk 19 optimal weight: 1.9990 chunk 38 optimal weight: 0.5980 chunk 33 optimal weight: 0.9990 chunk 24 optimal weight: 0.9990 chunk 31 optimal weight: 0.7980 chunk 49 optimal weight: 0.6980 chunk 18 optimal weight: 0.9980 chunk 37 optimal weight: 1.9990 chunk 5 optimal weight: 2.9990 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 89 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3652 r_free = 0.3652 target = 0.157378 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3414 r_free = 0.3414 target = 0.134983 restraints weight = 4191.135| |-----------------------------------------------------------------------------| r_work (start): 0.3415 rms_B_bonded: 0.98 r_work: 0.3222 rms_B_bonded: 2.37 restraints_weight: 0.5000 r_work: 0.3071 rms_B_bonded: 3.97 restraints_weight: 0.2500 r_work (final): 0.3071 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8105 moved from start: 0.1375 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.153 4614 Z= 0.149 Angle : 0.582 6.197 6330 Z= 0.267 Chirality : 0.039 0.123 692 Planarity : 0.005 0.047 790 Dihedral : 9.942 82.784 622 Min Nonbonded Distance : 2.532 Molprobity Statistics. All-atom Clashscore : 3.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.08 % Favored : 98.92 % Rotamer: Outliers : 3.30 % Allowed : 8.15 % Favored : 88.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: 2.84 (0.36), residues: 558 helix: 2.30 (0.25), residues: 436 sheet: None (None), residues: 0 loop : 0.41 (0.58), residues: 122 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP C 14 HIS 0.009 0.001 HIS C 89 PHE 0.009 0.001 PHE D 85 TYR 0.005 0.001 TYR A 42 ARG 0.003 0.000 ARG A 92 Details of bonding type rmsd hydrogen bonds : bond 0.03748 ( 343) hydrogen bonds : angle 4.02862 ( 978) covalent geometry : bond 0.00399 ( 4610) covalent geometry : angle 0.58248 ( 6330) Misc. bond : bond 0.10572 ( 4) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1116 Ramachandran restraints generated. 558 Oldfield, 0 Emsley, 558 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1116 Ramachandran restraints generated. 558 Oldfield, 0 Emsley, 558 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 57 residues out of total 454 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 42 time to evaluate : 0.464 Fit side-chains REVERT: A 60 LYS cc_start: 0.8094 (tptp) cc_final: 0.7571 (ttmm) REVERT: A 61 LYS cc_start: 0.8055 (mtpp) cc_final: 0.7562 (mtpt) REVERT: A 76 MET cc_start: 0.7353 (OUTLIER) cc_final: 0.6659 (mmt) REVERT: A 92 ARG cc_start: 0.8715 (mtt-85) cc_final: 0.7871 (mtm-85) REVERT: B 66 LYS cc_start: 0.8397 (mmmm) cc_final: 0.7806 (mtpt) REVERT: B 120 LYS cc_start: 0.7909 (OUTLIER) cc_final: 0.7342 (tttt) REVERT: C 60 LYS cc_start: 0.8038 (tptp) cc_final: 0.7353 (tppt) REVERT: C 76 MET cc_start: 0.7242 (OUTLIER) cc_final: 0.6848 (mtt) REVERT: D 43 GLU cc_start: 0.7465 (OUTLIER) cc_final: 0.6408 (pm20) REVERT: D 120 LYS cc_start: 0.7589 (mmtp) cc_final: 0.7278 (mmmt) outliers start: 15 outliers final: 8 residues processed: 50 average time/residue: 0.2279 time to fit residues: 13.9139 Evaluate side-chains 54 residues out of total 454 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 42 time to evaluate : 0.466 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 3 SER Chi-restraints excluded: chain A residue 34 LEU Chi-restraints excluded: chain A residue 76 MET Chi-restraints excluded: chain B residue 120 LYS Chi-restraints excluded: chain B residue 134 VAL Chi-restraints excluded: chain C residue 34 LEU Chi-restraints excluded: chain C residue 76 MET Chi-restraints excluded: chain C residue 89 HIS Chi-restraints excluded: chain D residue 17 LYS Chi-restraints excluded: chain D residue 43 GLU Chi-restraints excluded: chain D residue 78 LEU Chi-restraints excluded: chain D residue 141 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 56 random chunks: chunk 25 optimal weight: 1.9990 chunk 11 optimal weight: 0.9990 chunk 27 optimal weight: 0.3980 chunk 45 optimal weight: 0.5980 chunk 26 optimal weight: 0.6980 chunk 1 optimal weight: 0.6980 chunk 54 optimal weight: 4.9990 chunk 15 optimal weight: 0.7980 chunk 28 optimal weight: 2.9990 chunk 34 optimal weight: 0.9990 chunk 23 optimal weight: 1.9990 overall best weight: 0.6380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 89 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3652 r_free = 0.3652 target = 0.157655 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3416 r_free = 0.3416 target = 0.135258 restraints weight = 4262.293| |-----------------------------------------------------------------------------| r_work (start): 0.3415 rms_B_bonded: 0.99 r_work: 0.3228 rms_B_bonded: 2.34 restraints_weight: 0.5000 r_work: 0.3079 rms_B_bonded: 3.88 restraints_weight: 0.2500 r_work (final): 0.3079 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8101 moved from start: 0.1451 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.141 4614 Z= 0.137 Angle : 0.572 6.476 6330 Z= 0.261 Chirality : 0.039 0.122 692 Planarity : 0.005 0.047 790 Dihedral : 9.884 82.427 622 Min Nonbonded Distance : 2.542 Molprobity Statistics. All-atom Clashscore : 3.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.90 % Favored : 99.10 % Rotamer: Outliers : 3.30 % Allowed : 8.81 % Favored : 87.89 % 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: 2.91 (0.36), residues: 558 helix: 2.37 (0.25), residues: 436 sheet: None (None), residues: 0 loop : 0.35 (0.58), residues: 122 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 14 HIS 0.007 0.001 HIS C 89 PHE 0.008 0.001 PHE D 85 TYR 0.005 0.001 TYR B 35 ARG 0.003 0.000 ARG A 92 Details of bonding type rmsd hydrogen bonds : bond 0.03551 ( 343) hydrogen bonds : angle 4.00250 ( 978) covalent geometry : bond 0.00367 ( 4610) covalent geometry : angle 0.57188 ( 6330) Misc. bond : bond 0.09638 ( 4) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1116 Ramachandran restraints generated. 558 Oldfield, 0 Emsley, 558 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1116 Ramachandran restraints generated. 558 Oldfield, 0 Emsley, 558 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 57 residues out of total 454 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 42 time to evaluate : 0.379 Fit side-chains REVERT: A 60 LYS cc_start: 0.8106 (tptp) cc_final: 0.7586 (ttmm) REVERT: A 61 LYS cc_start: 0.8045 (mtpp) cc_final: 0.7575 (mtpt) REVERT: A 76 MET cc_start: 0.7445 (OUTLIER) cc_final: 0.6662 (mmt) REVERT: A 92 ARG cc_start: 0.8718 (mtt-85) cc_final: 0.7846 (mtm-85) REVERT: B 26 GLU cc_start: 0.7638 (OUTLIER) cc_final: 0.7420 (mm-30) REVERT: B 66 LYS cc_start: 0.8390 (mmmm) cc_final: 0.7826 (mtpt) REVERT: B 120 LYS cc_start: 0.7922 (OUTLIER) cc_final: 0.7371 (tttt) REVERT: C 60 LYS cc_start: 0.8008 (tptp) cc_final: 0.7335 (tppt) REVERT: C 76 MET cc_start: 0.7211 (OUTLIER) cc_final: 0.6789 (mtt) REVERT: D 43 GLU cc_start: 0.7538 (OUTLIER) cc_final: 0.6531 (pm20) REVERT: D 120 LYS cc_start: 0.7562 (mmtp) cc_final: 0.7230 (mmmt) outliers start: 15 outliers final: 9 residues processed: 49 average time/residue: 0.3284 time to fit residues: 19.6029 Evaluate side-chains 54 residues out of total 454 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 40 time to evaluate : 0.628 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 3 SER Chi-restraints excluded: chain A residue 34 LEU Chi-restraints excluded: chain A residue 76 MET Chi-restraints excluded: chain B residue 14 LEU Chi-restraints excluded: chain B residue 26 GLU Chi-restraints excluded: chain B residue 90 GLU Chi-restraints excluded: chain B residue 120 LYS Chi-restraints excluded: chain B residue 134 VAL Chi-restraints excluded: chain C residue 76 MET Chi-restraints excluded: chain C residue 89 HIS Chi-restraints excluded: chain D residue 17 LYS Chi-restraints excluded: chain D residue 43 GLU Chi-restraints excluded: chain D residue 78 LEU Chi-restraints excluded: chain D residue 141 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 56 random chunks: chunk 4 optimal weight: 0.0770 chunk 7 optimal weight: 3.9990 chunk 48 optimal weight: 0.9980 chunk 49 optimal weight: 1.9990 chunk 8 optimal weight: 0.8980 chunk 16 optimal weight: 2.9990 chunk 55 optimal weight: 0.5980 chunk 28 optimal weight: 0.9980 chunk 22 optimal weight: 0.0670 chunk 32 optimal weight: 0.8980 chunk 35 optimal weight: 3.9990 overall best weight: 0.5076 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 89 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3662 r_free = 0.3662 target = 0.158443 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3425 r_free = 0.3425 target = 0.135973 restraints weight = 4177.298| |-----------------------------------------------------------------------------| r_work (start): 0.3426 rms_B_bonded: 0.99 r_work: 0.3242 rms_B_bonded: 2.34 restraints_weight: 0.5000 r_work: 0.3092 rms_B_bonded: 3.93 restraints_weight: 0.2500 r_work (final): 0.3092 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8082 moved from start: 0.1514 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.135 4614 Z= 0.123 Angle : 0.557 6.231 6330 Z= 0.253 Chirality : 0.038 0.121 692 Planarity : 0.005 0.046 790 Dihedral : 9.673 82.084 620 Min Nonbonded Distance : 2.545 Molprobity Statistics. All-atom Clashscore : 3.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.08 % Favored : 98.92 % Rotamer: Outliers : 3.08 % Allowed : 9.25 % Favored : 87.67 % 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: 3.04 (0.36), residues: 558 helix: 2.47 (0.25), residues: 436 sheet: None (None), residues: 0 loop : 0.36 (0.58), residues: 122 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 14 HIS 0.006 0.001 HIS C 89 PHE 0.006 0.001 PHE C 43 TYR 0.005 0.001 TYR B 35 ARG 0.003 0.000 ARG A 92 Details of bonding type rmsd hydrogen bonds : bond 0.03307 ( 343) hydrogen bonds : angle 3.93692 ( 978) covalent geometry : bond 0.00329 ( 4610) covalent geometry : angle 0.55748 ( 6330) Misc. bond : bond 0.08952 ( 4) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1116 Ramachandran restraints generated. 558 Oldfield, 0 Emsley, 558 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1116 Ramachandran restraints generated. 558 Oldfield, 0 Emsley, 558 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 57 residues out of total 454 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 43 time to evaluate : 0.477 Fit side-chains REVERT: A 60 LYS cc_start: 0.8143 (tptp) cc_final: 0.7603 (ttmm) REVERT: A 61 LYS cc_start: 0.8026 (mtpp) cc_final: 0.7577 (mtpt) REVERT: A 76 MET cc_start: 0.7459 (OUTLIER) cc_final: 0.6697 (mmt) REVERT: A 92 ARG cc_start: 0.8701 (mtt-85) cc_final: 0.7844 (mtm-85) REVERT: B 26 GLU cc_start: 0.7669 (OUTLIER) cc_final: 0.7452 (mm-30) REVERT: B 66 LYS cc_start: 0.8356 (mmmm) cc_final: 0.7802 (mtpt) REVERT: B 120 LYS cc_start: 0.7925 (OUTLIER) cc_final: 0.7369 (tttt) REVERT: C 60 LYS cc_start: 0.7990 (tptp) cc_final: 0.7300 (tppt) REVERT: C 76 MET cc_start: 0.7207 (OUTLIER) cc_final: 0.6821 (mtt) REVERT: D 43 GLU cc_start: 0.7510 (OUTLIER) cc_final: 0.6591 (pm20) REVERT: D 120 LYS cc_start: 0.7543 (mmtp) cc_final: 0.7207 (mmmt) outliers start: 14 outliers final: 8 residues processed: 47 average time/residue: 0.2972 time to fit residues: 17.5502 Evaluate side-chains 54 residues out of total 454 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 41 time to evaluate : 1.513 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 34 LEU Chi-restraints excluded: chain A residue 76 MET Chi-restraints excluded: chain B residue 14 LEU Chi-restraints excluded: chain B residue 26 GLU Chi-restraints excluded: chain B residue 90 GLU Chi-restraints excluded: chain B residue 120 LYS Chi-restraints excluded: chain B residue 134 VAL Chi-restraints excluded: chain C residue 76 MET Chi-restraints excluded: chain C residue 89 HIS Chi-restraints excluded: chain D residue 17 LYS Chi-restraints excluded: chain D residue 43 GLU Chi-restraints excluded: chain D residue 78 LEU Chi-restraints excluded: chain D residue 141 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 56 random chunks: chunk 21 optimal weight: 0.0970 chunk 13 optimal weight: 0.7980 chunk 28 optimal weight: 1.9990 chunk 45 optimal weight: 0.8980 chunk 25 optimal weight: 3.9990 chunk 39 optimal weight: 0.9980 chunk 30 optimal weight: 0.8980 chunk 9 optimal weight: 0.8980 chunk 41 optimal weight: 0.0770 chunk 15 optimal weight: 1.9990 chunk 19 optimal weight: 0.2980 overall best weight: 0.4336 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 89 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3668 r_free = 0.3668 target = 0.159051 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3438 r_free = 0.3438 target = 0.137145 restraints weight = 4197.568| |-----------------------------------------------------------------------------| r_work (start): 0.3439 rms_B_bonded: 0.96 r_work: 0.3254 rms_B_bonded: 2.33 restraints_weight: 0.5000 r_work: 0.3105 rms_B_bonded: 3.91 restraints_weight: 0.2500 r_work (final): 0.3105 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8077 moved from start: 0.1530 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.131 4614 Z= 0.115 Angle : 0.549 6.065 6330 Z= 0.249 Chirality : 0.037 0.120 692 Planarity : 0.005 0.045 790 Dihedral : 9.635 81.732 620 Min Nonbonded Distance : 2.548 Molprobity Statistics. All-atom Clashscore : 3.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.08 % Favored : 98.92 % Rotamer: Outliers : 3.08 % Allowed : 9.69 % Favored : 87.22 % 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: 3.14 (0.36), residues: 558 helix: 2.55 (0.25), residues: 436 sheet: None (None), residues: 0 loop : 0.35 (0.59), residues: 122 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 14 HIS 0.005 0.001 HIS C 89 PHE 0.006 0.001 PHE C 43 TYR 0.005 0.001 TYR B 35 ARG 0.002 0.000 ARG A 92 Details of bonding type rmsd hydrogen bonds : bond 0.03151 ( 343) hydrogen bonds : angle 3.88347 ( 978) covalent geometry : bond 0.00308 ( 4610) covalent geometry : angle 0.54919 ( 6330) Misc. bond : bond 0.08442 ( 4) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1116 Ramachandran restraints generated. 558 Oldfield, 0 Emsley, 558 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1116 Ramachandran restraints generated. 558 Oldfield, 0 Emsley, 558 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 54 residues out of total 454 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 40 time to evaluate : 0.445 Fit side-chains REVERT: A 60 LYS cc_start: 0.8153 (tptp) cc_final: 0.7613 (ttmm) REVERT: A 61 LYS cc_start: 0.8022 (mtpp) cc_final: 0.7598 (mtpt) REVERT: A 76 MET cc_start: 0.7446 (OUTLIER) cc_final: 0.6587 (mmt) REVERT: A 92 ARG cc_start: 0.8691 (mtt-85) cc_final: 0.7846 (mtm-85) REVERT: B 26 GLU cc_start: 0.7638 (OUTLIER) cc_final: 0.7419 (mm-30) REVERT: B 66 LYS cc_start: 0.8371 (mmmm) cc_final: 0.7833 (mtpt) REVERT: B 120 LYS cc_start: 0.7886 (OUTLIER) cc_final: 0.7327 (tttt) REVERT: C 60 LYS cc_start: 0.7998 (tptp) cc_final: 0.7307 (tppt) REVERT: C 76 MET cc_start: 0.7176 (OUTLIER) cc_final: 0.6799 (mtt) REVERT: C 116 GLU cc_start: 0.7563 (mm-30) cc_final: 0.7324 (mp0) REVERT: D 43 GLU cc_start: 0.7533 (OUTLIER) cc_final: 0.6588 (pm20) REVERT: D 120 LYS cc_start: 0.7517 (mmtp) cc_final: 0.7190 (mmmt) outliers start: 14 outliers final: 8 residues processed: 45 average time/residue: 0.2384 time to fit residues: 13.0443 Evaluate side-chains 53 residues out of total 454 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 40 time to evaluate : 0.439 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 34 LEU Chi-restraints excluded: chain A residue 76 MET Chi-restraints excluded: chain B residue 14 LEU Chi-restraints excluded: chain B residue 26 GLU Chi-restraints excluded: chain B residue 90 GLU Chi-restraints excluded: chain B residue 120 LYS Chi-restraints excluded: chain B residue 134 VAL Chi-restraints excluded: chain C residue 34 LEU Chi-restraints excluded: chain C residue 76 MET Chi-restraints excluded: chain C residue 89 HIS Chi-restraints excluded: chain D residue 17 LYS Chi-restraints excluded: chain D residue 43 GLU Chi-restraints excluded: chain D residue 78 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 56 random chunks: chunk 41 optimal weight: 0.0060 chunk 37 optimal weight: 0.0980 chunk 0 optimal weight: 3.9990 chunk 42 optimal weight: 2.9990 chunk 51 optimal weight: 10.0000 chunk 22 optimal weight: 0.0980 chunk 27 optimal weight: 1.9990 chunk 48 optimal weight: 0.9980 chunk 15 optimal weight: 0.2980 chunk 18 optimal weight: 1.9990 chunk 16 optimal weight: 0.6980 overall best weight: 0.2396 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 102 ASN C 89 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3698 r_free = 0.3698 target = 0.161846 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3472 r_free = 0.3472 target = 0.140168 restraints weight = 4123.668| |-----------------------------------------------------------------------------| r_work (start): 0.3473 rms_B_bonded: 0.95 r_work: 0.3290 rms_B_bonded: 2.31 restraints_weight: 0.5000 r_work: 0.3142 rms_B_bonded: 3.89 restraints_weight: 0.2500 r_work (final): 0.3142 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8039 moved from start: 0.1602 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.118 4614 Z= 0.100 Angle : 0.530 5.554 6330 Z= 0.238 Chirality : 0.036 0.119 692 Planarity : 0.005 0.044 790 Dihedral : 9.542 82.229 620 Min Nonbonded Distance : 2.556 Molprobity Statistics. All-atom Clashscore : 3.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.25 % Favored : 98.75 % Rotamer: Outliers : 3.08 % Allowed : 9.69 % Favored : 87.22 % 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: 3.34 (0.36), residues: 558 helix: 2.71 (0.25), residues: 436 sheet: None (None), residues: 0 loop : 0.34 (0.59), residues: 122 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 14 HIS 0.007 0.001 HIS C 89 PHE 0.005 0.001 PHE C 117 TYR 0.004 0.001 TYR B 35 ARG 0.003 0.000 ARG A 92 Details of bonding type rmsd hydrogen bonds : bond 0.02792 ( 343) hydrogen bonds : angle 3.76670 ( 978) covalent geometry : bond 0.00260 ( 4610) covalent geometry : angle 0.53015 ( 6330) Misc. bond : bond 0.07090 ( 4) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1116 Ramachandran restraints generated. 558 Oldfield, 0 Emsley, 558 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1116 Ramachandran restraints generated. 558 Oldfield, 0 Emsley, 558 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 59 residues out of total 454 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 45 time to evaluate : 0.424 Fit side-chains revert: symmetry clash REVERT: A 60 LYS cc_start: 0.8127 (tptp) cc_final: 0.7608 (ttmm) REVERT: A 61 LYS cc_start: 0.7990 (mtpp) cc_final: 0.7596 (mtpt) REVERT: A 76 MET cc_start: 0.7433 (OUTLIER) cc_final: 0.6482 (mmt) REVERT: A 92 ARG cc_start: 0.8664 (mtt-85) cc_final: 0.7827 (mtm-85) REVERT: B 8 LYS cc_start: 0.7514 (tppt) cc_final: 0.7131 (mttm) REVERT: B 26 GLU cc_start: 0.7648 (OUTLIER) cc_final: 0.7315 (mm-30) REVERT: B 66 LYS cc_start: 0.8318 (mmmm) cc_final: 0.7805 (mtpt) REVERT: C 76 MET cc_start: 0.7185 (OUTLIER) cc_final: 0.6828 (mtt) REVERT: D 120 LYS cc_start: 0.7461 (mmtp) cc_final: 0.7136 (mmmt) outliers start: 14 outliers final: 10 residues processed: 50 average time/residue: 0.2230 time to fit residues: 13.6520 Evaluate side-chains 53 residues out of total 454 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 40 time to evaluate : 0.465 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 34 LEU Chi-restraints excluded: chain A residue 76 MET Chi-restraints excluded: chain B residue 14 LEU Chi-restraints excluded: chain B residue 26 GLU Chi-restraints excluded: chain B residue 90 GLU Chi-restraints excluded: chain B residue 134 VAL Chi-restraints excluded: chain C residue 34 LEU Chi-restraints excluded: chain C residue 76 MET Chi-restraints excluded: chain C residue 89 HIS Chi-restraints excluded: chain D residue 17 LYS Chi-restraints excluded: chain D residue 43 GLU Chi-restraints excluded: chain D residue 78 LEU Chi-restraints excluded: chain D residue 141 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 56 random chunks: chunk 51 optimal weight: 4.9990 chunk 14 optimal weight: 4.9990 chunk 41 optimal weight: 0.5980 chunk 24 optimal weight: 0.5980 chunk 39 optimal weight: 0.9980 chunk 47 optimal weight: 1.9990 chunk 33 optimal weight: 0.9980 chunk 31 optimal weight: 0.0980 chunk 19 optimal weight: 0.5980 chunk 1 optimal weight: 0.3980 chunk 36 optimal weight: 7.9990 overall best weight: 0.4580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 89 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3675 r_free = 0.3675 target = 0.159469 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3437 r_free = 0.3437 target = 0.137017 restraints weight = 4202.222| |-----------------------------------------------------------------------------| r_work (start): 0.3438 rms_B_bonded: 0.99 r_work: 0.3260 rms_B_bonded: 2.32 restraints_weight: 0.5000 r_work: 0.3112 rms_B_bonded: 3.94 restraints_weight: 0.2500 r_work (final): 0.3112 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8074 moved from start: 0.1665 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.131 4614 Z= 0.116 Angle : 0.545 6.096 6330 Z= 0.246 Chirality : 0.037 0.120 692 Planarity : 0.005 0.045 790 Dihedral : 9.602 81.746 620 Min Nonbonded Distance : 2.562 Molprobity Statistics. All-atom Clashscore : 3.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.25 % Favored : 98.75 % Rotamer: Outliers : 3.08 % Allowed : 9.25 % Favored : 87.67 % 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: 3.27 (0.36), residues: 558 helix: 2.66 (0.24), residues: 436 sheet: None (None), residues: 0 loop : 0.33 (0.59), residues: 122 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP C 14 HIS 0.006 0.001 HIS C 89 PHE 0.005 0.001 PHE C 43 TYR 0.005 0.001 TYR A 42 ARG 0.002 0.000 ARG A 92 Details of bonding type rmsd hydrogen bonds : bond 0.03097 ( 343) hydrogen bonds : angle 3.81851 ( 978) covalent geometry : bond 0.00311 ( 4610) covalent geometry : angle 0.54506 ( 6330) Misc. bond : bond 0.08661 ( 4) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1116 Ramachandran restraints generated. 558 Oldfield, 0 Emsley, 558 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1116 Ramachandran restraints generated. 558 Oldfield, 0 Emsley, 558 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 55 residues out of total 454 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 41 time to evaluate : 0.430 Fit side-chains REVERT: A 60 LYS cc_start: 0.8140 (tptp) cc_final: 0.7613 (ttmm) REVERT: A 61 LYS cc_start: 0.8002 (mtpp) cc_final: 0.7605 (mtpt) REVERT: A 76 MET cc_start: 0.7383 (OUTLIER) cc_final: 0.6665 (mmt) REVERT: A 92 ARG cc_start: 0.8687 (mtt-85) cc_final: 0.7850 (mtm-85) REVERT: B 8 LYS cc_start: 0.7503 (tppt) cc_final: 0.7118 (mttm) REVERT: B 26 GLU cc_start: 0.7703 (OUTLIER) cc_final: 0.7401 (mm-30) REVERT: B 66 LYS cc_start: 0.8361 (mmmm) cc_final: 0.7829 (mtpt) REVERT: C 60 LYS cc_start: 0.8038 (tptp) cc_final: 0.7355 (tppt) REVERT: C 76 MET cc_start: 0.7194 (OUTLIER) cc_final: 0.6849 (mtt) REVERT: D 43 GLU cc_start: 0.7485 (OUTLIER) cc_final: 0.6553 (pm20) REVERT: D 120 LYS cc_start: 0.7485 (mmtp) cc_final: 0.7149 (mmmt) outliers start: 14 outliers final: 9 residues processed: 47 average time/residue: 0.2525 time to fit residues: 14.4472 Evaluate side-chains 53 residues out of total 454 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 40 time to evaluate : 0.512 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 3 SER Chi-restraints excluded: chain A residue 34 LEU Chi-restraints excluded: chain A residue 76 MET Chi-restraints excluded: chain B residue 14 LEU Chi-restraints excluded: chain B residue 26 GLU Chi-restraints excluded: chain B residue 90 GLU Chi-restraints excluded: chain B residue 134 VAL Chi-restraints excluded: chain C residue 34 LEU Chi-restraints excluded: chain C residue 76 MET Chi-restraints excluded: chain C residue 89 HIS Chi-restraints excluded: chain D residue 17 LYS Chi-restraints excluded: chain D residue 43 GLU Chi-restraints excluded: chain D residue 78 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 56 random chunks: chunk 42 optimal weight: 2.9990 chunk 38 optimal weight: 1.9990 chunk 36 optimal weight: 6.9990 chunk 41 optimal weight: 0.0970 chunk 48 optimal weight: 0.8980 chunk 54 optimal weight: 0.9990 chunk 7 optimal weight: 2.9990 chunk 33 optimal weight: 0.6980 chunk 21 optimal weight: 0.6980 chunk 51 optimal weight: 7.9990 chunk 28 optimal weight: 0.7980 overall best weight: 0.6378 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 89 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3655 r_free = 0.3655 target = 0.157678 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3420 r_free = 0.3420 target = 0.135660 restraints weight = 4198.920| |-----------------------------------------------------------------------------| r_work (start): 0.3422 rms_B_bonded: 0.95 r_work: 0.3243 rms_B_bonded: 2.27 restraints_weight: 0.5000 r_work: 0.3097 rms_B_bonded: 3.83 restraints_weight: 0.2500 r_work (final): 0.3097 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8093 moved from start: 0.1723 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.142 4614 Z= 0.135 Angle : 0.564 6.519 6330 Z= 0.257 Chirality : 0.038 0.125 692 Planarity : 0.005 0.045 790 Dihedral : 9.657 82.529 620 Min Nonbonded Distance : 2.545 Molprobity Statistics. All-atom Clashscore : 3.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.43 % Favored : 98.57 % Rotamer: Outliers : 3.30 % Allowed : 9.47 % Favored : 87.22 % 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: 3.12 (0.36), residues: 558 helix: 2.57 (0.24), residues: 436 sheet: None (None), residues: 0 loop : 0.21 (0.58), residues: 122 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP C 14 HIS 0.007 0.001 HIS C 89 PHE 0.007 0.001 PHE D 85 TYR 0.005 0.001 TYR A 42 ARG 0.002 0.000 ARG A 92 Details of bonding type rmsd hydrogen bonds : bond 0.03418 ( 343) hydrogen bonds : angle 3.91752 ( 978) covalent geometry : bond 0.00364 ( 4610) covalent geometry : angle 0.56379 ( 6330) Misc. bond : bond 0.09685 ( 4) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1116 Ramachandran restraints generated. 558 Oldfield, 0 Emsley, 558 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1116 Ramachandran restraints generated. 558 Oldfield, 0 Emsley, 558 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 55 residues out of total 454 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 40 time to evaluate : 0.474 Fit side-chains REVERT: A 60 LYS cc_start: 0.8134 (tptp) cc_final: 0.7606 (ttmm) REVERT: A 61 LYS cc_start: 0.8004 (mtpp) cc_final: 0.7595 (mtpt) REVERT: A 92 ARG cc_start: 0.8687 (mtt-85) cc_final: 0.7844 (mtm-85) REVERT: B 8 LYS cc_start: 0.7541 (tppt) cc_final: 0.7154 (mttm) REVERT: B 26 GLU cc_start: 0.7698 (OUTLIER) cc_final: 0.7494 (mm-30) REVERT: B 66 LYS cc_start: 0.8380 (mmmm) cc_final: 0.7835 (mtpt) REVERT: C 60 LYS cc_start: 0.7987 (tptp) cc_final: 0.7311 (tppt) REVERT: C 76 MET cc_start: 0.7206 (OUTLIER) cc_final: 0.6847 (mtt) REVERT: D 43 GLU cc_start: 0.7511 (OUTLIER) cc_final: 0.6683 (pm20) REVERT: D 120 LYS cc_start: 0.7493 (mmtp) cc_final: 0.7150 (mmmt) outliers start: 15 outliers final: 10 residues processed: 48 average time/residue: 0.2304 time to fit residues: 13.5080 Evaluate side-chains 53 residues out of total 454 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 40 time to evaluate : 0.502 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 3 SER Chi-restraints excluded: chain A residue 34 LEU Chi-restraints excluded: chain B residue 14 LEU Chi-restraints excluded: chain B residue 21 ASP Chi-restraints excluded: chain B residue 26 GLU Chi-restraints excluded: chain B residue 90 GLU Chi-restraints excluded: chain B residue 134 VAL Chi-restraints excluded: chain C residue 34 LEU Chi-restraints excluded: chain C residue 76 MET Chi-restraints excluded: chain C residue 89 HIS Chi-restraints excluded: chain D residue 17 LYS Chi-restraints excluded: chain D residue 43 GLU Chi-restraints excluded: chain D residue 78 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 56 random chunks: chunk 30 optimal weight: 0.9980 chunk 35 optimal weight: 0.9980 chunk 19 optimal weight: 0.2980 chunk 53 optimal weight: 1.9990 chunk 16 optimal weight: 0.6980 chunk 38 optimal weight: 0.5980 chunk 33 optimal weight: 1.9990 chunk 0 optimal weight: 4.9990 chunk 41 optimal weight: 0.0770 chunk 31 optimal weight: 0.6980 chunk 42 optimal weight: 3.9990 overall best weight: 0.4738 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 89 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3668 r_free = 0.3668 target = 0.158859 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.3414 r_free = 0.3414 target = 0.134779 restraints weight = 4224.888| |-----------------------------------------------------------------------------| r_work (start): 0.3386 rms_B_bonded: 1.18 r_work: 0.3244 rms_B_bonded: 2.17 restraints_weight: 0.5000 r_work: 0.3088 rms_B_bonded: 3.66 restraints_weight: 0.2500 r_work (final): 0.3088 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7993 moved from start: 0.1719 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.135 4614 Z= 0.118 Angle : 0.549 6.277 6330 Z= 0.248 Chirality : 0.037 0.120 692 Planarity : 0.005 0.045 790 Dihedral : 9.607 82.127 620 Min Nonbonded Distance : 2.534 Molprobity Statistics. All-atom Clashscore : 3.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.61 % Favored : 98.39 % Rotamer: Outliers : 2.86 % Allowed : 9.69 % Favored : 87.44 % 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: 3.15 (0.36), residues: 558 helix: 2.60 (0.24), residues: 436 sheet: None (None), residues: 0 loop : 0.17 (0.58), residues: 122 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP C 14 HIS 0.005 0.001 HIS C 89 PHE 0.006 0.001 PHE C 43 TYR 0.005 0.001 TYR B 35 ARG 0.002 0.000 ARG A 92 Details of bonding type rmsd hydrogen bonds : bond 0.03174 ( 343) hydrogen bonds : angle 3.86683 ( 978) covalent geometry : bond 0.00316 ( 4610) covalent geometry : angle 0.54938 ( 6330) Misc. bond : bond 0.08852 ( 4) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3185.08 seconds wall clock time: 57 minutes 25.40 seconds (3445.40 seconds total)