Starting phenix.real_space_refine on Wed Sep 17 03:15:00 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8xh6_38342/09_2025/8xh6_38342_neut.cif Found real_map, /net/cci-nas-00/data/ceres_data/8xh6_38342/09_2025/8xh6_38342.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.52 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/8xh6_38342/09_2025/8xh6_38342_neut.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8xh6_38342/09_2025/8xh6_38342_neut.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8xh6_38342/09_2025/8xh6_38342.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8xh6_38342/09_2025/8xh6_38342.map" } resolution = 3.52 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.001 sd= 0.083 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 14 5.16 5 C 1870 2.51 5 N 378 2.21 5 O 372 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 2 residue(s): 0.00s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5805/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 2634 Number of models: 1 Model: "" Number of chains: 2 Chain: "A" Number of atoms: 1317 Number of conformers: 1 Conformer: "" Number of residues, atoms: 161, 1317 Classifications: {'peptide': 161} Link IDs: {'PTRANS': 1, 'TRANS': 159} Chain: "B" Number of atoms: 1317 Number of conformers: 1 Conformer: "" Number of residues, atoms: 161, 1317 Classifications: {'peptide': 161} Link IDs: {'PTRANS': 1, 'TRANS': 159} Time building chain proxies: 1.00, per 1000 atoms: 0.38 Number of scatterers: 2634 At special positions: 0 Unit cell: (57.2, 71.76, 70.72, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 14 16.00 O 372 8.00 N 378 7.00 C 1870 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: 0.17 Conformation dependent library (CDL) restraints added in 78.7 milliseconds Enol-peptide restraints added in 1.2 microseconds 636 Ramachandran restraints generated. 318 Oldfield, 0 Emsley, 318 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 600 Finding SS restraints... Secondary structure from input PDB file: 14 helices and 0 sheets defined 90.1% alpha, 0.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.08 Creating SS restraints... Processing helix chain 'A' and resid 24 through 45 removed outlier: 4.261A pdb=" N LEU A 37 " --> pdb=" O LEU A 33 " (cutoff:3.500A) removed outlier: 3.594A pdb=" N LEU A 40 " --> pdb=" O LEU A 36 " (cutoff:3.500A) removed outlier: 4.083A pdb=" N TYR A 41 " --> pdb=" O LEU A 37 " (cutoff:3.500A) Processing helix chain 'A' and resid 50 through 72 removed outlier: 4.057A pdb=" N VAL A 54 " --> pdb=" O GLY A 50 " (cutoff:3.500A) removed outlier: 3.750A pdb=" N LEU A 55 " --> pdb=" O ALA A 51 " (cutoff:3.500A) Processing helix chain 'A' and resid 73 through 77 removed outlier: 3.821A pdb=" N LEU A 76 " --> pdb=" O ARG A 73 " (cutoff:3.500A) Processing helix chain 'A' and resid 80 through 99 removed outlier: 4.399A pdb=" N ASN A 99 " --> pdb=" O ILE A 95 " (cutoff:3.500A) Processing helix chain 'A' and resid 103 through 132 removed outlier: 4.115A pdb=" N LEU A 107 " --> pdb=" O GLN A 103 " (cutoff:3.500A) removed outlier: 3.617A pdb=" N LEU A 111 " --> pdb=" O LEU A 107 " (cutoff:3.500A) Processing helix chain 'A' and resid 136 through 160 Processing helix chain 'A' and resid 162 through 183 removed outlier: 3.534A pdb=" N THR A 166 " --> pdb=" O GLN A 162 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N LEU A 168 " --> pdb=" O TRP A 164 " (cutoff:3.500A) Processing helix chain 'B' and resid 25 through 44 removed outlier: 3.734A pdb=" N MET B 44 " --> pdb=" O LEU B 40 " (cutoff:3.500A) Processing helix chain 'B' and resid 52 through 72 Processing helix chain 'B' and resid 73 through 77 removed outlier: 3.874A pdb=" N LEU B 76 " --> pdb=" O ARG B 73 " (cutoff:3.500A) Processing helix chain 'B' and resid 80 through 100 removed outlier: 4.401A pdb=" N ILE B 95 " --> pdb=" O THR B 91 " (cutoff:3.500A) removed outlier: 3.897A pdb=" N ALA B 96 " --> pdb=" O LEU B 92 " (cutoff:3.500A) removed outlier: 3.891A pdb=" N LEU B 100 " --> pdb=" O ALA B 96 " (cutoff:3.500A) Processing helix chain 'B' and resid 103 through 133 removed outlier: 4.065A pdb=" N LEU B 107 " --> pdb=" O GLN B 103 " (cutoff:3.500A) removed outlier: 3.526A pdb=" N LEU B 118 " --> pdb=" O PHE B 114 " (cutoff:3.500A) removed outlier: 3.704A pdb=" N GLY B 121 " --> pdb=" O LEU B 117 " (cutoff:3.500A) Processing helix chain 'B' and resid 136 through 160 removed outlier: 3.744A pdb=" N PHE B 143 " --> pdb=" O GLN B 139 " (cutoff:3.500A) removed outlier: 3.964A pdb=" N ILE B 144 " --> pdb=" O LEU B 140 " (cutoff:3.500A) removed outlier: 3.742A pdb=" N TYR B 159 " --> pdb=" O ILE B 155 " (cutoff:3.500A) Processing helix chain 'B' and resid 164 through 183 removed outlier: 4.109A pdb=" N LEU B 181 " --> pdb=" O PHE B 177 " (cutoff:3.500A) 213 hydrogen bonds defined for protein. 633 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 0.40 Time building geometry restraints manager: 0.22 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.34: 703 1.34 - 1.46: 689 1.46 - 1.58: 1292 1.58 - 1.69: 0 1.69 - 1.81: 24 Bond restraints: 2708 Sorted by residual: bond pdb=" CA TRP A 131 " pdb=" C TRP A 131 " ideal model delta sigma weight residual 1.522 1.499 0.023 1.41e-02 5.03e+03 2.74e+00 bond pdb=" CG1 ILE B 95 " pdb=" CD1 ILE B 95 " ideal model delta sigma weight residual 1.513 1.473 0.040 3.90e-02 6.57e+02 1.03e+00 bond pdb=" CG LEU B 60 " pdb=" CD1 LEU B 60 " ideal model delta sigma weight residual 1.521 1.494 0.027 3.30e-02 9.18e+02 6.69e-01 bond pdb=" CG ARG A 74 " pdb=" CD ARG A 74 " ideal model delta sigma weight residual 1.520 1.543 -0.023 3.00e-02 1.11e+03 5.85e-01 bond pdb=" N MET A 184 " pdb=" CA MET A 184 " ideal model delta sigma weight residual 1.458 1.472 -0.014 1.90e-02 2.77e+03 5.06e-01 ... (remaining 2703 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.23: 3548 1.23 - 2.47: 121 2.47 - 3.70: 25 3.70 - 4.94: 10 4.94 - 6.17: 4 Bond angle restraints: 3708 Sorted by residual: angle pdb=" C LEU A 130 " pdb=" N TRP A 131 " pdb=" CA TRP A 131 " ideal model delta sigma weight residual 120.60 125.40 -4.80 1.60e+00 3.91e-01 8.99e+00 angle pdb=" N ILE B 71 " pdb=" CA ILE B 71 " pdb=" C ILE B 71 " ideal model delta sigma weight residual 111.58 108.76 2.82 1.06e+00 8.90e-01 7.10e+00 angle pdb=" C TRP A 183 " pdb=" N MET A 184 " pdb=" CA MET A 184 " ideal model delta sigma weight residual 121.70 125.85 -4.15 1.80e+00 3.09e-01 5.31e+00 angle pdb=" CB MET A 61 " pdb=" CG MET A 61 " pdb=" SD MET A 61 " ideal model delta sigma weight residual 112.70 118.32 -5.62 3.00e+00 1.11e-01 3.51e+00 angle pdb=" C ILE A 109 " pdb=" CA ILE A 109 " pdb=" CB ILE A 109 " ideal model delta sigma weight residual 111.97 109.70 2.27 1.28e+00 6.10e-01 3.14e+00 ... (remaining 3703 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.00: 1320 16.00 - 32.01: 138 32.01 - 48.01: 31 48.01 - 64.02: 1 64.02 - 80.02: 4 Dihedral angle restraints: 1494 sinusoidal: 564 harmonic: 930 Sorted by residual: dihedral pdb=" CB MET B 89 " pdb=" CG MET B 89 " pdb=" SD MET B 89 " pdb=" CE MET B 89 " ideal model delta sinusoidal sigma weight residual 60.00 116.18 -56.18 3 1.50e+01 4.44e-03 9.39e+00 dihedral pdb=" CB GLU B 128 " pdb=" CG GLU B 128 " pdb=" CD GLU B 128 " pdb=" OE1 GLU B 128 " ideal model delta sinusoidal sigma weight residual 0.00 -80.02 80.02 1 3.00e+01 1.11e-03 8.82e+00 dihedral pdb=" CA LEU B 174 " pdb=" CB LEU B 174 " pdb=" CG LEU B 174 " pdb=" CD1 LEU B 174 " ideal model delta sinusoidal sigma weight residual 180.00 136.71 43.29 3 1.50e+01 4.44e-03 7.78e+00 ... (remaining 1491 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.021: 219 0.021 - 0.042: 137 0.042 - 0.063: 84 0.063 - 0.084: 27 0.084 - 0.106: 7 Chirality restraints: 474 Sorted by residual: chirality pdb=" CA CYS A 78 " pdb=" N CYS A 78 " pdb=" C CYS A 78 " pdb=" CB CYS A 78 " both_signs ideal model delta sigma weight residual False 2.51 2.40 0.11 2.00e-01 2.50e+01 2.78e-01 chirality pdb=" CA THR A 91 " pdb=" N THR A 91 " pdb=" C THR A 91 " pdb=" CB THR A 91 " both_signs ideal model delta sigma weight residual False 2.53 2.43 0.09 2.00e-01 2.50e+01 2.20e-01 chirality pdb=" CG LEU A 60 " pdb=" CB LEU A 60 " pdb=" CD1 LEU A 60 " pdb=" CD2 LEU A 60 " both_signs ideal model delta sigma weight residual False -2.59 -2.68 0.09 2.00e-01 2.50e+01 2.03e-01 ... (remaining 471 not shown) Planarity restraints: 402 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CD ARG A 74 " -0.102 9.50e-02 1.11e+02 4.62e-02 1.74e+00 pdb=" NE ARG A 74 " 0.010 2.00e-02 2.50e+03 pdb=" CZ ARG A 74 " -0.010 2.00e-02 2.50e+03 pdb=" NH1 ARG A 74 " 0.005 2.00e-02 2.50e+03 pdb=" NH2 ARG A 74 " 0.000 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C CYS B 78 " 0.015 5.00e-02 4.00e+02 2.32e-02 8.59e-01 pdb=" N PRO B 79 " -0.040 5.00e-02 4.00e+02 pdb=" CA PRO B 79 " 0.011 5.00e-02 4.00e+02 pdb=" CD PRO B 79 " 0.013 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C CYS A 78 " -0.015 5.00e-02 4.00e+02 2.23e-02 7.95e-01 pdb=" N PRO A 79 " 0.039 5.00e-02 4.00e+02 pdb=" CA PRO A 79 " -0.011 5.00e-02 4.00e+02 pdb=" CD PRO A 79 " -0.013 5.00e-02 4.00e+02 ... (remaining 399 not shown) Histogram of nonbonded interaction distances: 2.40 - 2.90: 919 2.90 - 3.40: 2794 3.40 - 3.90: 4364 3.90 - 4.40: 4625 4.40 - 4.90: 7627 Nonbonded interactions: 20329 Sorted by model distance: nonbonded pdb=" OD1 ASN B 99 " pdb=" N LEU B 100 " model vdw 2.397 3.120 nonbonded pdb=" O ASN B 46 " pdb=" ND2 ASN B 163 " model vdw 2.406 3.120 nonbonded pdb=" O THR A 48 " pdb=" OG1 THR A 48 " model vdw 2.460 3.040 nonbonded pdb=" O PHE B 70 " pdb=" NE ARG B 74 " model vdw 2.590 3.120 nonbonded pdb=" OG SER B 45 " pdb=" N ASN B 46 " model vdw 2.616 3.120 ... (remaining 20324 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 'B' } 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: 1.150 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: 0.050 Check model and map are aligned: 0.000 Set scattering table: 0.010 Process input model: 4.670 Find NCS groups from input model: 0.040 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:1.210 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 7.140 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7236 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 2708 Z= 0.140 Angle : 0.586 6.169 3708 Z= 0.297 Chirality : 0.036 0.106 474 Planarity : 0.003 0.046 402 Dihedral : 14.079 80.022 894 Min Nonbonded Distance : 2.397 Molprobity Statistics. All-atom Clashscore : 7.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.83 % Favored : 97.17 % Rotamer: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % 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 aren not related in a simple way. whole: 1.24 (0.47), residues: 318 helix: 1.16 (0.31), residues: 284 sheet: None (None), residues: 0 loop : -1.56 (1.07), residues: 34 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.001 ARG A 74 TYR 0.007 0.001 TYR A 159 PHE 0.011 0.001 PHE A 72 TRP 0.005 0.001 TRP A 164 HIS 0.001 0.001 HIS A 101 Details of bonding type rmsd covalent geometry : bond 0.00320 ( 2708) covalent geometry : angle 0.58618 ( 3708) hydrogen bonds : bond 0.15739 ( 213) hydrogen bonds : angle 5.18102 ( 633) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 636 Ramachandran restraints generated. 318 Oldfield, 0 Emsley, 318 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 636 Ramachandran restraints generated. 318 Oldfield, 0 Emsley, 318 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 37 residues out of total 276 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 37 time to evaluate : 0.091 Fit side-chains REVERT: A 161 GLN cc_start: 0.6670 (mt0) cc_final: 0.6451 (mt0) outliers start: 0 outliers final: 0 residues processed: 37 average time/residue: 0.0548 time to fit residues: 2.5681 Evaluate side-chains 32 residues out of total 276 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 32 time to evaluate : 0.097 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 32 random chunks: chunk 24 optimal weight: 0.6980 chunk 26 optimal weight: 0.7980 chunk 2 optimal weight: 0.9980 chunk 16 optimal weight: 1.9990 chunk 31 optimal weight: 1.9990 chunk 25 optimal weight: 0.8980 chunk 19 optimal weight: 0.9980 chunk 30 optimal weight: 0.5980 chunk 22 optimal weight: 0.8980 chunk 13 optimal weight: 0.9990 chunk 8 optimal weight: 0.0170 overall best weight: 0.6018 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4034 r_free = 0.4034 target = 0.174543 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3747 r_free = 0.3747 target = 0.146826 restraints weight = 3167.692| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 42)----------------| | r_work = 0.3789 r_free = 0.3789 target = 0.150804 restraints weight = 1883.539| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3817 r_free = 0.3817 target = 0.153444 restraints weight = 1370.753| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.3832 r_free = 0.3832 target = 0.154903 restraints weight = 1111.649| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 37)----------------| | r_work = 0.3845 r_free = 0.3845 target = 0.156111 restraints weight = 976.812| |-----------------------------------------------------------------------------| r_work (final): 0.3849 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7282 moved from start: 0.1262 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 2708 Z= 0.137 Angle : 0.535 5.868 3708 Z= 0.251 Chirality : 0.035 0.096 474 Planarity : 0.003 0.024 402 Dihedral : 3.798 10.454 336 Min Nonbonded Distance : 2.521 Molprobity Statistics. All-atom Clashscore : 7.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.83 % Favored : 97.17 % Rotamer: Outliers : 1.09 % Allowed : 11.23 % Favored : 87.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.65 (0.46), residues: 318 helix: 1.39 (0.30), residues: 288 sheet: None (None), residues: 0 loop : -1.47 (1.16), residues: 30 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG A 74 TYR 0.005 0.001 TYR B 125 PHE 0.014 0.001 PHE A 38 TRP 0.009 0.001 TRP A 131 HIS 0.001 0.001 HIS B 101 Details of bonding type rmsd covalent geometry : bond 0.00321 ( 2708) covalent geometry : angle 0.53532 ( 3708) hydrogen bonds : bond 0.03770 ( 213) hydrogen bonds : angle 3.41824 ( 633) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 636 Ramachandran restraints generated. 318 Oldfield, 0 Emsley, 318 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 636 Ramachandran restraints generated. 318 Oldfield, 0 Emsley, 318 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 43 residues out of total 276 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 40 time to evaluate : 0.092 Fit side-chains REVERT: A 161 GLN cc_start: 0.6792 (mt0) cc_final: 0.6492 (mt0) REVERT: B 184 MET cc_start: 0.5711 (tpp) cc_final: 0.5470 (mmm) outliers start: 3 outliers final: 2 residues processed: 42 average time/residue: 0.0470 time to fit residues: 2.5307 Evaluate side-chains 38 residues out of total 276 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 36 time to evaluate : 0.073 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 40 LEU Chi-restraints excluded: chain B residue 99 ASN Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 32 random chunks: chunk 6 optimal weight: 0.9990 chunk 4 optimal weight: 0.9990 chunk 8 optimal weight: 0.7980 chunk 31 optimal weight: 0.8980 chunk 2 optimal weight: 0.8980 chunk 14 optimal weight: 0.8980 chunk 22 optimal weight: 0.3980 chunk 13 optimal weight: 0.6980 chunk 11 optimal weight: 2.9990 chunk 25 optimal weight: 0.9990 chunk 12 optimal weight: 2.9990 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4011 r_free = 0.4011 target = 0.171615 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3710 r_free = 0.3710 target = 0.143011 restraints weight = 3208.000| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3748 r_free = 0.3748 target = 0.146731 restraints weight = 1936.759| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 42)----------------| | r_work = 0.3778 r_free = 0.3778 target = 0.149436 restraints weight = 1435.228| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3794 r_free = 0.3794 target = 0.150945 restraints weight = 1174.378| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3805 r_free = 0.3805 target = 0.152057 restraints weight = 1034.909| |-----------------------------------------------------------------------------| r_work (final): 0.3806 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7357 moved from start: 0.1688 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.026 2708 Z= 0.147 Angle : 0.522 6.359 3708 Z= 0.247 Chirality : 0.035 0.100 474 Planarity : 0.003 0.029 402 Dihedral : 3.732 11.632 336 Min Nonbonded Distance : 2.531 Molprobity Statistics. All-atom Clashscore : 7.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.14 % Favored : 96.86 % Rotamer: Outliers : 2.54 % Allowed : 14.49 % Favored : 82.97 % 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 aren not related in a simple way. whole: 1.86 (0.46), residues: 318 helix: 1.54 (0.30), residues: 288 sheet: None (None), residues: 0 loop : -1.49 (1.14), residues: 30 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG A 74 TYR 0.006 0.001 TYR A 125 PHE 0.008 0.001 PHE A 177 TRP 0.008 0.001 TRP A 131 HIS 0.001 0.000 HIS A 101 Details of bonding type rmsd covalent geometry : bond 0.00354 ( 2708) covalent geometry : angle 0.52199 ( 3708) hydrogen bonds : bond 0.03596 ( 213) hydrogen bonds : angle 3.20608 ( 633) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 636 Ramachandran restraints generated. 318 Oldfield, 0 Emsley, 318 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 636 Ramachandran restraints generated. 318 Oldfield, 0 Emsley, 318 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 46 residues out of total 276 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 39 time to evaluate : 0.096 Fit side-chains REVERT: A 161 GLN cc_start: 0.6823 (mt0) cc_final: 0.6580 (mt0) REVERT: B 147 PHE cc_start: 0.8566 (t80) cc_final: 0.8174 (t80) outliers start: 7 outliers final: 5 residues processed: 44 average time/residue: 0.0530 time to fit residues: 2.9290 Evaluate side-chains 43 residues out of total 276 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 38 time to evaluate : 0.096 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 36 LEU Chi-restraints excluded: chain A residue 129 ILE Chi-restraints excluded: chain B residue 40 LEU Chi-restraints excluded: chain B residue 99 ASN Chi-restraints excluded: chain B residue 100 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 32 random chunks: chunk 22 optimal weight: 0.5980 chunk 18 optimal weight: 2.9990 chunk 12 optimal weight: 0.6980 chunk 21 optimal weight: 2.9990 chunk 14 optimal weight: 0.9990 chunk 15 optimal weight: 0.9980 chunk 24 optimal weight: 0.9990 chunk 7 optimal weight: 0.8980 chunk 16 optimal weight: 2.9990 chunk 10 optimal weight: 1.9990 chunk 25 optimal weight: 1.9990 overall best weight: 0.8382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3988 r_free = 0.3988 target = 0.169221 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3686 r_free = 0.3686 target = 0.140863 restraints weight = 3194.562| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.3727 r_free = 0.3727 target = 0.144697 restraints weight = 1931.186| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.3754 r_free = 0.3754 target = 0.147285 restraints weight = 1428.132| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3769 r_free = 0.3769 target = 0.148690 restraints weight = 1171.656| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 36)----------------| | r_work = 0.3782 r_free = 0.3782 target = 0.149866 restraints weight = 1037.543| |-----------------------------------------------------------------------------| r_work (final): 0.3783 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7377 moved from start: 0.1900 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.026 2708 Z= 0.159 Angle : 0.527 6.051 3708 Z= 0.250 Chirality : 0.035 0.103 474 Planarity : 0.003 0.030 402 Dihedral : 3.783 12.121 336 Min Nonbonded Distance : 2.528 Molprobity Statistics. All-atom Clashscore : 7.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.46 % Favored : 96.54 % Rotamer: Outliers : 2.90 % Allowed : 19.57 % Favored : 77.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.99 (0.47), residues: 318 helix: 1.61 (0.30), residues: 288 sheet: None (None), residues: 0 loop : -1.31 (1.21), residues: 30 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.001 ARG A 74 TYR 0.006 0.001 TYR A 125 PHE 0.009 0.001 PHE A 177 TRP 0.008 0.001 TRP A 131 HIS 0.001 0.000 HIS A 101 Details of bonding type rmsd covalent geometry : bond 0.00384 ( 2708) covalent geometry : angle 0.52716 ( 3708) hydrogen bonds : bond 0.03594 ( 213) hydrogen bonds : angle 3.15405 ( 633) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 636 Ramachandran restraints generated. 318 Oldfield, 0 Emsley, 318 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 636 Ramachandran restraints generated. 318 Oldfield, 0 Emsley, 318 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 45 residues out of total 276 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 37 time to evaluate : 0.093 Fit side-chains REVERT: A 159 TYR cc_start: 0.6718 (m-10) cc_final: 0.6385 (m-80) REVERT: A 161 GLN cc_start: 0.6923 (mt0) cc_final: 0.6614 (mt0) REVERT: A 172 LEU cc_start: 0.7789 (tt) cc_final: 0.7310 (mt) REVERT: B 147 PHE cc_start: 0.8557 (t80) cc_final: 0.8143 (t80) REVERT: B 184 MET cc_start: 0.6369 (tpp) cc_final: 0.5459 (mmt) outliers start: 8 outliers final: 4 residues processed: 44 average time/residue: 0.0569 time to fit residues: 3.0526 Evaluate side-chains 40 residues out of total 276 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 36 time to evaluate : 0.080 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 54 VAL Chi-restraints excluded: chain A residue 129 ILE Chi-restraints excluded: chain B residue 40 LEU Chi-restraints excluded: chain B residue 100 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 32 random chunks: chunk 22 optimal weight: 0.5980 chunk 17 optimal weight: 0.5980 chunk 5 optimal weight: 2.9990 chunk 0 optimal weight: 2.9990 chunk 1 optimal weight: 0.5980 chunk 29 optimal weight: 0.1980 chunk 3 optimal weight: 0.2980 chunk 9 optimal weight: 0.8980 chunk 16 optimal weight: 0.8980 chunk 19 optimal weight: 0.9990 chunk 4 optimal weight: 0.7980 overall best weight: 0.4580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4012 r_free = 0.4012 target = 0.171592 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3709 r_free = 0.3709 target = 0.143186 restraints weight = 3145.605| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 23)----------------| | r_work = 0.3749 r_free = 0.3749 target = 0.147048 restraints weight = 1909.732| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 41)----------------| | r_work = 0.3780 r_free = 0.3780 target = 0.149696 restraints weight = 1404.381| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3795 r_free = 0.3795 target = 0.151227 restraints weight = 1149.783| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 36)----------------| | r_work = 0.3810 r_free = 0.3810 target = 0.152491 restraints weight = 1012.351| |-----------------------------------------------------------------------------| r_work (final): 0.3809 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7321 moved from start: 0.2043 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 2708 Z= 0.109 Angle : 0.474 6.177 3708 Z= 0.224 Chirality : 0.034 0.100 474 Planarity : 0.002 0.028 402 Dihedral : 3.619 10.959 336 Min Nonbonded Distance : 2.478 Molprobity Statistics. All-atom Clashscore : 7.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.77 % Favored : 96.23 % Rotamer: Outliers : 2.54 % Allowed : 22.46 % Favored : 75.00 % 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 aren not related in a simple way. whole: 2.43 (0.46), residues: 318 helix: 1.90 (0.30), residues: 288 sheet: None (None), residues: 0 loop : -1.14 (1.21), residues: 30 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 74 TYR 0.006 0.001 TYR A 125 PHE 0.007 0.001 PHE A 177 TRP 0.005 0.001 TRP A 131 HIS 0.001 0.000 HIS A 101 Details of bonding type rmsd covalent geometry : bond 0.00251 ( 2708) covalent geometry : angle 0.47350 ( 3708) hydrogen bonds : bond 0.03222 ( 213) hydrogen bonds : angle 2.97591 ( 633) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 636 Ramachandran restraints generated. 318 Oldfield, 0 Emsley, 318 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 636 Ramachandran restraints generated. 318 Oldfield, 0 Emsley, 318 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 40 residues out of total 276 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 33 time to evaluate : 0.082 Fit side-chains REVERT: A 159 TYR cc_start: 0.6647 (m-10) cc_final: 0.6366 (m-80) REVERT: A 161 GLN cc_start: 0.6761 (mt0) cc_final: 0.6442 (mt0) REVERT: B 147 PHE cc_start: 0.8576 (t80) cc_final: 0.8190 (t80) REVERT: B 184 MET cc_start: 0.6103 (tpp) cc_final: 0.5384 (mmt) outliers start: 7 outliers final: 3 residues processed: 40 average time/residue: 0.0582 time to fit residues: 2.8611 Evaluate side-chains 35 residues out of total 276 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 32 time to evaluate : 0.058 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 36 LEU Chi-restraints excluded: chain A residue 129 ILE Chi-restraints excluded: chain B residue 42 ILE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 32 random chunks: chunk 29 optimal weight: 0.9990 chunk 18 optimal weight: 2.9990 chunk 17 optimal weight: 0.5980 chunk 9 optimal weight: 0.8980 chunk 16 optimal weight: 0.3980 chunk 14 optimal weight: 0.6980 chunk 26 optimal weight: 2.9990 chunk 13 optimal weight: 0.6980 chunk 15 optimal weight: 0.8980 chunk 2 optimal weight: 2.9990 chunk 8 optimal weight: 2.9990 overall best weight: 0.6580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3994 r_free = 0.3994 target = 0.169520 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3683 r_free = 0.3683 target = 0.140857 restraints weight = 3150.717| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3727 r_free = 0.3727 target = 0.144854 restraints weight = 1905.619| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3756 r_free = 0.3756 target = 0.147461 restraints weight = 1407.616| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 35)----------------| | r_work = 0.3775 r_free = 0.3775 target = 0.149159 restraints weight = 1151.247| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3784 r_free = 0.3784 target = 0.149994 restraints weight = 1004.263| |-----------------------------------------------------------------------------| r_work (final): 0.3790 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7364 moved from start: 0.2129 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 2708 Z= 0.135 Angle : 0.513 6.866 3708 Z= 0.237 Chirality : 0.035 0.101 474 Planarity : 0.002 0.029 402 Dihedral : 3.638 10.644 336 Min Nonbonded Distance : 2.501 Molprobity Statistics. All-atom Clashscore : 7.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.77 % Favored : 96.23 % Rotamer: Outliers : 3.62 % Allowed : 21.38 % Favored : 75.00 % 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 aren not related in a simple way. whole: 2.48 (0.46), residues: 318 helix: 1.92 (0.29), residues: 288 sheet: None (None), residues: 0 loop : -0.99 (1.25), residues: 30 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 132 TYR 0.005 0.001 TYR A 125 PHE 0.007 0.001 PHE A 177 TRP 0.007 0.001 TRP A 131 HIS 0.001 0.000 HIS A 101 Details of bonding type rmsd covalent geometry : bond 0.00319 ( 2708) covalent geometry : angle 0.51337 ( 3708) hydrogen bonds : bond 0.03370 ( 213) hydrogen bonds : angle 2.98533 ( 633) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 636 Ramachandran restraints generated. 318 Oldfield, 0 Emsley, 318 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 636 Ramachandran restraints generated. 318 Oldfield, 0 Emsley, 318 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 47 residues out of total 276 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 37 time to evaluate : 0.107 Fit side-chains REVERT: A 159 TYR cc_start: 0.6703 (m-10) cc_final: 0.6443 (m-80) REVERT: A 161 GLN cc_start: 0.6789 (mt0) cc_final: 0.6502 (mt0) REVERT: A 172 LEU cc_start: 0.7826 (tt) cc_final: 0.7284 (mt) REVERT: B 147 PHE cc_start: 0.8556 (t80) cc_final: 0.8166 (t80) outliers start: 10 outliers final: 5 residues processed: 45 average time/residue: 0.0749 time to fit residues: 4.0058 Evaluate side-chains 39 residues out of total 276 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 34 time to evaluate : 0.069 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 36 LEU Chi-restraints excluded: chain A residue 54 VAL Chi-restraints excluded: chain A residue 129 ILE Chi-restraints excluded: chain A residue 184 MET Chi-restraints excluded: chain B residue 42 ILE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 32 random chunks: chunk 21 optimal weight: 0.3980 chunk 25 optimal weight: 0.9990 chunk 12 optimal weight: 0.6980 chunk 22 optimal weight: 0.5980 chunk 26 optimal weight: 1.9990 chunk 30 optimal weight: 2.9990 chunk 13 optimal weight: 0.5980 chunk 29 optimal weight: 0.0980 chunk 23 optimal weight: 0.2980 chunk 9 optimal weight: 0.6980 chunk 14 optimal weight: 0.5980 overall best weight: 0.3980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4023 r_free = 0.4023 target = 0.172453 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3717 r_free = 0.3717 target = 0.143808 restraints weight = 3148.807| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3761 r_free = 0.3761 target = 0.147941 restraints weight = 1904.174| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.3792 r_free = 0.3792 target = 0.150671 restraints weight = 1397.240| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 35)----------------| | r_work = 0.3810 r_free = 0.3810 target = 0.152386 restraints weight = 1135.513| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3820 r_free = 0.3820 target = 0.153307 restraints weight = 989.511| |-----------------------------------------------------------------------------| r_work (final): 0.3823 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7314 moved from start: 0.2226 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.026 2708 Z= 0.109 Angle : 0.554 8.858 3708 Z= 0.247 Chirality : 0.034 0.104 474 Planarity : 0.003 0.050 402 Dihedral : 3.596 9.953 336 Min Nonbonded Distance : 2.494 Molprobity Statistics. All-atom Clashscore : 7.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.77 % Favored : 96.23 % Rotamer: Outliers : 2.54 % Allowed : 23.19 % Favored : 74.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 2.73 (0.46), residues: 318 helix: 2.10 (0.29), residues: 288 sheet: None (None), residues: 0 loop : -1.11 (1.18), residues: 30 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.002 ARG A 74 TYR 0.005 0.001 TYR A 125 PHE 0.006 0.001 PHE A 177 TRP 0.006 0.001 TRP A 39 HIS 0.001 0.000 HIS A 101 Details of bonding type rmsd covalent geometry : bond 0.00247 ( 2708) covalent geometry : angle 0.55448 ( 3708) hydrogen bonds : bond 0.03108 ( 213) hydrogen bonds : angle 2.89484 ( 633) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 636 Ramachandran restraints generated. 318 Oldfield, 0 Emsley, 318 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 636 Ramachandran restraints generated. 318 Oldfield, 0 Emsley, 318 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 43 residues out of total 276 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 36 time to evaluate : 0.117 Fit side-chains REVERT: B 147 PHE cc_start: 0.8563 (t80) cc_final: 0.8201 (t80) REVERT: B 184 MET cc_start: 0.6221 (tpp) cc_final: 0.5381 (mmm) outliers start: 7 outliers final: 4 residues processed: 41 average time/residue: 0.0837 time to fit residues: 4.0685 Evaluate side-chains 39 residues out of total 276 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 35 time to evaluate : 0.095 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 36 LEU Chi-restraints excluded: chain A residue 54 VAL Chi-restraints excluded: chain A residue 184 MET Chi-restraints excluded: chain B residue 42 ILE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 32 random chunks: chunk 16 optimal weight: 1.9990 chunk 25 optimal weight: 0.7980 chunk 13 optimal weight: 0.7980 chunk 4 optimal weight: 0.7980 chunk 22 optimal weight: 0.5980 chunk 0 optimal weight: 2.9990 chunk 8 optimal weight: 2.9990 chunk 28 optimal weight: 0.9990 chunk 20 optimal weight: 0.6980 chunk 5 optimal weight: 0.0870 chunk 3 optimal weight: 0.7980 overall best weight: 0.5958 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4003 r_free = 0.4003 target = 0.170620 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3688 r_free = 0.3688 target = 0.141471 restraints weight = 3225.461| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 41)----------------| | r_work = 0.3734 r_free = 0.3734 target = 0.145548 restraints weight = 1946.379| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3759 r_free = 0.3759 target = 0.147948 restraints weight = 1434.565| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 33)----------------| | r_work = 0.3780 r_free = 0.3780 target = 0.149774 restraints weight = 1187.155| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3790 r_free = 0.3790 target = 0.150738 restraints weight = 1036.917| |-----------------------------------------------------------------------------| r_work (final): 0.3793 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7351 moved from start: 0.2312 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 2708 Z= 0.127 Angle : 0.566 8.515 3708 Z= 0.250 Chirality : 0.035 0.135 474 Planarity : 0.003 0.029 402 Dihedral : 3.596 10.141 336 Min Nonbonded Distance : 2.492 Molprobity Statistics. All-atom Clashscore : 7.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.46 % Favored : 96.54 % Rotamer: Outliers : 2.17 % Allowed : 23.55 % Favored : 74.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 2.77 (0.46), residues: 318 helix: 2.13 (0.29), residues: 288 sheet: None (None), residues: 0 loop : -1.18 (1.16), residues: 30 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG A 74 TYR 0.004 0.001 TYR B 41 PHE 0.007 0.001 PHE A 177 TRP 0.005 0.001 TRP A 131 HIS 0.001 0.000 HIS A 101 Details of bonding type rmsd covalent geometry : bond 0.00296 ( 2708) covalent geometry : angle 0.56566 ( 3708) hydrogen bonds : bond 0.03238 ( 213) hydrogen bonds : angle 2.93110 ( 633) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 636 Ramachandran restraints generated. 318 Oldfield, 0 Emsley, 318 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 636 Ramachandran restraints generated. 318 Oldfield, 0 Emsley, 318 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 42 residues out of total 276 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 36 time to evaluate : 0.094 Fit side-chains REVERT: B 74 ARG cc_start: 0.8104 (mpt-90) cc_final: 0.7840 (ttm170) REVERT: B 147 PHE cc_start: 0.8579 (t80) cc_final: 0.8209 (t80) REVERT: B 184 MET cc_start: 0.6040 (tpp) cc_final: 0.5269 (mmm) outliers start: 6 outliers final: 5 residues processed: 41 average time/residue: 0.0771 time to fit residues: 3.7378 Evaluate side-chains 41 residues out of total 276 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 36 time to evaluate : 0.127 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 36 LEU Chi-restraints excluded: chain A residue 54 VAL Chi-restraints excluded: chain A residue 184 MET Chi-restraints excluded: chain B residue 42 ILE Chi-restraints excluded: chain B residue 100 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 32 random chunks: chunk 28 optimal weight: 2.9990 chunk 15 optimal weight: 0.5980 chunk 22 optimal weight: 0.9980 chunk 5 optimal weight: 0.0170 chunk 18 optimal weight: 0.4980 chunk 6 optimal weight: 0.5980 chunk 9 optimal weight: 0.8980 chunk 0 optimal weight: 4.9990 chunk 31 optimal weight: 0.8980 chunk 10 optimal weight: 0.9990 chunk 11 optimal weight: 0.9990 overall best weight: 0.5218 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4003 r_free = 0.4003 target = 0.170541 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3688 r_free = 0.3688 target = 0.141439 restraints weight = 3198.028| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 43)----------------| | r_work = 0.3734 r_free = 0.3734 target = 0.145579 restraints weight = 1917.864| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3762 r_free = 0.3762 target = 0.148208 restraints weight = 1400.858| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 39)----------------| | r_work = 0.3782 r_free = 0.3782 target = 0.149923 restraints weight = 1144.266| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3792 r_free = 0.3792 target = 0.150880 restraints weight = 1002.426| |-----------------------------------------------------------------------------| r_work (final): 0.3799 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7333 moved from start: 0.2373 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 2708 Z= 0.117 Angle : 0.568 8.927 3708 Z= 0.248 Chirality : 0.034 0.116 474 Planarity : 0.003 0.028 402 Dihedral : 3.549 10.107 336 Min Nonbonded Distance : 2.491 Molprobity Statistics. All-atom Clashscore : 7.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.14 % Favored : 96.86 % Rotamer: Outliers : 2.17 % Allowed : 23.55 % Favored : 74.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 2.88 (0.46), residues: 318 helix: 2.19 (0.29), residues: 288 sheet: None (None), residues: 0 loop : -1.02 (1.19), residues: 30 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG A 74 TYR 0.004 0.001 TYR B 41 PHE 0.007 0.001 PHE A 177 TRP 0.006 0.001 TRP A 131 HIS 0.001 0.000 HIS A 101 Details of bonding type rmsd covalent geometry : bond 0.00272 ( 2708) covalent geometry : angle 0.56813 ( 3708) hydrogen bonds : bond 0.03125 ( 213) hydrogen bonds : angle 2.89213 ( 633) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 636 Ramachandran restraints generated. 318 Oldfield, 0 Emsley, 318 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 636 Ramachandran restraints generated. 318 Oldfield, 0 Emsley, 318 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 40 residues out of total 276 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 34 time to evaluate : 0.091 Fit side-chains REVERT: B 74 ARG cc_start: 0.8074 (mpt-90) cc_final: 0.7859 (ttm170) REVERT: B 147 PHE cc_start: 0.8561 (t80) cc_final: 0.8211 (t80) REVERT: B 184 MET cc_start: 0.6102 (tpp) cc_final: 0.5098 (mmm) outliers start: 6 outliers final: 5 residues processed: 39 average time/residue: 0.0792 time to fit residues: 3.6604 Evaluate side-chains 39 residues out of total 276 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 34 time to evaluate : 0.066 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 36 LEU Chi-restraints excluded: chain A residue 54 VAL Chi-restraints excluded: chain A residue 184 MET Chi-restraints excluded: chain B residue 42 ILE Chi-restraints excluded: chain B residue 100 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 32 random chunks: chunk 19 optimal weight: 0.6980 chunk 30 optimal weight: 0.5980 chunk 4 optimal weight: 0.7980 chunk 20 optimal weight: 0.1980 chunk 15 optimal weight: 0.7980 chunk 23 optimal weight: 0.8980 chunk 14 optimal weight: 0.9990 chunk 1 optimal weight: 0.0470 chunk 5 optimal weight: 0.9990 chunk 11 optimal weight: 0.9990 chunk 9 optimal weight: 0.6980 overall best weight: 0.4478 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4029 r_free = 0.4029 target = 0.172647 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3717 r_free = 0.3717 target = 0.143584 restraints weight = 3224.453| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 42)----------------| | r_work = 0.3763 r_free = 0.3763 target = 0.147749 restraints weight = 1943.907| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3793 r_free = 0.3793 target = 0.150477 restraints weight = 1422.083| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 37)----------------| | r_work = 0.3813 r_free = 0.3813 target = 0.152269 restraints weight = 1160.662| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 33)----------------| | r_work = 0.3824 r_free = 0.3824 target = 0.153293 restraints weight = 1010.060| |-----------------------------------------------------------------------------| r_work (final): 0.3825 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7315 moved from start: 0.2427 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 2708 Z= 0.114 Angle : 0.556 9.418 3708 Z= 0.245 Chirality : 0.035 0.116 474 Planarity : 0.002 0.029 402 Dihedral : 3.547 12.088 336 Min Nonbonded Distance : 2.484 Molprobity Statistics. All-atom Clashscore : 7.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.14 % Favored : 96.86 % Rotamer: Outliers : 2.17 % Allowed : 24.28 % Favored : 73.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 2.93 (0.46), residues: 318 helix: 2.22 (0.29), residues: 288 sheet: None (None), residues: 0 loop : -0.93 (1.20), residues: 30 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 132 TYR 0.004 0.001 TYR B 41 PHE 0.006 0.001 PHE A 177 TRP 0.009 0.001 TRP A 39 HIS 0.001 0.000 HIS A 101 Details of bonding type rmsd covalent geometry : bond 0.00261 ( 2708) covalent geometry : angle 0.55570 ( 3708) hydrogen bonds : bond 0.03109 ( 213) hydrogen bonds : angle 2.89684 ( 633) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 636 Ramachandran restraints generated. 318 Oldfield, 0 Emsley, 318 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 636 Ramachandran restraints generated. 318 Oldfield, 0 Emsley, 318 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 41 residues out of total 276 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 35 time to evaluate : 0.090 Fit side-chains REVERT: B 147 PHE cc_start: 0.8527 (t80) cc_final: 0.8182 (t80) REVERT: B 184 MET cc_start: 0.6019 (tpp) cc_final: 0.5068 (mmm) outliers start: 6 outliers final: 5 residues processed: 41 average time/residue: 0.0801 time to fit residues: 3.9591 Evaluate side-chains 40 residues out of total 276 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 35 time to evaluate : 0.115 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 36 LEU Chi-restraints excluded: chain A residue 54 VAL Chi-restraints excluded: chain A residue 144 ILE Chi-restraints excluded: chain B residue 42 ILE Chi-restraints excluded: chain B residue 100 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 32 random chunks: chunk 14 optimal weight: 0.6980 chunk 19 optimal weight: 0.6980 chunk 31 optimal weight: 0.4980 chunk 12 optimal weight: 0.9990 chunk 9 optimal weight: 0.6980 chunk 26 optimal weight: 2.9990 chunk 21 optimal weight: 0.9980 chunk 22 optimal weight: 0.8980 chunk 2 optimal weight: 0.5980 chunk 24 optimal weight: 0.0570 chunk 17 optimal weight: 0.6980 overall best weight: 0.5098 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4028 r_free = 0.4028 target = 0.172546 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3717 r_free = 0.3717 target = 0.143436 restraints weight = 3196.995| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.3762 r_free = 0.3762 target = 0.147555 restraints weight = 1917.664| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3787 r_free = 0.3787 target = 0.150025 restraints weight = 1409.477| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 41)----------------| | r_work = 0.3809 r_free = 0.3809 target = 0.151877 restraints weight = 1162.483| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.3816 r_free = 0.3816 target = 0.152490 restraints weight = 1016.168| |-----------------------------------------------------------------------------| r_work (final): 0.3819 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7343 moved from start: 0.2474 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 2708 Z= 0.120 Angle : 0.569 9.605 3708 Z= 0.249 Chirality : 0.035 0.168 474 Planarity : 0.002 0.029 402 Dihedral : 3.533 11.512 336 Min Nonbonded Distance : 2.484 Molprobity Statistics. All-atom Clashscore : 7.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.46 % Favored : 96.54 % Rotamer: Outliers : 2.17 % Allowed : 23.91 % Favored : 73.91 % 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 aren not related in a simple way. whole: 2.96 (0.46), residues: 318 helix: 2.24 (0.29), residues: 288 sheet: None (None), residues: 0 loop : -0.88 (1.20), residues: 30 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 132 TYR 0.004 0.001 TYR B 41 PHE 0.006 0.001 PHE A 177 TRP 0.009 0.001 TRP A 39 HIS 0.001 0.000 HIS A 101 Details of bonding type rmsd covalent geometry : bond 0.00278 ( 2708) covalent geometry : angle 0.56875 ( 3708) hydrogen bonds : bond 0.03125 ( 213) hydrogen bonds : angle 2.90309 ( 633) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 634.10 seconds wall clock time: 11 minutes 34.60 seconds (694.60 seconds total)