Starting phenix.real_space_refine on Tue Aug 4 11:44:14 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9vjd_60696/08_2026/9vjd_60696.cif Found real_map, /net/cci-nas-00/data/ceres_data/9vjd_60696/08_2026/9vjd_60696.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.86 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9vjd_60696/08_2026/9vjd_60696.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9vjd_60696/08_2026/9vjd_60696.map" model { file = "/net/cci-nas-00/data/ceres_data/9vjd_60696/08_2026/9vjd_60696.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9vjd_60696/08_2026/9vjd_60696.cif" } resolution = 2.86 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= 0.088 sd= 0.463 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: 3 Type Number sf(0) Gaussians C 751 2.51 5 N 200 2.21 5 O 235 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 9 residue(s): 0.00s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.2rc3-6140/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 1186 Number of models: 1 Model: "" Number of chains: 1 Chain: "A" Number of atoms: 1186 Number of conformers: 1 Conformer: "" Number of residues, atoms: 155, 1186 Classifications: {'peptide': 155} Link IDs: {'PCIS': 1, 'PTRANS': 8, 'TRANS': 145} Time building chain proxies: 0.57, per 1000 atoms: 0.48 Number of scatterers: 1186 At special positions: 0 Unit cell: (80.04, 53.82, 48.3, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 3 Type Number sf(0) O 235 8.00 N 200 7.00 C 751 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: 0.10 Conformation dependent library (CDL) restraints added in 52.2 milliseconds 306 Ramachandran restraints generated. 153 Oldfield, 0 Emsley, 153 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 300 Finding SS restraints... Secondary structure from input PDB file: 8 helices and 2 sheets defined 65.2% alpha, 4.5% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.02 Creating SS restraints... Processing helix chain 'A' and resid 7 through 15 removed outlier: 3.762A pdb=" N LEU A 11 " --> pdb=" O PRO A 8 " (cutoff:3.500A) removed outlier: 4.483A pdb=" N ILE A 12 " --> pdb=" O SER A 9 " (cutoff:3.500A) Processing helix chain 'A' and resid 21 through 31 Processing helix chain 'A' and resid 32 through 34 No H-bonds generated for 'chain 'A' and resid 32 through 34' Processing helix chain 'A' and resid 38 through 52 Processing helix chain 'A' and resid 76 through 89 removed outlier: 4.388A pdb=" N ILE A 80 " --> pdb=" O VAL A 76 " (cutoff:3.500A) removed outlier: 3.501A pdb=" N ASP A 89 " --> pdb=" O LEU A 85 " (cutoff:3.500A) Processing helix chain 'A' and resid 92 through 98 removed outlier: 3.565A pdb=" N GLU A 96 " --> pdb=" O ASN A 92 " (cutoff:3.500A) Processing helix chain 'A' and resid 104 through 135 Processing helix chain 'A' and resid 141 through 150 Processing sheet with id=AA1, first strand: chain 'A' and resid 3 through 4 Processing sheet with id=AA2, first strand: chain 'A' and resid 18 through 20 72 hydrogen bonds defined for protein. 198 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: 0.10 Time building geometry restraints manager: 0.14 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.29: 200 1.29 - 1.35: 194 1.35 - 1.42: 125 1.42 - 1.48: 192 1.48 - 1.55: 500 Bond restraints: 1211 Sorted by residual: bond pdb=" C ASN A 102 " pdb=" N PRO A 103 " ideal model delta sigma weight residual 1.332 1.365 -0.033 1.12e-02 7.97e+03 8.58e+00 bond pdb=" CB ASP A 127 " pdb=" CG ASP A 127 " ideal model delta sigma weight residual 1.516 1.545 -0.029 2.50e-02 1.60e+03 1.36e+00 bond pdb=" C SER A 119 " pdb=" O SER A 119 " ideal model delta sigma weight residual 1.237 1.246 -0.009 1.17e-02 7.31e+03 6.45e-01 bond pdb=" CB PRO A 53 " pdb=" CG PRO A 53 " ideal model delta sigma weight residual 1.492 1.453 0.039 5.00e-02 4.00e+02 6.22e-01 bond pdb=" N ALA A 121 " pdb=" CA ALA A 121 " ideal model delta sigma weight residual 1.459 1.449 0.010 1.23e-02 6.61e+03 6.11e-01 ... (remaining 1206 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.18: 1533 1.18 - 2.35: 94 2.35 - 3.53: 16 3.53 - 4.70: 6 4.70 - 5.88: 4 Bond angle restraints: 1653 Sorted by residual: angle pdb=" N VAL A 56 " pdb=" CA VAL A 56 " pdb=" C VAL A 56 " ideal model delta sigma weight residual 113.53 109.73 3.80 9.80e-01 1.04e+00 1.50e+01 angle pdb=" CA ASP A 89 " pdb=" C ASP A 89 " pdb=" N THR A 90 " ideal model delta sigma weight residual 114.76 118.22 -3.46 1.14e+00 7.69e-01 9.20e+00 angle pdb=" C VAL A 98 " pdb=" N ASP A 99 " pdb=" CA ASP A 99 " ideal model delta sigma weight residual 121.80 127.68 -5.88 2.44e+00 1.68e-01 5.80e+00 angle pdb=" CA ASP A 127 " pdb=" CB ASP A 127 " pdb=" CG ASP A 127 " ideal model delta sigma weight residual 112.60 114.94 -2.34 1.00e+00 1.00e+00 5.46e+00 angle pdb=" N ASN A 102 " pdb=" CA ASN A 102 " pdb=" C ASN A 102 " ideal model delta sigma weight residual 109.81 114.93 -5.12 2.21e+00 2.05e-01 5.36e+00 ... (remaining 1648 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 14.29: 618 14.29 - 28.58: 76 28.58 - 42.87: 29 42.87 - 57.16: 4 57.16 - 71.45: 3 Dihedral angle restraints: 730 sinusoidal: 272 harmonic: 458 Sorted by residual: dihedral pdb=" CA TYR A 140 " pdb=" C TYR A 140 " pdb=" N ASP A 141 " pdb=" CA ASP A 141 " ideal model delta harmonic sigma weight residual 180.00 159.93 20.07 0 5.00e+00 4.00e-02 1.61e+01 dihedral pdb=" CA GLN A 37 " pdb=" CB GLN A 37 " pdb=" CG GLN A 37 " pdb=" CD GLN A 37 " ideal model delta sinusoidal sigma weight residual -60.00 -119.15 59.15 3 1.50e+01 4.44e-03 9.48e+00 dihedral pdb=" N SER A 154 " pdb=" CA SER A 154 " pdb=" CB SER A 154 " pdb=" OG SER A 154 " ideal model delta sinusoidal sigma weight residual 60.00 2.18 57.82 3 1.50e+01 4.44e-03 9.45e+00 ... (remaining 727 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.028: 107 0.028 - 0.055: 59 0.055 - 0.083: 14 0.083 - 0.110: 10 0.110 - 0.137: 4 Chirality restraints: 194 Sorted by residual: chirality pdb=" CA VAL A 19 " pdb=" N VAL A 19 " pdb=" C VAL A 19 " pdb=" CB VAL A 19 " both_signs ideal model delta sigma weight residual False 2.44 2.58 -0.14 2.00e-01 2.50e+01 4.71e-01 chirality pdb=" CA GLU A 125 " pdb=" N GLU A 125 " pdb=" C GLU A 125 " pdb=" CB GLU A 125 " both_signs ideal model delta sigma weight residual False 2.51 2.40 0.12 2.00e-01 2.50e+01 3.32e-01 chirality pdb=" CA VAL A 139 " pdb=" N VAL A 139 " pdb=" C VAL A 139 " pdb=" CB VAL A 139 " both_signs ideal model delta sigma weight residual False 2.44 2.55 -0.11 2.00e-01 2.50e+01 3.06e-01 ... (remaining 191 not shown) Planarity restraints: 217 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA ARG A 78 " 0.008 2.00e-02 2.50e+03 1.60e-02 2.57e+00 pdb=" C ARG A 78 " -0.028 2.00e-02 2.50e+03 pdb=" O ARG A 78 " 0.010 2.00e-02 2.50e+03 pdb=" N PRO A 79 " 0.010 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CG GLU A 125 " 0.006 2.00e-02 2.50e+03 1.16e-02 1.34e+00 pdb=" CD GLU A 125 " -0.020 2.00e-02 2.50e+03 pdb=" OE1 GLU A 125 " 0.007 2.00e-02 2.50e+03 pdb=" OE2 GLU A 125 " 0.007 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA GLU A 125 " -0.006 2.00e-02 2.50e+03 1.12e-02 1.25e+00 pdb=" C GLU A 125 " 0.019 2.00e-02 2.50e+03 pdb=" O GLU A 125 " -0.007 2.00e-02 2.50e+03 pdb=" N ILE A 126 " -0.007 2.00e-02 2.50e+03 ... (remaining 214 not shown) Histogram of nonbonded interaction distances: 2.32 - 2.83: 401 2.83 - 3.35: 1094 3.35 - 3.87: 2002 3.87 - 4.38: 2075 4.38 - 4.90: 3826 Nonbonded interactions: 9398 Sorted by model distance: nonbonded pdb=" O PHE A 27 " pdb=" OG SER A 31 " model vdw 2.315 3.040 nonbonded pdb=" O PHE A 63 " pdb=" NH2 ARG A 142 " model vdw 2.384 3.120 nonbonded pdb=" O GLU A 131 " pdb=" OG SER A 134 " model vdw 2.508 3.040 nonbonded pdb=" O GLN A 32 " pdb=" NH1 ARG A 123 " model vdw 2.520 3.120 nonbonded pdb=" N ASP A 65 " pdb=" OD1 ASP A 65 " model vdw 2.534 3.120 ... (remaining 9393 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. 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: 1.250 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: 0.010 Check model and map are aligned: 0.010 Set scattering table: 0.000 Process input model: 3.650 Find NCS groups from input model: 0.000 Set up NCS constraints: 0.000 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:5.830 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 10.750 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9081 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 1211 Z= 0.202 Angle : 0.718 5.876 1653 Z= 0.440 Chirality : 0.042 0.137 194 Planarity : 0.004 0.024 217 Dihedral : 15.447 71.449 430 Min Nonbonded Distance : 2.315 Molprobity Statistics. All-atom Clashscore : 5.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.31 % Favored : 98.69 % Rotamer: Outliers : 1.53 % Allowed : 22.90 % Favored : 75.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 11.11 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.00 (0.68), residues: 153 helix: 2.44 (0.60), residues: 83 sheet: None (None), residues: 0 loop : -0.02 (0.69), residues: 70 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG A 78 TYR 0.003 0.001 TYR A 18 PHE 0.013 0.002 PHE A 81 TRP 0.002 0.001 TRP A 153 Details of bonding type rmsd/Z covalent geometry : bond 0.00377 / 0.20 ( 1211) covalent geometry : angle 0.71805 / 0.44 ( 1653) hydrogen bonds : bond 0.15116 / 9.82 ( 72) hydrogen bonds : angle 3.99684 / 2.57 ( 198) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 306 Ramachandran restraints generated. 153 Oldfield, 0 Emsley, 153 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 306 Ramachandran restraints generated. 153 Oldfield, 0 Emsley, 153 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 26 residues out of total 131 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 24 time to evaluate : 0.072 Fit side-chains outliers start: 2 outliers final: 1 residues processed: 26 average time/residue: 0.3929 time to fit residues: 10.4350 Evaluate side-chains 24 residues out of total 131 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 23 time to evaluate : 0.043 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 154 SER Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 15 random chunks: chunk 13 optimal weight: 7.9990 chunk 6 optimal weight: 9.9990 chunk 12 optimal weight: 2.9990 chunk 14 optimal weight: 9.9990 chunk 0 optimal weight: 10.0000 chunk 4 optimal weight: 10.0000 chunk 8 optimal weight: 5.9990 chunk 7 optimal weight: 10.0000 chunk 5 optimal weight: 0.9990 chunk 9 optimal weight: 6.9990 chunk 3 optimal weight: 10.0000 overall best weight: 4.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2788 r_free = 0.2788 target = 0.069928 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.2617 r_free = 0.2617 target = 0.060782 restraints weight = 2300.588| |-----------------------------------------------------------------------------| r_work (start): 0.2615 rms_B_bonded: 1.80 r_work: 0.2512 rms_B_bonded: 2.21 restraints_weight: 0.5000 r_work: 0.2414 rms_B_bonded: 3.68 restraints_weight: 0.2500 r_work (final): 0.2414 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9159 moved from start: 0.1493 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.048 1211 Z= 0.188 Angle : 0.617 6.113 1653 Z= 0.319 Chirality : 0.042 0.110 194 Planarity : 0.004 0.026 217 Dihedral : 4.416 30.446 169 Min Nonbonded Distance : 2.602 Molprobity Statistics. All-atom Clashscore : 2.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.61 % Favored : 97.39 % Rotamer: Outliers : 3.82 % Allowed : 19.85 % Favored : 76.34 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 11.11 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.48 (0.67), residues: 153 helix: 3.09 (0.54), residues: 83 sheet: None (None), residues: 0 loop : -0.16 (0.70), residues: 70 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 42 TYR 0.005 0.001 TYR A 69 PHE 0.014 0.002 PHE A 81 TRP 0.004 0.001 TRP A 153 Details of bonding type rmsd/Z covalent geometry : bond 0.00483 / 0.19 ( 1211) covalent geometry : angle 0.61691 / 0.32 ( 1653) hydrogen bonds : bond 0.05160 / 3.59 ( 72) hydrogen bonds : angle 3.29887 / 2.20 ( 198) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 306 Ramachandran restraints generated. 153 Oldfield, 0 Emsley, 153 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 306 Ramachandran restraints generated. 153 Oldfield, 0 Emsley, 153 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 26 residues out of total 131 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 21 time to evaluate : 0.045 Fit side-chains REVERT: A 58 ASP cc_start: 0.8442 (t0) cc_final: 0.8127 (t0) REVERT: A 93 ARG cc_start: 0.8793 (OUTLIER) cc_final: 0.4756 (ttt180) REVERT: A 127 ASP cc_start: 0.8796 (t70) cc_final: 0.8567 (t0) outliers start: 5 outliers final: 4 residues processed: 26 average time/residue: 0.5682 time to fit residues: 14.9918 Evaluate side-chains 25 residues out of total 131 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 20 time to evaluate : 0.047 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 93 ARG Chi-restraints excluded: chain A residue 98 VAL Chi-restraints excluded: chain A residue 105 THR Chi-restraints excluded: chain A residue 119 SER Chi-restraints excluded: chain A residue 154 SER Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 15 random chunks: chunk 11 optimal weight: 5.9990 chunk 6 optimal weight: 10.0000 chunk 3 optimal weight: 4.9990 chunk 4 optimal weight: 5.9990 chunk 14 optimal weight: 10.0000 chunk 10 optimal weight: 1.9990 chunk 0 optimal weight: 9.9990 chunk 8 optimal weight: 5.9990 chunk 13 optimal weight: 2.9990 chunk 1 optimal weight: 0.9990 chunk 9 optimal weight: 7.9990 overall best weight: 3.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2807 r_free = 0.2807 target = 0.070869 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.2641 r_free = 0.2641 target = 0.061872 restraints weight = 2296.442| |-----------------------------------------------------------------------------| r_work (start): 0.2633 rms_B_bonded: 1.79 r_work: 0.2533 rms_B_bonded: 2.20 restraints_weight: 0.5000 r_work: 0.2434 rms_B_bonded: 3.69 restraints_weight: 0.2500 r_work (final): 0.2434 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9155 moved from start: 0.1650 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 1211 Z= 0.144 Angle : 0.574 5.625 1653 Z= 0.293 Chirality : 0.040 0.108 194 Planarity : 0.004 0.026 217 Dihedral : 3.632 20.687 169 Min Nonbonded Distance : 2.620 Molprobity Statistics. All-atom Clashscore : 2.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.96 % Favored : 98.04 % Rotamer: Outliers : 3.05 % Allowed : 19.85 % Favored : 77.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 11.11 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.65 (0.67), residues: 153 helix: 3.21 (0.54), residues: 83 sheet: None (None), residues: 0 loop : -0.06 (0.70), residues: 70 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG A 142 TYR 0.004 0.001 TYR A 69 PHE 0.012 0.001 PHE A 81 TRP 0.003 0.001 TRP A 153 Details of bonding type rmsd/Z covalent geometry : bond 0.00373 / 0.14 ( 1211) covalent geometry : angle 0.57373 / 0.29 ( 1653) hydrogen bonds : bond 0.04396 / 3.07 ( 72) hydrogen bonds : angle 3.27489 / 2.17 ( 198) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 306 Ramachandran restraints generated. 153 Oldfield, 0 Emsley, 153 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 306 Ramachandran restraints generated. 153 Oldfield, 0 Emsley, 153 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 27 residues out of total 131 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 23 time to evaluate : 0.080 Fit side-chains REVERT: A 58 ASP cc_start: 0.8483 (t0) cc_final: 0.8113 (t0) REVERT: A 93 ARG cc_start: 0.8841 (OUTLIER) cc_final: 0.4760 (ttt180) REVERT: A 127 ASP cc_start: 0.8773 (t70) cc_final: 0.8539 (t0) outliers start: 4 outliers final: 3 residues processed: 27 average time/residue: 0.5659 time to fit residues: 15.5092 Evaluate side-chains 26 residues out of total 131 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 22 time to evaluate : 0.047 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 93 ARG Chi-restraints excluded: chain A residue 98 VAL Chi-restraints excluded: chain A residue 119 SER Chi-restraints excluded: chain A residue 130 ILE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 15 random chunks: chunk 12 optimal weight: 20.0000 chunk 14 optimal weight: 20.0000 chunk 6 optimal weight: 10.0000 chunk 0 optimal weight: 20.0000 chunk 7 optimal weight: 10.0000 chunk 11 optimal weight: 6.9990 chunk 8 optimal weight: 5.9990 chunk 3 optimal weight: 2.9990 chunk 4 optimal weight: 6.9990 chunk 2 optimal weight: 5.9990 chunk 5 optimal weight: 9.9990 overall best weight: 5.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2751 r_free = 0.2751 target = 0.067787 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.2577 r_free = 0.2577 target = 0.058903 restraints weight = 2369.604| |-----------------------------------------------------------------------------| r_work (start): 0.2571 rms_B_bonded: 1.82 r_work: 0.2466 rms_B_bonded: 2.21 restraints_weight: 0.5000 r_work: 0.2366 rms_B_bonded: 3.68 restraints_weight: 0.2500 r_work (final): 0.2366 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9194 moved from start: 0.1940 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.051 1211 Z= 0.203 Angle : 0.605 6.031 1653 Z= 0.311 Chirality : 0.042 0.110 194 Planarity : 0.005 0.027 217 Dihedral : 3.726 20.822 168 Min Nonbonded Distance : 2.614 Molprobity Statistics. All-atom Clashscore : 3.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.61 % Favored : 97.39 % Rotamer: Outliers : 3.82 % Allowed : 17.56 % Favored : 78.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 11.11 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.57 (0.66), residues: 153 helix: 3.20 (0.53), residues: 83 sheet: None (None), residues: 0 loop : -0.19 (0.71), residues: 70 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 42 TYR 0.005 0.001 TYR A 69 PHE 0.013 0.002 PHE A 81 TRP 0.005 0.002 TRP A 153 Details of bonding type rmsd/Z covalent geometry : bond 0.00519 / 0.20 ( 1211) covalent geometry : angle 0.60549 / 0.31 ( 1653) hydrogen bonds : bond 0.04989 / 3.50 ( 72) hydrogen bonds : angle 3.34769 / 2.24 ( 198) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 306 Ramachandran restraints generated. 153 Oldfield, 0 Emsley, 153 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 306 Ramachandran restraints generated. 153 Oldfield, 0 Emsley, 153 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 27 residues out of total 131 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 22 time to evaluate : 0.054 Fit side-chains REVERT: A 32 GLN cc_start: 0.9271 (OUTLIER) cc_final: 0.8451 (mt0) REVERT: A 58 ASP cc_start: 0.8491 (t0) cc_final: 0.8075 (t0) REVERT: A 93 ARG cc_start: 0.8943 (OUTLIER) cc_final: 0.4739 (ttt180) REVERT: A 127 ASP cc_start: 0.8839 (t70) cc_final: 0.8591 (t0) outliers start: 5 outliers final: 4 residues processed: 27 average time/residue: 0.5276 time to fit residues: 14.4704 Evaluate side-chains 28 residues out of total 131 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 22 time to evaluate : 0.051 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 32 GLN Chi-restraints excluded: chain A residue 93 ARG Chi-restraints excluded: chain A residue 97 VAL Chi-restraints excluded: chain A residue 98 VAL Chi-restraints excluded: chain A residue 119 SER Chi-restraints excluded: chain A residue 130 ILE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 15 random chunks: chunk 9 optimal weight: 2.9990 chunk 4 optimal weight: 9.9990 chunk 13 optimal weight: 10.0000 chunk 10 optimal weight: 7.9990 chunk 6 optimal weight: 10.0000 chunk 5 optimal weight: 9.9990 chunk 11 optimal weight: 6.9990 chunk 14 optimal weight: 5.9990 chunk 1 optimal weight: 0.7980 chunk 7 optimal weight: 4.9990 chunk 3 optimal weight: 2.9990 overall best weight: 3.5588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2784 r_free = 0.2784 target = 0.069373 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.2614 r_free = 0.2614 target = 0.060601 restraints weight = 2259.805| |-----------------------------------------------------------------------------| r_work (start): 0.2607 rms_B_bonded: 1.78 r_work: 0.2504 rms_B_bonded: 2.17 restraints_weight: 0.5000 r_work: 0.2405 rms_B_bonded: 3.64 restraints_weight: 0.2500 r_work (final): 0.2405 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9174 moved from start: 0.1984 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 1211 Z= 0.144 Angle : 0.561 5.614 1653 Z= 0.286 Chirality : 0.041 0.107 194 Planarity : 0.004 0.026 217 Dihedral : 3.583 21.099 168 Min Nonbonded Distance : 2.622 Molprobity Statistics. All-atom Clashscore : 2.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.96 % Favored : 98.04 % Rotamer: Outliers : 3.05 % Allowed : 19.08 % Favored : 77.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 11.11 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.77 (0.67), residues: 153 helix: 3.34 (0.53), residues: 83 sheet: None (None), residues: 0 loop : -0.04 (0.71), residues: 70 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG A 42 TYR 0.004 0.001 TYR A 69 PHE 0.011 0.001 PHE A 81 TRP 0.002 0.001 TRP A 153 Details of bonding type rmsd/Z covalent geometry : bond 0.00371 / 0.14 ( 1211) covalent geometry : angle 0.56088 / 0.29 ( 1653) hydrogen bonds : bond 0.04302 / 3.00 ( 72) hydrogen bonds : angle 3.30789 / 2.19 ( 198) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 306 Ramachandran restraints generated. 153 Oldfield, 0 Emsley, 153 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 306 Ramachandran restraints generated. 153 Oldfield, 0 Emsley, 153 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 27 residues out of total 131 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 23 time to evaluate : 0.082 Fit side-chains REVERT: A 58 ASP cc_start: 0.8516 (t0) cc_final: 0.8065 (t0) REVERT: A 93 ARG cc_start: 0.8919 (OUTLIER) cc_final: 0.4720 (ttt180) REVERT: A 127 ASP cc_start: 0.8810 (t70) cc_final: 0.8567 (t0) outliers start: 4 outliers final: 4 residues processed: 27 average time/residue: 0.4800 time to fit residues: 13.1612 Evaluate side-chains 27 residues out of total 131 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 22 time to evaluate : 0.044 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 93 ARG Chi-restraints excluded: chain A residue 95 ILE Chi-restraints excluded: chain A residue 97 VAL Chi-restraints excluded: chain A residue 98 VAL Chi-restraints excluded: chain A residue 130 ILE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 15 random chunks: chunk 0 optimal weight: 20.0000 chunk 6 optimal weight: 8.9990 chunk 2 optimal weight: 3.9990 chunk 12 optimal weight: 10.0000 chunk 3 optimal weight: 10.0000 chunk 1 optimal weight: 0.9990 chunk 9 optimal weight: 6.9990 chunk 10 optimal weight: 8.9990 chunk 14 optimal weight: 5.9990 chunk 5 optimal weight: 5.9990 chunk 4 optimal weight: 5.9990 overall best weight: 4.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2765 r_free = 0.2765 target = 0.068655 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.2593 r_free = 0.2593 target = 0.059726 restraints weight = 2316.933| |-----------------------------------------------------------------------------| r_work (start): 0.2592 rms_B_bonded: 1.86 r_work: 0.2484 rms_B_bonded: 2.26 restraints_weight: 0.5000 r_work: 0.2383 rms_B_bonded: 3.78 restraints_weight: 0.2500 r_work (final): 0.2383 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9142 moved from start: 0.1997 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.047 1211 Z= 0.170 Angle : 0.580 5.673 1653 Z= 0.296 Chirality : 0.041 0.109 194 Planarity : 0.004 0.027 217 Dihedral : 3.625 21.367 168 Min Nonbonded Distance : 2.618 Molprobity Statistics. All-atom Clashscore : 2.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.61 % Favored : 97.39 % Rotamer: Outliers : 3.82 % Allowed : 17.56 % Favored : 78.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 11.11 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.78 (0.66), residues: 153 helix: 3.32 (0.53), residues: 83 sheet: None (None), residues: 0 loop : -0.00 (0.71), residues: 70 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 42 TYR 0.004 0.001 TYR A 69 PHE 0.012 0.002 PHE A 81 TRP 0.003 0.001 TRP A 153 Details of bonding type rmsd/Z covalent geometry : bond 0.00437 / 0.17 ( 1211) covalent geometry : angle 0.57950 / 0.30 ( 1653) hydrogen bonds : bond 0.04523 / 3.17 ( 72) hydrogen bonds : angle 3.31194 / 2.20 ( 198) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 306 Ramachandran restraints generated. 153 Oldfield, 0 Emsley, 153 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 306 Ramachandran restraints generated. 153 Oldfield, 0 Emsley, 153 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 28 residues out of total 131 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 23 time to evaluate : 0.048 Fit side-chains REVERT: A 58 ASP cc_start: 0.8624 (t0) cc_final: 0.8117 (t0) REVERT: A 65 ASP cc_start: 0.8796 (p0) cc_final: 0.8566 (p0) REVERT: A 93 ARG cc_start: 0.8914 (OUTLIER) cc_final: 0.4673 (ttt180) REVERT: A 127 ASP cc_start: 0.8795 (t70) cc_final: 0.8560 (t0) outliers start: 5 outliers final: 5 residues processed: 28 average time/residue: 0.4744 time to fit residues: 13.4898 Evaluate side-chains 29 residues out of total 131 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 23 time to evaluate : 0.041 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 93 ARG Chi-restraints excluded: chain A residue 95 ILE Chi-restraints excluded: chain A residue 97 VAL Chi-restraints excluded: chain A residue 98 VAL Chi-restraints excluded: chain A residue 119 SER Chi-restraints excluded: chain A residue 130 ILE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 15 random chunks: chunk 5 optimal weight: 8.9990 chunk 14 optimal weight: 10.0000 chunk 13 optimal weight: 6.9990 chunk 10 optimal weight: 10.0000 chunk 7 optimal weight: 6.9990 chunk 9 optimal weight: 4.9990 chunk 11 optimal weight: 5.9990 chunk 12 optimal weight: 5.9990 chunk 2 optimal weight: 0.9990 chunk 0 optimal weight: 9.9990 chunk 6 optimal weight: 1.9990 overall best weight: 3.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2772 r_free = 0.2772 target = 0.068925 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.2602 r_free = 0.2602 target = 0.060088 restraints weight = 2320.999| |-----------------------------------------------------------------------------| r_work (start): 0.2594 rms_B_bonded: 1.79 r_work: 0.2490 rms_B_bonded: 2.19 restraints_weight: 0.5000 r_work: 0.2390 rms_B_bonded: 3.68 restraints_weight: 0.2500 r_work (final): 0.2390 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9174 moved from start: 0.1944 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 1211 Z= 0.153 Angle : 0.564 5.578 1653 Z= 0.287 Chirality : 0.041 0.109 194 Planarity : 0.004 0.026 217 Dihedral : 3.577 21.547 168 Min Nonbonded Distance : 2.612 Molprobity Statistics. All-atom Clashscore : 2.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.96 % Favored : 98.04 % Rotamer: Outliers : 3.05 % Allowed : 18.32 % Favored : 78.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 11.11 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.92 (0.66), residues: 153 helix: 3.39 (0.53), residues: 83 sheet: None (None), residues: 0 loop : 0.13 (0.72), residues: 70 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG A 42 TYR 0.004 0.001 TYR A 69 PHE 0.010 0.002 PHE A 81 TRP 0.004 0.001 TRP A 153 Details of bonding type rmsd/Z covalent geometry : bond 0.00394 / 0.15 ( 1211) covalent geometry : angle 0.56405 / 0.29 ( 1653) hydrogen bonds : bond 0.04353 / 3.04 ( 72) hydrogen bonds : angle 3.28616 / 2.18 ( 198) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 306 Ramachandran restraints generated. 153 Oldfield, 0 Emsley, 153 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 306 Ramachandran restraints generated. 153 Oldfield, 0 Emsley, 153 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 27 residues out of total 131 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 23 time to evaluate : 0.052 Fit side-chains REVERT: A 58 ASP cc_start: 0.8603 (t0) cc_final: 0.8114 (t0) REVERT: A 65 ASP cc_start: 0.8778 (p0) cc_final: 0.8562 (p0) REVERT: A 93 ARG cc_start: 0.8952 (OUTLIER) cc_final: 0.4728 (ttt180) REVERT: A 127 ASP cc_start: 0.8822 (t70) cc_final: 0.8578 (t0) outliers start: 4 outliers final: 4 residues processed: 27 average time/residue: 0.5089 time to fit residues: 13.9475 Evaluate side-chains 28 residues out of total 131 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 23 time to evaluate : 0.047 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 93 ARG Chi-restraints excluded: chain A residue 95 ILE Chi-restraints excluded: chain A residue 98 VAL Chi-restraints excluded: chain A residue 119 SER Chi-restraints excluded: chain A residue 130 ILE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 15 random chunks: chunk 2 optimal weight: 0.9980 chunk 7 optimal weight: 0.8980 chunk 3 optimal weight: 0.7980 chunk 0 optimal weight: 20.0000 chunk 8 optimal weight: 4.9990 chunk 12 optimal weight: 5.9990 chunk 14 optimal weight: 20.0000 chunk 6 optimal weight: 1.9990 chunk 4 optimal weight: 6.9990 chunk 13 optimal weight: 1.9990 chunk 10 optimal weight: 9.9990 overall best weight: 1.3384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2841 r_free = 0.2841 target = 0.072319 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.2670 r_free = 0.2670 target = 0.063224 restraints weight = 2214.074| |-----------------------------------------------------------------------------| r_work (start): 0.2684 rms_B_bonded: 1.84 r_work: 0.2586 rms_B_bonded: 2.21 restraints_weight: 0.5000 r_work: 0.2487 rms_B_bonded: 3.73 restraints_weight: 0.2500 r_work (final): 0.2487 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9119 moved from start: 0.2057 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 1211 Z= 0.106 Angle : 0.530 5.078 1653 Z= 0.268 Chirality : 0.039 0.111 194 Planarity : 0.004 0.025 217 Dihedral : 3.311 21.295 168 Min Nonbonded Distance : 2.613 Molprobity Statistics. All-atom Clashscore : 3.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.61 % Favored : 97.39 % Rotamer: Outliers : 3.05 % Allowed : 18.32 % Favored : 78.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 11.11 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 3.33 (0.68), residues: 153 helix: 3.69 (0.55), residues: 83 sheet: None (None), residues: 0 loop : 0.36 (0.72), residues: 70 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG A 91 TYR 0.003 0.001 TYR A 140 PHE 0.009 0.001 PHE A 81 TRP 0.002 0.000 TRP A 153 Details of bonding type rmsd/Z covalent geometry : bond 0.00264 / 0.11 ( 1211) covalent geometry : angle 0.53033 / 0.27 ( 1653) hydrogen bonds : bond 0.03306 / 2.27 ( 72) hydrogen bonds : angle 3.24370 / 2.11 ( 198) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 306 Ramachandran restraints generated. 153 Oldfield, 0 Emsley, 153 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 306 Ramachandran restraints generated. 153 Oldfield, 0 Emsley, 153 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 26 residues out of total 131 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 22 time to evaluate : 0.047 Fit side-chains REVERT: A 58 ASP cc_start: 0.8484 (t0) cc_final: 0.8024 (t0) REVERT: A 93 ARG cc_start: 0.8731 (OUTLIER) cc_final: 0.4549 (ttt180) REVERT: A 127 ASP cc_start: 0.8726 (t70) cc_final: 0.8483 (t0) outliers start: 4 outliers final: 3 residues processed: 25 average time/residue: 0.4839 time to fit residues: 12.2736 Evaluate side-chains 25 residues out of total 131 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 21 time to evaluate : 0.048 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 93 ARG Chi-restraints excluded: chain A residue 98 VAL Chi-restraints excluded: chain A residue 119 SER Chi-restraints excluded: chain A residue 130 ILE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 15 random chunks: chunk 10 optimal weight: 2.9990 chunk 5 optimal weight: 0.6980 chunk 9 optimal weight: 2.9990 chunk 12 optimal weight: 4.9990 chunk 6 optimal weight: 9.9990 chunk 1 optimal weight: 6.9990 chunk 11 optimal weight: 6.9990 chunk 0 optimal weight: 2.9990 chunk 2 optimal weight: 2.9990 chunk 8 optimal weight: 1.9990 chunk 14 optimal weight: 0.9990 overall best weight: 1.9388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2829 r_free = 0.2829 target = 0.071741 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.2654 r_free = 0.2654 target = 0.062555 restraints weight = 2190.540| |-----------------------------------------------------------------------------| r_work (start): 0.2667 rms_B_bonded: 1.83 r_work: 0.2566 rms_B_bonded: 2.24 restraints_weight: 0.5000 r_work: 0.2466 rms_B_bonded: 3.75 restraints_weight: 0.2500 r_work (final): 0.2466 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9130 moved from start: 0.2049 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 1211 Z= 0.114 Angle : 0.549 5.193 1653 Z= 0.278 Chirality : 0.040 0.112 194 Planarity : 0.004 0.026 217 Dihedral : 3.338 21.562 168 Min Nonbonded Distance : 2.601 Molprobity Statistics. All-atom Clashscore : 3.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.61 % Favored : 97.39 % Rotamer: Outliers : 2.29 % Allowed : 19.85 % Favored : 77.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 11.11 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 3.38 (0.68), residues: 153 helix: 3.72 (0.55), residues: 83 sheet: None (None), residues: 0 loop : 0.40 (0.72), residues: 70 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.000 0.000 ARG A 42 TYR 0.004 0.001 TYR A 140 PHE 0.009 0.001 PHE A 81 TRP 0.002 0.001 TRP A 153 Details of bonding type rmsd/Z covalent geometry : bond 0.00289 / 0.11 ( 1211) covalent geometry : angle 0.54867 / 0.28 ( 1653) hydrogen bonds : bond 0.03552 / 2.47 ( 72) hydrogen bonds : angle 3.23345 / 2.12 ( 198) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 306 Ramachandran restraints generated. 153 Oldfield, 0 Emsley, 153 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 306 Ramachandran restraints generated. 153 Oldfield, 0 Emsley, 153 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 24 residues out of total 131 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 21 time to evaluate : 0.052 Fit side-chains REVERT: A 58 ASP cc_start: 0.8543 (t0) cc_final: 0.8063 (t0) REVERT: A 93 ARG cc_start: 0.8754 (OUTLIER) cc_final: 0.4557 (ttt180) REVERT: A 127 ASP cc_start: 0.8716 (t70) cc_final: 0.8477 (t0) outliers start: 3 outliers final: 3 residues processed: 24 average time/residue: 0.5212 time to fit residues: 12.6972 Evaluate side-chains 25 residues out of total 131 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 21 time to evaluate : 0.047 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 93 ARG Chi-restraints excluded: chain A residue 98 VAL Chi-restraints excluded: chain A residue 119 SER Chi-restraints excluded: chain A residue 130 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 15 random chunks: chunk 11 optimal weight: 6.9990 chunk 14 optimal weight: 9.9990 chunk 5 optimal weight: 2.9990 chunk 1 optimal weight: 5.9990 chunk 9 optimal weight: 4.9990 chunk 10 optimal weight: 5.9990 chunk 13 optimal weight: 8.9990 chunk 8 optimal weight: 2.9990 chunk 3 optimal weight: 9.9990 chunk 4 optimal weight: 6.9990 chunk 0 optimal weight: 2.9990 overall best weight: 3.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2797 r_free = 0.2797 target = 0.070046 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.2623 r_free = 0.2623 target = 0.060845 restraints weight = 2260.577| |-----------------------------------------------------------------------------| r_work (start): 0.2622 rms_B_bonded: 1.86 r_work: 0.2518 rms_B_bonded: 2.21 restraints_weight: 0.5000 r_work: 0.2415 rms_B_bonded: 3.71 restraints_weight: 0.2500 r_work (final): 0.2415 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9155 moved from start: 0.2068 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 1211 Z= 0.154 Angle : 0.575 5.505 1653 Z= 0.293 Chirality : 0.041 0.111 194 Planarity : 0.004 0.026 217 Dihedral : 3.474 21.493 168 Min Nonbonded Distance : 2.599 Molprobity Statistics. All-atom Clashscore : 3.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.61 % Favored : 97.39 % Rotamer: Outliers : 2.29 % Allowed : 20.61 % Favored : 77.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 11.11 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 3.25 (0.67), residues: 153 helix: 3.62 (0.54), residues: 83 sheet: None (None), residues: 0 loop : 0.34 (0.72), residues: 70 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG A 42 TYR 0.003 0.001 TYR A 3 PHE 0.011 0.002 PHE A 81 TRP 0.004 0.001 TRP A 153 Details of bonding type rmsd/Z covalent geometry : bond 0.00395 / 0.15 ( 1211) covalent geometry : angle 0.57452 / 0.29 ( 1653) hydrogen bonds : bond 0.04271 / 3.00 ( 72) hydrogen bonds : angle 3.30525 / 2.19 ( 198) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 306 Ramachandran restraints generated. 153 Oldfield, 0 Emsley, 153 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 306 Ramachandran restraints generated. 153 Oldfield, 0 Emsley, 153 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 26 residues out of total 131 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 23 time to evaluate : 0.032 Fit side-chains REVERT: A 58 ASP cc_start: 0.8552 (t0) cc_final: 0.8090 (t0) REVERT: A 93 ARG cc_start: 0.8906 (OUTLIER) cc_final: 0.4691 (ttt180) REVERT: A 127 ASP cc_start: 0.8756 (t70) cc_final: 0.8520 (t0) outliers start: 3 outliers final: 3 residues processed: 26 average time/residue: 0.4809 time to fit residues: 12.6901 Evaluate side-chains 26 residues out of total 131 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 22 time to evaluate : 0.060 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 93 ARG Chi-restraints excluded: chain A residue 98 VAL Chi-restraints excluded: chain A residue 119 SER Chi-restraints excluded: chain A residue 130 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 15 random chunks: chunk 4 optimal weight: 9.9990 chunk 13 optimal weight: 6.9990 chunk 14 optimal weight: 6.9990 chunk 9 optimal weight: 0.5980 chunk 0 optimal weight: 20.0000 chunk 3 optimal weight: 5.9990 chunk 7 optimal weight: 5.9990 chunk 1 optimal weight: 0.0870 chunk 6 optimal weight: 4.9990 chunk 5 optimal weight: 0.0050 chunk 11 optimal weight: 7.9990 overall best weight: 2.3376 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2821 r_free = 0.2821 target = 0.071266 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.2647 r_free = 0.2647 target = 0.062102 restraints weight = 2258.208| |-----------------------------------------------------------------------------| r_work (start): 0.2648 rms_B_bonded: 1.86 r_work: 0.2544 rms_B_bonded: 2.24 restraints_weight: 0.5000 r_work: 0.2443 rms_B_bonded: 3.75 restraints_weight: 0.2500 r_work (final): 0.2443 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9135 moved from start: 0.2090 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 1211 Z= 0.117 Angle : 0.545 5.246 1653 Z= 0.275 Chirality : 0.040 0.111 194 Planarity : 0.004 0.026 217 Dihedral : 3.390 21.608 168 Min Nonbonded Distance : 2.598 Molprobity Statistics. All-atom Clashscore : 2.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.61 % Favored : 97.39 % Rotamer: Outliers : 2.29 % Allowed : 21.37 % Favored : 76.34 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 11.11 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 3.33 (0.67), residues: 153 helix: 3.67 (0.54), residues: 83 sheet: None (None), residues: 0 loop : 0.39 (0.72), residues: 70 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG A 42 TYR 0.003 0.001 TYR A 140 PHE 0.010 0.001 PHE A 81 TRP 0.004 0.001 TRP A 153 Details of bonding type rmsd/Z covalent geometry : bond 0.00298 / 0.12 ( 1211) covalent geometry : angle 0.54470 / 0.28 ( 1653) hydrogen bonds : bond 0.03750 / 2.61 ( 72) hydrogen bonds : angle 3.25079 / 2.13 ( 198) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 648.87 seconds wall clock time: 12 minutes 1.01 seconds (721.01 seconds total)