Starting phenix.real_space_refine on Wed Sep 17 04:49:37 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9ccu_45458/09_2025/9ccu_45458.cif Found real_map, /net/cci-nas-00/data/ceres_data/9ccu_45458/09_2025/9ccu_45458.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.8 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9ccu_45458/09_2025/9ccu_45458.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9ccu_45458/09_2025/9ccu_45458.map" model { file = "/net/cci-nas-00/data/ceres_data/9ccu_45458/09_2025/9ccu_45458.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9ccu_45458/09_2025/9ccu_45458.cif" } resolution = 3.8 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.001 sd= 0.022 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 2853 2.51 5 N 736 2.21 5 O 896 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 5 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: 4499 Number of models: 1 Model: "" Number of chains: 3 Chain: "A" Number of atoms: 1200 Number of conformers: 1 Conformer: "" Number of residues, atoms: 160, 1200 Classifications: {'peptide': 160} Link IDs: {'PCIS': 1, 'PTRANS': 9, 'TRANS': 149} Chain: "B" Number of atoms: 1621 Number of conformers: 1 Conformer: "" Number of residues, atoms: 213, 1621 Classifications: {'peptide': 213} Link IDs: {'PCIS': 2, 'PTRANS': 9, 'TRANS': 201} Chain: "C" Number of atoms: 1678 Number of conformers: 1 Conformer: "" Number of residues, atoms: 222, 1678 Classifications: {'peptide': 222} Link IDs: {'PTRANS': 14, 'TRANS': 207} Time building chain proxies: 1.43, per 1000 atoms: 0.32 Number of scatterers: 4499 At special positions: 0 Unit cell: (55.648, 72.224, 127.872, 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 896 8.00 N 736 7.00 C 2853 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=5, symmetry=0 Simple disulfide: pdb=" SG CYS A 3 " - pdb=" SG CYS A 44 " distance=2.03 Simple disulfide: pdb=" SG CYS B 28 " - pdb=" SG CYS B 94 " distance=2.04 Simple disulfide: pdb=" SG CYS B 140 " - pdb=" SG CYS B 200 " distance=2.04 Simple disulfide: pdb=" SG CYS C 27 " - pdb=" SG CYS C 101 " distance=2.04 Simple disulfide: pdb=" SG CYS C 151 " - pdb=" SG CYS C 207 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 0.35 Conformation dependent library (CDL) restraints added in 231.2 milliseconds Enol-peptide restraints added in 953.7 nanoseconds 1178 Ramachandran restraints generated. 589 Oldfield, 0 Emsley, 589 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1094 Finding SS restraints... Secondary structure from input PDB file: 5 helices and 11 sheets defined 4.5% alpha, 23.5% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.18 Creating SS restraints... Processing helix chain 'A' and resid 37 through 41 Processing helix chain 'A' and resid 66 through 70 Processing helix chain 'B' and resid 128 through 133 Processing helix chain 'B' and resid 189 through 194 Processing helix chain 'C' and resid 140 through 144 removed outlier: 3.912A pdb=" N SER C 143 " --> pdb=" O LYS C 140 " (cutoff:3.500A) 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 16 through 22 removed outlier: 6.366A pdb=" N GLY A 16 " --> pdb=" O VAL A 145 " (cutoff:3.500A) removed outlier: 8.027A pdb=" N ASN A 147 " --> pdb=" O GLY A 16 " (cutoff:3.500A) removed outlier: 6.598A pdb=" N ALA A 18 " --> pdb=" O ASN A 147 " (cutoff:3.500A) removed outlier: 7.522A pdb=" N TYR A 149 " --> pdb=" O ALA A 18 " (cutoff:3.500A) removed outlier: 6.102A pdb=" N VAL A 20 " --> pdb=" O TYR A 149 " (cutoff:3.500A) removed outlier: 3.534A pdb=" N PHE A 142 " --> pdb=" O GLN A 133 " (cutoff:3.500A) removed outlier: 3.816A pdb=" N ALA A 127 " --> pdb=" O ILE A 148 " (cutoff:3.500A) removed outlier: 6.930A pdb=" N ALA A 150 " --> pdb=" O LEU A 125 " (cutoff:3.500A) removed outlier: 6.446A pdb=" N LEU A 125 " --> pdb=" O ALA A 150 " (cutoff:3.500A) removed outlier: 3.530A pdb=" N ARG A 60 " --> pdb=" O ILE A 130 " (cutoff:3.500A) removed outlier: 6.379A pdb=" N ARG A 132 " --> pdb=" O LEU A 58 " (cutoff:3.500A) removed outlier: 5.525A pdb=" N LEU A 58 " --> pdb=" O ARG A 132 " (cutoff:3.500A) removed outlier: 7.136A pdb=" N THR A 134 " --> pdb=" O VAL A 56 " (cutoff:3.500A) removed outlier: 4.851A pdb=" N VAL A 56 " --> pdb=" O THR A 134 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 35 through 36 Processing sheet with id=AA4, first strand: chain 'B' and resid 10 through 12 removed outlier: 3.509A pdb=" N THR B 10 " --> pdb=" O SER B 29 " (cutoff:3.500A) removed outlier: 3.571A pdb=" N SER B 29 " --> pdb=" O THR B 10 " (cutoff:3.500A) removed outlier: 3.881A pdb=" N SER B 12 " --> pdb=" O THR B 27 " (cutoff:3.500A) removed outlier: 4.370A pdb=" N THR B 27 " --> pdb=" O SER B 12 " (cutoff:3.500A) removed outlier: 3.620A pdb=" N SER B 78 " --> pdb=" O SER B 71 " (cutoff:3.500A) removed outlier: 3.580A pdb=" N SER B 71 " --> pdb=" O SER B 78 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 51 through 55 removed outlier: 6.354A pdb=" N TRP B 41 " --> pdb=" O TRP B 53 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 120 through 124 removed outlier: 6.094A pdb=" N TYR B 179 " --> pdb=" O ASN B 144 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 135 through 136 removed outlier: 3.982A pdb=" N LEU B 187 " --> pdb=" O ALA B 136 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 160 through 161 removed outlier: 4.454A pdb=" N TRP B 154 " --> pdb=" O GLN B 161 " (cutoff:3.500A) removed outlier: 4.555A pdb=" N TYR B 198 " --> pdb=" O PHE B 215 " (cutoff:3.500A) removed outlier: 4.061A pdb=" N PHE B 215 " --> pdb=" O TYR B 198 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'C' and resid 9 through 10 Processing sheet with id=AB1, first strand: chain 'C' and resid 61 through 65 removed outlier: 4.339A pdb=" N THR C 63 " --> pdb=" O LEU C 55 " (cutoff:3.500A) removed outlier: 6.894A pdb=" N LEU C 55 " --> pdb=" O THR C 63 " (cutoff:3.500A) removed outlier: 4.888A pdb=" N TYR C 65 " --> pdb=" O ILE C 53 " (cutoff:3.500A) removed outlier: 8.351A pdb=" N ILE C 53 " --> pdb=" O TYR C 65 " (cutoff:3.500A) removed outlier: 6.762A pdb=" N TRP C 41 " --> pdb=" O ILE C 53 " (cutoff:3.500A) removed outlier: 4.644A pdb=" N LEU C 55 " --> pdb=" O ILE C 39 " (cutoff:3.500A) removed outlier: 6.865A pdb=" N ILE C 39 " --> pdb=" O LEU C 55 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'C' and resid 133 through 135 removed outlier: 3.683A pdb=" N LEU C 152 " --> pdb=" O PHE C 133 " (cutoff:3.500A) removed outlier: 3.681A pdb=" N GLY C 150 " --> pdb=" O LEU C 135 " (cutoff:3.500A) 98 hydrogen bonds defined for protein. 213 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: 0.66 Time building geometry restraints manager: 0.49 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 1409 1.34 - 1.47: 1189 1.47 - 1.59: 1997 1.59 - 1.71: 2 1.71 - 1.83: 17 Bond restraints: 4614 Sorted by residual: bond pdb=" CG1 ILE B 34 " pdb=" CD1 ILE B 34 " ideal model delta sigma weight residual 1.513 1.443 0.070 3.90e-02 6.57e+02 3.18e+00 bond pdb=" CB GLN C 67 " pdb=" CG GLN C 67 " ideal model delta sigma weight residual 1.520 1.562 -0.042 3.00e-02 1.11e+03 1.93e+00 bond pdb=" CA TYR B 55 " pdb=" CB TYR B 55 " ideal model delta sigma weight residual 1.539 1.603 -0.063 4.88e-02 4.20e+02 1.67e+00 bond pdb=" CG1 ILE C 25 " pdb=" CD1 ILE C 25 " ideal model delta sigma weight residual 1.513 1.468 0.045 3.90e-02 6.57e+02 1.32e+00 bond pdb=" CA LYS C 72 " pdb=" CB LYS C 72 " ideal model delta sigma weight residual 1.539 1.595 -0.055 4.88e-02 4.20e+02 1.28e+00 ... (remaining 4609 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.03: 6029 2.03 - 4.06: 228 4.06 - 6.09: 34 6.09 - 8.12: 11 8.12 - 10.15: 2 Bond angle restraints: 6304 Sorted by residual: angle pdb=" N ILE B 34 " pdb=" CA ILE B 34 " pdb=" C ILE B 34 " ideal model delta sigma weight residual 109.34 118.84 -9.50 2.08e+00 2.31e-01 2.09e+01 angle pdb=" N ILE B 34 " pdb=" CA ILE B 34 " pdb=" CB ILE B 34 " ideal model delta sigma weight residual 111.23 103.98 7.25 1.65e+00 3.67e-01 1.93e+01 angle pdb=" CA TYR B 55 " pdb=" CB TYR B 55 " pdb=" CG TYR B 55 " ideal model delta sigma weight residual 113.90 120.78 -6.88 1.80e+00 3.09e-01 1.46e+01 angle pdb=" C LYS C 221 " pdb=" N VAL C 222 " pdb=" CA VAL C 222 " ideal model delta sigma weight residual 121.97 128.49 -6.52 1.80e+00 3.09e-01 1.31e+01 angle pdb=" N VAL C 23 " pdb=" CA VAL C 23 " pdb=" C VAL C 23 " ideal model delta sigma weight residual 112.96 109.43 3.53 1.00e+00 1.00e+00 1.25e+01 ... (remaining 6299 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.38: 2290 17.38 - 34.77: 326 34.77 - 52.15: 79 52.15 - 69.53: 18 69.53 - 86.91: 8 Dihedral angle restraints: 2721 sinusoidal: 1002 harmonic: 1719 Sorted by residual: dihedral pdb=" CA SER B 33 " pdb=" C SER B 33 " pdb=" N ILE B 34 " pdb=" CA ILE B 34 " ideal model delta harmonic sigma weight residual 180.00 -159.24 -20.76 0 5.00e+00 4.00e-02 1.72e+01 dihedral pdb=" CA VAL A 30 " pdb=" C VAL A 30 " pdb=" N GLY A 31 " pdb=" CA GLY A 31 " ideal model delta harmonic sigma weight residual -180.00 -159.77 -20.23 0 5.00e+00 4.00e-02 1.64e+01 dihedral pdb=" CA LEU B 15 " pdb=" C LEU B 15 " pdb=" N MET B 16 " pdb=" CA MET B 16 " ideal model delta harmonic sigma weight residual 180.00 161.02 18.98 0 5.00e+00 4.00e-02 1.44e+01 ... (remaining 2718 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.076: 607 0.076 - 0.153: 104 0.153 - 0.229: 6 0.229 - 0.306: 2 0.306 - 0.382: 1 Chirality restraints: 720 Sorted by residual: chirality pdb=" CB VAL C 15 " pdb=" CA VAL C 15 " pdb=" CG1 VAL C 15 " pdb=" CG2 VAL C 15 " both_signs ideal model delta sigma weight residual False -2.63 -2.25 -0.38 2.00e-01 2.50e+01 3.65e+00 chirality pdb=" CB THR B 103 " pdb=" CA THR B 103 " pdb=" OG1 THR B 103 " pdb=" CG2 THR B 103 " both_signs ideal model delta sigma weight residual False 2.55 2.28 0.27 2.00e-01 2.50e+01 1.82e+00 chirality pdb=" CB ILE B 34 " pdb=" CA ILE B 34 " pdb=" CG1 ILE B 34 " pdb=" CG2 ILE B 34 " both_signs ideal model delta sigma weight residual False 2.64 2.40 0.24 2.00e-01 2.50e+01 1.49e+00 ... (remaining 717 not shown) Planarity restraints: 800 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C VAL A 156 " 0.044 5.00e-02 4.00e+02 6.66e-02 7.09e+00 pdb=" N PRO A 157 " -0.115 5.00e-02 4.00e+02 pdb=" CA PRO A 157 " 0.035 5.00e-02 4.00e+02 pdb=" CD PRO A 157 " 0.037 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C GLY C 129 " -0.042 5.00e-02 4.00e+02 6.44e-02 6.63e+00 pdb=" N PRO C 130 " 0.111 5.00e-02 4.00e+02 pdb=" CA PRO C 130 " -0.034 5.00e-02 4.00e+02 pdb=" CD PRO C 130 " -0.035 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C THR A 90 " -0.038 5.00e-02 4.00e+02 5.75e-02 5.29e+00 pdb=" N PRO A 91 " 0.099 5.00e-02 4.00e+02 pdb=" CA PRO A 91 " -0.030 5.00e-02 4.00e+02 pdb=" CD PRO A 91 " -0.032 5.00e-02 4.00e+02 ... (remaining 797 not shown) Histogram of nonbonded interaction distances: 2.25 - 2.78: 1002 2.78 - 3.31: 4382 3.31 - 3.84: 7665 3.84 - 4.37: 8671 4.37 - 4.90: 14595 Nonbonded interactions: 36315 Sorted by model distance: nonbonded pdb=" O SER A 139 " pdb=" OG SER A 139 " model vdw 2.249 3.040 nonbonded pdb=" OE2 GLU B 201 " pdb=" OG1 THR B 203 " model vdw 2.252 3.040 nonbonded pdb=" O THR B 48 " pdb=" OH TYR C 100 " model vdw 2.294 3.040 nonbonded pdb=" O ILE B 112 " pdb=" OH TYR B 146 " model vdw 2.300 3.040 nonbonded pdb=" O SER C 188 " pdb=" OG SER C 188 " model vdw 2.303 3.040 ... (remaining 36310 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 ========== 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 group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.870 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.090 Check model and map are aligned: 0.020 Set scattering table: 0.010 Process input model: 6.870 Find NCS groups from input model: 0.020 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:1.390 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 9.290 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6089 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 : 0.005 0.070 4619 Z= 0.213 Angle : 0.914 10.147 6314 Z= 0.485 Chirality : 0.056 0.382 720 Planarity : 0.007 0.067 800 Dihedral : 17.794 86.915 1612 Min Nonbonded Distance : 2.249 Molprobity Statistics. All-atom Clashscore : 15.79 Ramachandran Plot: Outliers : 0.34 % Allowed : 16.81 % Favored : 82.85 % Rotamer: Outliers : 1.38 % Allowed : 34.18 % Favored : 64.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.57 % 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: -3.22 (0.33), residues: 589 helix: -3.51 (0.92), residues: 20 sheet: -1.22 (0.35), residues: 215 loop : -2.78 (0.32), residues: 354 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG A 92 TYR 0.018 0.002 TYR B 55 PHE 0.018 0.002 PHE B 122 TRP 0.035 0.003 TRP B 154 HIS 0.009 0.002 HIS B 195 Details of bonding type rmsd covalent geometry : bond 0.00478 ( 4614) covalent geometry : angle 0.91314 ( 6304) SS BOND : bond 0.00774 ( 5) SS BOND : angle 1.35936 ( 10) hydrogen bonds : bond 0.18991 ( 98) hydrogen bonds : angle 9.79919 ( 213) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1178 Ramachandran restraints generated. 589 Oldfield, 0 Emsley, 589 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1178 Ramachandran restraints generated. 589 Oldfield, 0 Emsley, 589 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 100 residues out of total 509 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 93 time to evaluate : 0.178 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 161 VAL cc_start: 0.8282 (p) cc_final: 0.7952 (m) outliers start: 7 outliers final: 4 residues processed: 97 average time/residue: 0.0621 time to fit residues: 8.0681 Evaluate side-chains 94 residues out of total 509 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 90 time to evaluate : 0.126 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 34 LEU Chi-restraints excluded: chain B residue 43 GLN Chi-restraints excluded: chain C residue 108 TYR Chi-restraints excluded: chain C residue 166 ASN Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 59 random chunks: chunk 54 optimal weight: 1.9990 chunk 24 optimal weight: 0.6980 chunk 48 optimal weight: 4.9990 chunk 56 optimal weight: 0.0770 chunk 26 optimal weight: 0.9990 chunk 2 optimal weight: 0.9980 chunk 16 optimal weight: 0.9990 chunk 32 optimal weight: 4.9990 chunk 31 optimal weight: 0.4980 chunk 25 optimal weight: 0.6980 chunk 58 optimal weight: 0.9980 overall best weight: 0.5938 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 11 GLN B 43 GLN ** B 95 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 130 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4385 r_free = 0.4385 target = 0.189426 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.4123 r_free = 0.4123 target = 0.166185 restraints weight = 7060.560| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.4191 r_free = 0.4191 target = 0.172020 restraints weight = 4052.880| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.4236 r_free = 0.4236 target = 0.175971 restraints weight = 2616.984| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 31)----------------| | r_work = 0.4266 r_free = 0.4266 target = 0.178598 restraints weight = 1824.776| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 31)----------------| | r_work = 0.4288 r_free = 0.4288 target = 0.180545 restraints weight = 1361.929| |-----------------------------------------------------------------------------| r_work (final): 0.4272 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6011 moved from start: 0.0877 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.069 4619 Z= 0.163 Angle : 0.722 6.852 6314 Z= 0.373 Chirality : 0.047 0.208 720 Planarity : 0.006 0.054 800 Dihedral : 6.302 45.677 644 Min Nonbonded Distance : 2.502 Molprobity Statistics. All-atom Clashscore : 15.79 Ramachandran Plot: Outliers : 0.34 % Allowed : 14.77 % Favored : 84.89 % Rotamer: Outliers : 5.30 % Allowed : 29.67 % Favored : 65.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.57 % 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: -3.04 (0.34), residues: 589 helix: -2.79 (1.27), residues: 14 sheet: -1.37 (0.35), residues: 216 loop : -2.51 (0.32), residues: 359 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 92 TYR 0.020 0.002 TYR B 55 PHE 0.013 0.002 PHE A 1 TRP 0.016 0.002 TRP A 103 HIS 0.008 0.002 HIS B 40 Details of bonding type rmsd covalent geometry : bond 0.00369 ( 4614) covalent geometry : angle 0.72166 ( 6304) SS BOND : bond 0.00615 ( 5) SS BOND : angle 1.07156 ( 10) hydrogen bonds : bond 0.04116 ( 98) hydrogen bonds : angle 7.97114 ( 213) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1178 Ramachandran restraints generated. 589 Oldfield, 0 Emsley, 589 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1178 Ramachandran restraints generated. 589 Oldfield, 0 Emsley, 589 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 119 residues out of total 509 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 92 time to evaluate : 0.173 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 38 PHE cc_start: 0.6565 (m-80) cc_final: 0.6291 (m-80) REVERT: C 149 LEU cc_start: 0.8015 (OUTLIER) cc_final: 0.7648 (pp) REVERT: C 217 LYS cc_start: 0.7622 (OUTLIER) cc_final: 0.7324 (tptp) outliers start: 27 outliers final: 10 residues processed: 112 average time/residue: 0.0665 time to fit residues: 9.7437 Evaluate side-chains 103 residues out of total 509 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 91 time to evaluate : 0.166 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 24 VAL Chi-restraints excluded: chain B residue 43 GLN Chi-restraints excluded: chain B residue 120 SER Chi-restraints excluded: chain C residue 50 LEU Chi-restraints excluded: chain C residue 52 TRP Chi-restraints excluded: chain C residue 82 SER Chi-restraints excluded: chain C residue 101 CYS Chi-restraints excluded: chain C residue 108 TYR Chi-restraints excluded: chain C residue 132 VAL Chi-restraints excluded: chain C residue 149 LEU Chi-restraints excluded: chain C residue 166 ASN Chi-restraints excluded: chain C residue 217 LYS Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 59 random chunks: chunk 8 optimal weight: 0.8980 chunk 31 optimal weight: 4.9990 chunk 20 optimal weight: 0.5980 chunk 54 optimal weight: 0.0010 chunk 28 optimal weight: 0.7980 chunk 55 optimal weight: 2.9990 chunk 44 optimal weight: 2.9990 chunk 9 optimal weight: 3.9990 chunk 50 optimal weight: 5.9990 chunk 16 optimal weight: 0.4980 chunk 21 optimal weight: 0.9980 overall best weight: 0.5586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 95 GLN ** C 11 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 166 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4379 r_free = 0.4379 target = 0.188567 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.4124 r_free = 0.4124 target = 0.165767 restraints weight = 7056.792| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.4189 r_free = 0.4189 target = 0.171382 restraints weight = 4104.539| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.4230 r_free = 0.4230 target = 0.175079 restraints weight = 2676.269| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 36)----------------| | r_work = 0.4263 r_free = 0.4263 target = 0.177847 restraints weight = 1890.014| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.4283 r_free = 0.4283 target = 0.179702 restraints weight = 1397.905| |-----------------------------------------------------------------------------| r_work (final): 0.4272 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6009 moved from start: 0.1185 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.063 4619 Z= 0.157 Angle : 0.707 7.379 6314 Z= 0.363 Chirality : 0.046 0.207 720 Planarity : 0.005 0.054 800 Dihedral : 5.734 37.356 642 Min Nonbonded Distance : 2.533 Molprobity Statistics. All-atom Clashscore : 16.58 Ramachandran Plot: Outliers : 0.34 % Allowed : 16.13 % Favored : 83.53 % Rotamer: Outliers : 6.68 % Allowed : 29.08 % Favored : 64.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.57 % 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: -3.07 (0.34), residues: 589 helix: -3.26 (0.98), residues: 20 sheet: -1.40 (0.35), residues: 211 loop : -2.46 (0.33), residues: 358 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 67 TYR 0.019 0.002 TYR B 55 PHE 0.014 0.002 PHE C 69 TRP 0.011 0.002 TRP B 154 HIS 0.005 0.002 HIS B 40 Details of bonding type rmsd covalent geometry : bond 0.00361 ( 4614) covalent geometry : angle 0.70642 ( 6304) SS BOND : bond 0.00571 ( 5) SS BOND : angle 1.03323 ( 10) hydrogen bonds : bond 0.03707 ( 98) hydrogen bonds : angle 7.48962 ( 213) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1178 Ramachandran restraints generated. 589 Oldfield, 0 Emsley, 589 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1178 Ramachandran restraints generated. 589 Oldfield, 0 Emsley, 589 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 125 residues out of total 509 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 91 time to evaluate : 0.227 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 141 ASP cc_start: 0.6494 (OUTLIER) cc_final: 0.6100 (t0) REVERT: B 154 TRP cc_start: 0.6273 (m100) cc_final: 0.6066 (m100) REVERT: C 36 ASP cc_start: 0.5891 (OUTLIER) cc_final: 0.5335 (t70) REVERT: C 38 PHE cc_start: 0.6663 (m-80) cc_final: 0.6336 (m-80) REVERT: C 149 LEU cc_start: 0.7974 (OUTLIER) cc_final: 0.7612 (pp) REVERT: C 159 GLU cc_start: 0.7585 (tp30) cc_final: 0.6882 (tp30) REVERT: C 217 LYS cc_start: 0.7632 (OUTLIER) cc_final: 0.7294 (tptp) outliers start: 34 outliers final: 21 residues processed: 112 average time/residue: 0.0596 time to fit residues: 8.9456 Evaluate side-chains 114 residues out of total 509 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 89 time to evaluate : 0.175 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 34 LEU Chi-restraints excluded: chain A residue 40 THR Chi-restraints excluded: chain A residue 48 TYR Chi-restraints excluded: chain A residue 67 VAL Chi-restraints excluded: chain A residue 105 VAL Chi-restraints excluded: chain A residue 141 ASP Chi-restraints excluded: chain A residue 158 THR Chi-restraints excluded: chain B residue 24 VAL Chi-restraints excluded: chain B residue 95 GLN Chi-restraints excluded: chain B residue 200 CYS Chi-restraints excluded: chain C residue 26 SER Chi-restraints excluded: chain C residue 36 ASP Chi-restraints excluded: chain C residue 50 LEU Chi-restraints excluded: chain C residue 52 TRP Chi-restraints excluded: chain C residue 74 THR Chi-restraints excluded: chain C residue 82 SER Chi-restraints excluded: chain C residue 101 CYS Chi-restraints excluded: chain C residue 108 TYR Chi-restraints excluded: chain C residue 132 VAL Chi-restraints excluded: chain C residue 149 LEU Chi-restraints excluded: chain C residue 153 VAL Chi-restraints excluded: chain C residue 162 THR Chi-restraints excluded: chain C residue 166 ASN Chi-restraints excluded: chain C residue 192 VAL Chi-restraints excluded: chain C residue 217 LYS Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 59 random chunks: chunk 17 optimal weight: 2.9990 chunk 8 optimal weight: 0.8980 chunk 37 optimal weight: 0.9990 chunk 30 optimal weight: 1.9990 chunk 28 optimal weight: 0.0980 chunk 5 optimal weight: 0.4980 chunk 41 optimal weight: 1.9990 chunk 55 optimal weight: 4.9990 chunk 22 optimal weight: 4.9990 chunk 44 optimal weight: 2.9990 chunk 26 optimal weight: 3.9990 overall best weight: 0.8984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 95 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4355 r_free = 0.4355 target = 0.185852 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.4076 r_free = 0.4076 target = 0.161441 restraints weight = 7105.349| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.4148 r_free = 0.4148 target = 0.167582 restraints weight = 3999.562| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.4197 r_free = 0.4197 target = 0.171769 restraints weight = 2573.841| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 37)----------------| | r_work = 0.4230 r_free = 0.4230 target = 0.174664 restraints weight = 1789.962| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.4251 r_free = 0.4251 target = 0.176588 restraints weight = 1317.276| |-----------------------------------------------------------------------------| r_work (final): 0.4233 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6080 moved from start: 0.1428 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.052 4619 Z= 0.205 Angle : 0.745 9.908 6314 Z= 0.382 Chirality : 0.048 0.233 720 Planarity : 0.005 0.052 800 Dihedral : 5.723 37.292 639 Min Nonbonded Distance : 2.548 Molprobity Statistics. All-atom Clashscore : 18.61 Ramachandran Plot: Outliers : 0.34 % Allowed : 15.79 % Favored : 83.87 % Rotamer: Outliers : 8.06 % Allowed : 27.31 % Favored : 64.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.57 % 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: -3.07 (0.35), residues: 589 helix: -3.19 (1.01), residues: 20 sheet: -1.27 (0.36), residues: 213 loop : -2.57 (0.34), residues: 356 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 217 TYR 0.019 0.002 TYR B 55 PHE 0.012 0.002 PHE B 122 TRP 0.018 0.002 TRP A 103 HIS 0.008 0.002 HIS B 40 Details of bonding type rmsd covalent geometry : bond 0.00450 ( 4614) covalent geometry : angle 0.74332 ( 6304) SS BOND : bond 0.00736 ( 5) SS BOND : angle 1.37942 ( 10) hydrogen bonds : bond 0.04012 ( 98) hydrogen bonds : angle 7.53092 ( 213) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1178 Ramachandran restraints generated. 589 Oldfield, 0 Emsley, 589 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1178 Ramachandran restraints generated. 589 Oldfield, 0 Emsley, 589 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 138 residues out of total 509 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 97 time to evaluate : 0.174 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 154 TRP cc_start: 0.6314 (m100) cc_final: 0.5978 (m100) REVERT: C 36 ASP cc_start: 0.5901 (OUTLIER) cc_final: 0.5442 (t70) REVERT: C 38 PHE cc_start: 0.6705 (m-80) cc_final: 0.6346 (m-80) REVERT: C 149 LEU cc_start: 0.8081 (OUTLIER) cc_final: 0.7725 (pp) REVERT: C 217 LYS cc_start: 0.7612 (OUTLIER) cc_final: 0.7297 (tptp) outliers start: 41 outliers final: 23 residues processed: 126 average time/residue: 0.0649 time to fit residues: 10.7838 Evaluate side-chains 123 residues out of total 509 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 97 time to evaluate : 0.173 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 34 LEU Chi-restraints excluded: chain A residue 40 THR Chi-restraints excluded: chain A residue 48 TYR Chi-restraints excluded: chain A residue 67 VAL Chi-restraints excluded: chain A residue 105 VAL Chi-restraints excluded: chain A residue 138 ASN Chi-restraints excluded: chain A residue 141 ASP Chi-restraints excluded: chain A residue 148 ILE Chi-restraints excluded: chain A residue 158 THR Chi-restraints excluded: chain B residue 24 VAL Chi-restraints excluded: chain B residue 26 ILE Chi-restraints excluded: chain B residue 95 GLN Chi-restraints excluded: chain B residue 200 CYS Chi-restraints excluded: chain C residue 26 SER Chi-restraints excluded: chain C residue 36 ASP Chi-restraints excluded: chain C residue 50 LEU Chi-restraints excluded: chain C residue 52 TRP Chi-restraints excluded: chain C residue 82 SER Chi-restraints excluded: chain C residue 101 CYS Chi-restraints excluded: chain C residue 108 TYR Chi-restraints excluded: chain C residue 132 VAL Chi-restraints excluded: chain C residue 149 LEU Chi-restraints excluded: chain C residue 171 THR Chi-restraints excluded: chain C residue 192 VAL Chi-restraints excluded: chain C residue 194 THR Chi-restraints excluded: chain C residue 217 LYS Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 59 random chunks: chunk 36 optimal weight: 0.0570 chunk 20 optimal weight: 0.7980 chunk 33 optimal weight: 0.9980 chunk 53 optimal weight: 2.9990 chunk 18 optimal weight: 0.0870 chunk 57 optimal weight: 2.9990 chunk 9 optimal weight: 0.9990 chunk 25 optimal weight: 0.6980 chunk 42 optimal weight: 2.9990 chunk 29 optimal weight: 0.6980 chunk 56 optimal weight: 5.9990 overall best weight: 0.4676 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 59 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 95 GLN B 205 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4370 r_free = 0.4370 target = 0.187152 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.4104 r_free = 0.4104 target = 0.163690 restraints weight = 7058.266| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.4170 r_free = 0.4170 target = 0.169408 restraints weight = 4081.429| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.4215 r_free = 0.4215 target = 0.173361 restraints weight = 2682.176| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.4244 r_free = 0.4244 target = 0.175937 restraints weight = 1890.967| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 43)----------------| | r_work = 0.4268 r_free = 0.4268 target = 0.177981 restraints weight = 1425.668| |-----------------------------------------------------------------------------| r_work (final): 0.4269 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6026 moved from start: 0.1581 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.058 4619 Z= 0.148 Angle : 0.714 8.873 6314 Z= 0.364 Chirality : 0.046 0.204 720 Planarity : 0.005 0.051 800 Dihedral : 5.524 37.302 637 Min Nonbonded Distance : 2.557 Molprobity Statistics. All-atom Clashscore : 17.25 Ramachandran Plot: Outliers : 0.34 % Allowed : 15.45 % Favored : 84.21 % Rotamer: Outliers : 6.29 % Allowed : 29.67 % Favored : 64.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.57 % 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: -2.91 (0.35), residues: 589 helix: -2.57 (1.36), residues: 14 sheet: -1.27 (0.36), residues: 209 loop : -2.42 (0.34), residues: 366 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 92 TYR 0.019 0.002 TYR B 55 PHE 0.013 0.002 PHE A 1 TRP 0.016 0.001 TRP A 103 HIS 0.006 0.002 HIS B 40 Details of bonding type rmsd covalent geometry : bond 0.00341 ( 4614) covalent geometry : angle 0.71287 ( 6304) SS BOND : bond 0.00563 ( 5) SS BOND : angle 1.17208 ( 10) hydrogen bonds : bond 0.03361 ( 98) hydrogen bonds : angle 7.16159 ( 213) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1178 Ramachandran restraints generated. 589 Oldfield, 0 Emsley, 589 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1178 Ramachandran restraints generated. 589 Oldfield, 0 Emsley, 589 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 131 residues out of total 509 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 99 time to evaluate : 0.172 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 141 ASP cc_start: 0.6378 (OUTLIER) cc_final: 0.5971 (t0) REVERT: B 154 TRP cc_start: 0.6387 (m100) cc_final: 0.6003 (m100) REVERT: B 166 GLN cc_start: 0.7116 (tm-30) cc_final: 0.6854 (tm-30) REVERT: C 38 PHE cc_start: 0.6659 (m-80) cc_final: 0.6353 (m-80) REVERT: C 149 LEU cc_start: 0.8017 (OUTLIER) cc_final: 0.7655 (pp) REVERT: C 159 GLU cc_start: 0.7658 (tp30) cc_final: 0.7372 (tp30) REVERT: C 161 VAL cc_start: 0.8362 (p) cc_final: 0.8069 (m) REVERT: C 217 LYS cc_start: 0.7593 (OUTLIER) cc_final: 0.7190 (tptp) outliers start: 32 outliers final: 21 residues processed: 118 average time/residue: 0.0614 time to fit residues: 9.6487 Evaluate side-chains 119 residues out of total 509 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 95 time to evaluate : 0.166 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 34 LEU Chi-restraints excluded: chain A residue 40 THR Chi-restraints excluded: chain A residue 48 TYR Chi-restraints excluded: chain A residue 57 THR Chi-restraints excluded: chain A residue 67 VAL Chi-restraints excluded: chain A residue 105 VAL Chi-restraints excluded: chain A residue 138 ASN Chi-restraints excluded: chain A residue 141 ASP Chi-restraints excluded: chain A residue 158 THR Chi-restraints excluded: chain B residue 24 VAL Chi-restraints excluded: chain B residue 95 GLN Chi-restraints excluded: chain B residue 160 LEU Chi-restraints excluded: chain B residue 200 CYS Chi-restraints excluded: chain B residue 205 GLN Chi-restraints excluded: chain C residue 50 LEU Chi-restraints excluded: chain C residue 52 TRP Chi-restraints excluded: chain C residue 82 SER Chi-restraints excluded: chain C residue 101 CYS Chi-restraints excluded: chain C residue 108 TYR Chi-restraints excluded: chain C residue 132 VAL Chi-restraints excluded: chain C residue 149 LEU Chi-restraints excluded: chain C residue 153 VAL Chi-restraints excluded: chain C residue 192 VAL Chi-restraints excluded: chain C residue 217 LYS Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 59 random chunks: chunk 7 optimal weight: 2.9990 chunk 58 optimal weight: 2.9990 chunk 43 optimal weight: 0.9990 chunk 44 optimal weight: 0.7980 chunk 13 optimal weight: 0.4980 chunk 1 optimal weight: 4.9990 chunk 32 optimal weight: 0.8980 chunk 9 optimal weight: 6.9990 chunk 6 optimal weight: 0.1980 chunk 52 optimal weight: 0.6980 chunk 42 optimal weight: 0.9980 overall best weight: 0.6180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 59 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 95 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 204 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4372 r_free = 0.4372 target = 0.187222 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.4107 r_free = 0.4107 target = 0.163748 restraints weight = 7133.035| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.4174 r_free = 0.4174 target = 0.169530 restraints weight = 4099.373| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.4220 r_free = 0.4220 target = 0.173571 restraints weight = 2665.944| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.4248 r_free = 0.4248 target = 0.176155 restraints weight = 1861.904| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.4271 r_free = 0.4271 target = 0.178134 restraints weight = 1392.988| |-----------------------------------------------------------------------------| r_work (final): 0.4262 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6036 moved from start: 0.1682 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.060 4619 Z= 0.166 Angle : 0.720 10.152 6314 Z= 0.369 Chirality : 0.047 0.172 720 Planarity : 0.005 0.051 800 Dihedral : 5.557 37.738 637 Min Nonbonded Distance : 2.500 Molprobity Statistics. All-atom Clashscore : 18.49 Ramachandran Plot: Outliers : 0.34 % Allowed : 15.62 % Favored : 84.04 % Rotamer: Outliers : 7.86 % Allowed : 28.88 % Favored : 63.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.57 % 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 (0.35), residues: 589 helix: -2.62 (1.33), residues: 14 sheet: -1.27 (0.36), residues: 208 loop : -2.47 (0.33), residues: 367 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 92 TYR 0.021 0.001 TYR B 55 PHE 0.012 0.002 PHE A 1 TRP 0.018 0.002 TRP A 103 HIS 0.006 0.002 HIS B 40 Details of bonding type rmsd covalent geometry : bond 0.00378 ( 4614) covalent geometry : angle 0.71837 ( 6304) SS BOND : bond 0.00615 ( 5) SS BOND : angle 1.29164 ( 10) hydrogen bonds : bond 0.03367 ( 98) hydrogen bonds : angle 7.19170 ( 213) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1178 Ramachandran restraints generated. 589 Oldfield, 0 Emsley, 589 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1178 Ramachandran restraints generated. 589 Oldfield, 0 Emsley, 589 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 141 residues out of total 509 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 101 time to evaluate : 0.162 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 166 GLN cc_start: 0.7116 (tm-30) cc_final: 0.6880 (tm-30) REVERT: C 36 ASP cc_start: 0.5886 (OUTLIER) cc_final: 0.5411 (t70) REVERT: C 38 PHE cc_start: 0.6668 (m-80) cc_final: 0.6379 (m-80) REVERT: C 149 LEU cc_start: 0.8044 (OUTLIER) cc_final: 0.7682 (pp) REVERT: C 159 GLU cc_start: 0.7819 (tp30) cc_final: 0.7551 (tp30) REVERT: C 161 VAL cc_start: 0.8378 (p) cc_final: 0.8072 (m) REVERT: C 217 LYS cc_start: 0.7605 (OUTLIER) cc_final: 0.7188 (tptp) REVERT: C 220 LYS cc_start: 0.4871 (OUTLIER) cc_final: 0.4063 (ptpp) outliers start: 40 outliers final: 22 residues processed: 130 average time/residue: 0.0552 time to fit residues: 9.6160 Evaluate side-chains 122 residues out of total 509 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 96 time to evaluate : 0.162 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 34 LEU Chi-restraints excluded: chain A residue 40 THR Chi-restraints excluded: chain A residue 48 TYR Chi-restraints excluded: chain A residue 57 THR Chi-restraints excluded: chain A residue 67 VAL Chi-restraints excluded: chain A residue 105 VAL Chi-restraints excluded: chain A residue 138 ASN Chi-restraints excluded: chain A residue 148 ILE Chi-restraints excluded: chain A residue 158 THR Chi-restraints excluded: chain B residue 24 VAL Chi-restraints excluded: chain B residue 121 VAL Chi-restraints excluded: chain B residue 200 CYS Chi-restraints excluded: chain B residue 205 GLN Chi-restraints excluded: chain C residue 36 ASP Chi-restraints excluded: chain C residue 50 LEU Chi-restraints excluded: chain C residue 52 TRP Chi-restraints excluded: chain C residue 82 SER Chi-restraints excluded: chain C residue 101 CYS Chi-restraints excluded: chain C residue 108 TYR Chi-restraints excluded: chain C residue 132 VAL Chi-restraints excluded: chain C residue 149 LEU Chi-restraints excluded: chain C residue 153 VAL Chi-restraints excluded: chain C residue 171 THR Chi-restraints excluded: chain C residue 192 VAL Chi-restraints excluded: chain C residue 217 LYS Chi-restraints excluded: chain C residue 220 LYS Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 59 random chunks: chunk 27 optimal weight: 0.6980 chunk 48 optimal weight: 0.9990 chunk 10 optimal weight: 0.9980 chunk 54 optimal weight: 1.9990 chunk 46 optimal weight: 1.9990 chunk 13 optimal weight: 3.9990 chunk 21 optimal weight: 1.9990 chunk 28 optimal weight: 0.9990 chunk 4 optimal weight: 2.9990 chunk 37 optimal weight: 0.5980 chunk 52 optimal weight: 0.0980 overall best weight: 0.6782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 59 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 95 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4379 r_free = 0.4379 target = 0.187812 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.4114 r_free = 0.4114 target = 0.164611 restraints weight = 7042.650| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.4181 r_free = 0.4181 target = 0.170286 restraints weight = 4088.372| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.4227 r_free = 0.4227 target = 0.174204 restraints weight = 2671.350| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.4255 r_free = 0.4255 target = 0.176778 restraints weight = 1871.224| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 38)----------------| | r_work = 0.4278 r_free = 0.4278 target = 0.178726 restraints weight = 1403.021| |-----------------------------------------------------------------------------| r_work (final): 0.4267 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6043 moved from start: 0.1897 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.053 4619 Z= 0.175 Angle : 0.742 12.163 6314 Z= 0.380 Chirality : 0.047 0.199 720 Planarity : 0.005 0.050 800 Dihedral : 5.629 37.669 637 Min Nonbonded Distance : 2.491 Molprobity Statistics. All-atom Clashscore : 20.07 Ramachandran Plot: Outliers : 0.34 % Allowed : 15.28 % Favored : 84.38 % Rotamer: Outliers : 6.68 % Allowed : 29.67 % Favored : 63.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.57 % 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 (0.34), residues: 589 helix: -2.59 (1.35), residues: 14 sheet: -1.27 (0.36), residues: 206 loop : -2.44 (0.33), residues: 369 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 217 TYR 0.019 0.002 TYR B 55 PHE 0.014 0.002 PHE C 69 TRP 0.024 0.002 TRP A 103 HIS 0.007 0.001 HIS B 195 Details of bonding type rmsd covalent geometry : bond 0.00393 ( 4614) covalent geometry : angle 0.74126 ( 6304) SS BOND : bond 0.00603 ( 5) SS BOND : angle 1.19761 ( 10) hydrogen bonds : bond 0.03579 ( 98) hydrogen bonds : angle 7.20346 ( 213) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1178 Ramachandran restraints generated. 589 Oldfield, 0 Emsley, 589 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1178 Ramachandran restraints generated. 589 Oldfield, 0 Emsley, 589 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 131 residues out of total 509 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 97 time to evaluate : 0.164 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 143 GLN cc_start: 0.6914 (mm-40) cc_final: 0.6664 (mm-40) REVERT: B 154 TRP cc_start: 0.6403 (m100) cc_final: 0.6096 (m100) REVERT: B 166 GLN cc_start: 0.7134 (tm-30) cc_final: 0.6899 (tm-30) REVERT: C 36 ASP cc_start: 0.5954 (OUTLIER) cc_final: 0.5334 (t70) REVERT: C 38 PHE cc_start: 0.6671 (m-80) cc_final: 0.6372 (m-80) REVERT: C 149 LEU cc_start: 0.8052 (OUTLIER) cc_final: 0.7701 (pp) REVERT: C 159 GLU cc_start: 0.7772 (tp30) cc_final: 0.7138 (tp30) REVERT: C 161 VAL cc_start: 0.8403 (p) cc_final: 0.8079 (m) REVERT: C 217 LYS cc_start: 0.7599 (OUTLIER) cc_final: 0.7138 (tptp) REVERT: C 220 LYS cc_start: 0.4643 (OUTLIER) cc_final: 0.3804 (ptpp) outliers start: 34 outliers final: 21 residues processed: 119 average time/residue: 0.0630 time to fit residues: 9.9795 Evaluate side-chains 122 residues out of total 509 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 97 time to evaluate : 0.174 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 34 LEU Chi-restraints excluded: chain A residue 40 THR Chi-restraints excluded: chain A residue 48 TYR Chi-restraints excluded: chain A residue 67 VAL Chi-restraints excluded: chain A residue 105 VAL Chi-restraints excluded: chain A residue 138 ASN Chi-restraints excluded: chain A residue 148 ILE Chi-restraints excluded: chain A residue 158 THR Chi-restraints excluded: chain B residue 24 VAL Chi-restraints excluded: chain B residue 26 ILE Chi-restraints excluded: chain B residue 95 GLN Chi-restraints excluded: chain B residue 121 VAL Chi-restraints excluded: chain B residue 200 CYS Chi-restraints excluded: chain C residue 36 ASP Chi-restraints excluded: chain C residue 50 LEU Chi-restraints excluded: chain C residue 52 TRP Chi-restraints excluded: chain C residue 82 SER Chi-restraints excluded: chain C residue 101 CYS Chi-restraints excluded: chain C residue 108 TYR Chi-restraints excluded: chain C residue 132 VAL Chi-restraints excluded: chain C residue 149 LEU Chi-restraints excluded: chain C residue 153 VAL Chi-restraints excluded: chain C residue 171 THR Chi-restraints excluded: chain C residue 217 LYS Chi-restraints excluded: chain C residue 220 LYS Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 59 random chunks: chunk 50 optimal weight: 2.9990 chunk 32 optimal weight: 3.9990 chunk 26 optimal weight: 0.7980 chunk 21 optimal weight: 1.9990 chunk 36 optimal weight: 1.9990 chunk 15 optimal weight: 0.8980 chunk 38 optimal weight: 0.7980 chunk 39 optimal weight: 0.5980 chunk 51 optimal weight: 1.9990 chunk 19 optimal weight: 0.9990 chunk 49 optimal weight: 0.6980 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 59 GLN B 38 ASN ** B 95 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4346 r_free = 0.4346 target = 0.184341 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.4083 r_free = 0.4083 target = 0.161349 restraints weight = 7084.925| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.4148 r_free = 0.4148 target = 0.166803 restraints weight = 4182.321| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.4192 r_free = 0.4192 target = 0.170545 restraints weight = 2769.952| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.4219 r_free = 0.4219 target = 0.172930 restraints weight = 1966.589| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 32)----------------| | r_work = 0.4241 r_free = 0.4241 target = 0.174816 restraints weight = 1495.133| |-----------------------------------------------------------------------------| r_work (final): 0.4234 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6074 moved from start: 0.2016 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.055 4619 Z= 0.186 Angle : 0.759 12.825 6314 Z= 0.386 Chirality : 0.049 0.191 720 Planarity : 0.005 0.050 800 Dihedral : 5.672 37.856 637 Min Nonbonded Distance : 2.484 Molprobity Statistics. All-atom Clashscore : 20.30 Ramachandran Plot: Outliers : 0.34 % Allowed : 15.62 % Favored : 84.04 % Rotamer: Outliers : 5.50 % Allowed : 30.84 % Favored : 63.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.57 % 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: -2.94 (0.34), residues: 589 helix: -2.62 (1.34), residues: 14 sheet: -1.23 (0.36), residues: 206 loop : -2.47 (0.33), residues: 369 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 132 TYR 0.020 0.002 TYR B 55 PHE 0.017 0.002 PHE C 69 TRP 0.020 0.002 TRP A 103 HIS 0.006 0.001 HIS B 195 Details of bonding type rmsd covalent geometry : bond 0.00414 ( 4614) covalent geometry : angle 0.75846 ( 6304) SS BOND : bond 0.00562 ( 5) SS BOND : angle 1.14199 ( 10) hydrogen bonds : bond 0.03661 ( 98) hydrogen bonds : angle 7.19884 ( 213) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1178 Ramachandran restraints generated. 589 Oldfield, 0 Emsley, 589 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1178 Ramachandran restraints generated. 589 Oldfield, 0 Emsley, 589 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 128 residues out of total 509 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 100 time to evaluate : 0.164 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 143 GLN cc_start: 0.6852 (mm-40) cc_final: 0.6580 (mm-40) REVERT: B 154 TRP cc_start: 0.6473 (m100) cc_final: 0.6134 (m100) REVERT: B 166 GLN cc_start: 0.7141 (tm-30) cc_final: 0.6910 (tm-30) REVERT: B 200 CYS cc_start: 0.1668 (OUTLIER) cc_final: 0.1410 (p) REVERT: C 36 ASP cc_start: 0.5990 (OUTLIER) cc_final: 0.5475 (t70) REVERT: C 38 PHE cc_start: 0.6588 (m-80) cc_final: 0.6323 (m-80) REVERT: C 149 LEU cc_start: 0.8098 (OUTLIER) cc_final: 0.7753 (pp) REVERT: C 159 GLU cc_start: 0.7619 (tp30) cc_final: 0.6978 (tp30) REVERT: C 161 VAL cc_start: 0.8415 (p) cc_final: 0.8095 (m) REVERT: C 217 LYS cc_start: 0.7607 (OUTLIER) cc_final: 0.7152 (tptp) REVERT: C 220 LYS cc_start: 0.4606 (OUTLIER) cc_final: 0.3735 (ptpp) outliers start: 28 outliers final: 22 residues processed: 118 average time/residue: 0.0668 time to fit residues: 10.3417 Evaluate side-chains 124 residues out of total 509 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 97 time to evaluate : 0.164 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 34 LEU Chi-restraints excluded: chain A residue 40 THR Chi-restraints excluded: chain A residue 48 TYR Chi-restraints excluded: chain A residue 57 THR Chi-restraints excluded: chain A residue 67 VAL Chi-restraints excluded: chain A residue 105 VAL Chi-restraints excluded: chain A residue 138 ASN Chi-restraints excluded: chain A residue 158 THR Chi-restraints excluded: chain B residue 24 VAL Chi-restraints excluded: chain B residue 34 ILE Chi-restraints excluded: chain B residue 116 VAL Chi-restraints excluded: chain B residue 121 VAL Chi-restraints excluded: chain B residue 200 CYS Chi-restraints excluded: chain C residue 36 ASP Chi-restraints excluded: chain C residue 50 LEU Chi-restraints excluded: chain C residue 52 TRP Chi-restraints excluded: chain C residue 82 SER Chi-restraints excluded: chain C residue 94 GLU Chi-restraints excluded: chain C residue 101 CYS Chi-restraints excluded: chain C residue 106 ARG Chi-restraints excluded: chain C residue 108 TYR Chi-restraints excluded: chain C residue 132 VAL Chi-restraints excluded: chain C residue 149 LEU Chi-restraints excluded: chain C residue 153 VAL Chi-restraints excluded: chain C residue 171 THR Chi-restraints excluded: chain C residue 217 LYS Chi-restraints excluded: chain C residue 220 LYS Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 59 random chunks: chunk 30 optimal weight: 2.9990 chunk 51 optimal weight: 4.9990 chunk 33 optimal weight: 0.9990 chunk 42 optimal weight: 0.8980 chunk 28 optimal weight: 0.6980 chunk 26 optimal weight: 1.9990 chunk 0 optimal weight: 8.9990 chunk 38 optimal weight: 0.6980 chunk 50 optimal weight: 0.6980 chunk 54 optimal weight: 0.8980 chunk 40 optimal weight: 1.9990 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 95 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4341 r_free = 0.4341 target = 0.183720 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 26)----------------| | r_work = 0.4082 r_free = 0.4082 target = 0.161095 restraints weight = 7009.365| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.4148 r_free = 0.4148 target = 0.166630 restraints weight = 4077.725| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 41)----------------| | r_work = 0.4192 r_free = 0.4192 target = 0.170384 restraints weight = 2664.585| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 36)----------------| | r_work = 0.4221 r_free = 0.4221 target = 0.172935 restraints weight = 1875.329| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.4241 r_free = 0.4241 target = 0.174642 restraints weight = 1396.705| |-----------------------------------------------------------------------------| r_work (final): 0.4235 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6075 moved from start: 0.2192 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.067 4619 Z= 0.191 Angle : 0.770 13.382 6314 Z= 0.394 Chirality : 0.049 0.185 720 Planarity : 0.006 0.050 800 Dihedral : 5.783 38.410 637 Min Nonbonded Distance : 2.477 Molprobity Statistics. All-atom Clashscore : 19.96 Ramachandran Plot: Outliers : 0.34 % Allowed : 16.30 % Favored : 83.36 % Rotamer: Outliers : 6.09 % Allowed : 30.26 % Favored : 63.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.57 % 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: -3.19 (0.34), residues: 589 helix: -3.54 (0.77), residues: 26 sheet: -1.25 (0.36), residues: 204 loop : -2.66 (0.32), residues: 359 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 217 TYR 0.022 0.002 TYR B 55 PHE 0.014 0.002 PHE C 69 TRP 0.030 0.002 TRP A 103 HIS 0.007 0.002 HIS B 195 Details of bonding type rmsd covalent geometry : bond 0.00423 ( 4614) covalent geometry : angle 0.76901 ( 6304) SS BOND : bond 0.00639 ( 5) SS BOND : angle 1.23956 ( 10) hydrogen bonds : bond 0.03734 ( 98) hydrogen bonds : angle 7.25496 ( 213) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1178 Ramachandran restraints generated. 589 Oldfield, 0 Emsley, 589 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1178 Ramachandran restraints generated. 589 Oldfield, 0 Emsley, 589 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 130 residues out of total 509 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 99 time to evaluate : 0.165 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 143 GLN cc_start: 0.6854 (mm-40) cc_final: 0.6653 (mp10) REVERT: B 154 TRP cc_start: 0.6495 (m100) cc_final: 0.6134 (m100) REVERT: B 166 GLN cc_start: 0.7175 (tm-30) cc_final: 0.6924 (tm-30) REVERT: B 200 CYS cc_start: 0.1689 (OUTLIER) cc_final: 0.1404 (p) REVERT: C 36 ASP cc_start: 0.5981 (OUTLIER) cc_final: 0.5448 (t70) REVERT: C 38 PHE cc_start: 0.6577 (m-80) cc_final: 0.6299 (m-80) REVERT: C 149 LEU cc_start: 0.8092 (OUTLIER) cc_final: 0.7775 (pp) REVERT: C 159 GLU cc_start: 0.7599 (tp30) cc_final: 0.6953 (tp30) REVERT: C 161 VAL cc_start: 0.8416 (p) cc_final: 0.8097 (m) REVERT: C 217 LYS cc_start: 0.7605 (OUTLIER) cc_final: 0.7136 (tptp) REVERT: C 220 LYS cc_start: 0.4561 (OUTLIER) cc_final: 0.3691 (ptpp) outliers start: 31 outliers final: 23 residues processed: 120 average time/residue: 0.0671 time to fit residues: 10.5727 Evaluate side-chains 124 residues out of total 509 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 96 time to evaluate : 0.168 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 34 LEU Chi-restraints excluded: chain A residue 40 THR Chi-restraints excluded: chain A residue 48 TYR Chi-restraints excluded: chain A residue 67 VAL Chi-restraints excluded: chain A residue 75 VAL Chi-restraints excluded: chain A residue 105 VAL Chi-restraints excluded: chain A residue 138 ASN Chi-restraints excluded: chain A residue 148 ILE Chi-restraints excluded: chain A residue 158 THR Chi-restraints excluded: chain B residue 24 VAL Chi-restraints excluded: chain B residue 26 ILE Chi-restraints excluded: chain B residue 34 ILE Chi-restraints excluded: chain B residue 39 LEU Chi-restraints excluded: chain B residue 116 VAL Chi-restraints excluded: chain B residue 121 VAL Chi-restraints excluded: chain B residue 200 CYS Chi-restraints excluded: chain C residue 36 ASP Chi-restraints excluded: chain C residue 50 LEU Chi-restraints excluded: chain C residue 52 TRP Chi-restraints excluded: chain C residue 82 SER Chi-restraints excluded: chain C residue 94 GLU Chi-restraints excluded: chain C residue 101 CYS Chi-restraints excluded: chain C residue 108 TYR Chi-restraints excluded: chain C residue 149 LEU Chi-restraints excluded: chain C residue 153 VAL Chi-restraints excluded: chain C residue 171 THR Chi-restraints excluded: chain C residue 217 LYS Chi-restraints excluded: chain C residue 220 LYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 59 random chunks: chunk 58 optimal weight: 0.0980 chunk 53 optimal weight: 4.9990 chunk 25 optimal weight: 0.9990 chunk 21 optimal weight: 0.5980 chunk 42 optimal weight: 2.9990 chunk 52 optimal weight: 0.5980 chunk 5 optimal weight: 0.3980 chunk 2 optimal weight: 0.0570 chunk 23 optimal weight: 5.9990 chunk 3 optimal weight: 0.8980 chunk 16 optimal weight: 3.9990 overall best weight: 0.3498 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 95 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4420 r_free = 0.4420 target = 0.191866 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.4159 r_free = 0.4159 target = 0.168605 restraints weight = 6970.233| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.4231 r_free = 0.4231 target = 0.174598 restraints weight = 3958.425| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.4276 r_free = 0.4276 target = 0.178557 restraints weight = 2531.947| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.4306 r_free = 0.4306 target = 0.181220 restraints weight = 1750.261| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 34)----------------| | r_work = 0.4328 r_free = 0.4328 target = 0.183234 restraints weight = 1287.996| |-----------------------------------------------------------------------------| r_work (final): 0.4302 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5992 moved from start: 0.2247 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.068 4619 Z= 0.138 Angle : 0.746 11.594 6314 Z= 0.381 Chirality : 0.048 0.176 720 Planarity : 0.006 0.058 800 Dihedral : 5.618 38.216 637 Min Nonbonded Distance : 2.497 Molprobity Statistics. All-atom Clashscore : 17.48 Ramachandran Plot: Outliers : 0.34 % Allowed : 14.94 % Favored : 84.72 % Rotamer: Outliers : 5.11 % Allowed : 31.83 % Favored : 63.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.57 % 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: -2.83 (0.35), residues: 589 helix: -2.58 (1.35), residues: 14 sheet: -1.11 (0.38), residues: 201 loop : -2.42 (0.33), residues: 374 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG A 98 TYR 0.018 0.001 TYR B 55 PHE 0.025 0.002 PHE C 69 TRP 0.023 0.002 TRP A 103 HIS 0.006 0.002 HIS B 195 Details of bonding type rmsd covalent geometry : bond 0.00325 ( 4614) covalent geometry : angle 0.74610 ( 6304) SS BOND : bond 0.00465 ( 5) SS BOND : angle 0.85734 ( 10) hydrogen bonds : bond 0.03194 ( 98) hydrogen bonds : angle 6.93191 ( 213) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1178 Ramachandran restraints generated. 589 Oldfield, 0 Emsley, 589 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1178 Ramachandran restraints generated. 589 Oldfield, 0 Emsley, 589 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 119 residues out of total 509 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 93 time to evaluate : 0.148 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 154 TRP cc_start: 0.6456 (m100) cc_final: 0.6092 (m100) REVERT: B 200 CYS cc_start: 0.1381 (OUTLIER) cc_final: 0.1104 (p) REVERT: C 36 ASP cc_start: 0.5915 (OUTLIER) cc_final: 0.5375 (t70) REVERT: C 38 PHE cc_start: 0.6609 (m-80) cc_final: 0.6390 (m-80) REVERT: C 149 LEU cc_start: 0.8044 (pp) cc_final: 0.7696 (pp) REVERT: C 217 LYS cc_start: 0.7562 (OUTLIER) cc_final: 0.7057 (tptp) REVERT: C 220 LYS cc_start: 0.4620 (OUTLIER) cc_final: 0.3820 (ptpp) outliers start: 26 outliers final: 18 residues processed: 110 average time/residue: 0.0573 time to fit residues: 8.4254 Evaluate side-chains 111 residues out of total 509 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 89 time to evaluate : 0.185 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 34 LEU Chi-restraints excluded: chain A residue 40 THR Chi-restraints excluded: chain A residue 48 TYR Chi-restraints excluded: chain A residue 67 VAL Chi-restraints excluded: chain A residue 75 VAL Chi-restraints excluded: chain A residue 105 VAL Chi-restraints excluded: chain A residue 148 ILE Chi-restraints excluded: chain A residue 158 THR Chi-restraints excluded: chain B residue 24 VAL Chi-restraints excluded: chain B residue 34 ILE Chi-restraints excluded: chain B residue 39 LEU Chi-restraints excluded: chain B residue 121 VAL Chi-restraints excluded: chain B residue 200 CYS Chi-restraints excluded: chain C residue 36 ASP Chi-restraints excluded: chain C residue 50 LEU Chi-restraints excluded: chain C residue 52 TRP Chi-restraints excluded: chain C residue 101 CYS Chi-restraints excluded: chain C residue 108 TYR Chi-restraints excluded: chain C residue 153 VAL Chi-restraints excluded: chain C residue 171 THR Chi-restraints excluded: chain C residue 217 LYS Chi-restraints excluded: chain C residue 220 LYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 59 random chunks: chunk 55 optimal weight: 4.9990 chunk 35 optimal weight: 0.8980 chunk 4 optimal weight: 3.9990 chunk 49 optimal weight: 0.9980 chunk 51 optimal weight: 0.6980 chunk 3 optimal weight: 0.3980 chunk 56 optimal weight: 0.9980 chunk 44 optimal weight: 1.9990 chunk 36 optimal weight: 0.1980 chunk 34 optimal weight: 1.9990 chunk 12 optimal weight: 1.9990 overall best weight: 0.6380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 143 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4359 r_free = 0.4359 target = 0.185560 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.4100 r_free = 0.4100 target = 0.162939 restraints weight = 7046.779| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.4164 r_free = 0.4164 target = 0.168338 restraints weight = 4186.120| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.4207 r_free = 0.4207 target = 0.172017 restraints weight = 2762.829| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.4235 r_free = 0.4235 target = 0.174453 restraints weight = 1963.611| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 37)----------------| | r_work = 0.4257 r_free = 0.4257 target = 0.176399 restraints weight = 1482.575| |-----------------------------------------------------------------------------| r_work (final): 0.4254 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6046 moved from start: 0.2349 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.065 4619 Z= 0.171 Angle : 0.793 13.919 6314 Z= 0.401 Chirality : 0.048 0.171 720 Planarity : 0.006 0.053 800 Dihedral : 5.727 38.629 637 Min Nonbonded Distance : 2.479 Molprobity Statistics. All-atom Clashscore : 19.17 Ramachandran Plot: Outliers : 0.34 % Allowed : 16.13 % Favored : 83.53 % Rotamer: Outliers : 5.11 % Allowed : 32.22 % Favored : 62.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.57 % 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: -2.87 (0.35), residues: 589 helix: -2.43 (1.43), residues: 14 sheet: -1.19 (0.37), residues: 206 loop : -2.43 (0.33), residues: 369 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG A 98 TYR 0.020 0.002 TYR B 55 PHE 0.024 0.002 PHE C 69 TRP 0.026 0.002 TRP A 103 HIS 0.007 0.002 HIS B 195 Details of bonding type rmsd covalent geometry : bond 0.00391 ( 4614) covalent geometry : angle 0.79198 ( 6304) SS BOND : bond 0.00586 ( 5) SS BOND : angle 1.20118 ( 10) hydrogen bonds : bond 0.03593 ( 98) hydrogen bonds : angle 7.00840 ( 213) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 987.18 seconds wall clock time: 17 minutes 49.06 seconds (1069.06 seconds total)