Starting phenix.real_space_refine on Wed Jul 23 22:35:52 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9ccu_45458/07_2025/9ccu_45458.cif Found real_map, /net/cci-nas-00/data/ceres_data/9ccu_45458/07_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_45458/07_2025/9ccu_45458.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9ccu_45458/07_2025/9ccu_45458.map" model { file = "/net/cci-nas-00/data/ceres_data/9ccu_45458/07_2025/9ccu_45458.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9ccu_45458/07_2025/9ccu_45458.cif" } resolution = 3.8 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.001 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): 0.01s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5711/modules/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: 3.34, per 1000 atoms: 0.74 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: 1.23 Conformation dependent library (CDL) restraints added in 575.4 milliseconds 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: 0.62 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: 1.10 Time building geometry restraints manager: 1.42 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: 0.620 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: 0.190 Check model and map are aligned: 0.040 Set scattering table: 0.040 Process input model: 15.360 Find NCS groups from input model: 0.050 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.930 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 19.250 ------------------------------------------------------------------------------- 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 : 15.90 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.22 (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 TRP 0.035 0.003 TRP B 154 HIS 0.009 0.002 HIS B 195 PHE 0.018 0.002 PHE B 122 TYR 0.018 0.002 TYR B 55 ARG 0.004 0.001 ARG A 92 Details of bonding type rmsd hydrogen bonds : bond 0.18991 ( 98) hydrogen bonds : angle 9.79919 ( 213) SS BOND : bond 0.00774 ( 5) SS BOND : angle 1.35936 ( 10) covalent geometry : bond 0.00478 ( 4614) covalent geometry : angle 0.91314 ( 6304) *********************** 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 : 0.377 Fit side-chains 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: 0.1301 time to fit residues: 16.8848 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 : 0.448 ------------------------------------------------------------------------------- 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 49 optimal weight: 0.9990 chunk 44 optimal weight: 2.9990 chunk 24 optimal weight: 0.6980 chunk 15 optimal weight: 2.9990 chunk 30 optimal weight: 0.7980 chunk 23 optimal weight: 2.9990 chunk 46 optimal weight: 1.9990 chunk 17 optimal weight: 0.7980 chunk 28 optimal weight: 0.7980 chunk 34 optimal weight: 0.9990 chunk 53 optimal weight: 4.9990 overall best weight: 0.8182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 43 GLN ** B 95 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 130 GLN C 10 GLN C 166 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4359 r_free = 0.4359 target = 0.186883 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.4103 r_free = 0.4103 target = 0.164301 restraints weight = 6986.637| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.4168 r_free = 0.4168 target = 0.169864 restraints weight = 4048.442| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.4214 r_free = 0.4214 target = 0.173733 restraints weight = 2640.747| |-----------------------------------------------------------------------------| r_work (final): 0.4203 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6108 moved from start: 0.0983 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.068 4619 Z= 0.195 Angle : 0.746 7.454 6314 Z= 0.386 Chirality : 0.048 0.212 720 Planarity : 0.006 0.056 800 Dihedral : 6.380 45.701 644 Min Nonbonded Distance : 2.494 Molprobity Statistics. All-atom Clashscore : 17.14 Ramachandran Plot: Outliers : 0.34 % Allowed : 15.28 % Favored : 84.38 % Rotamer: Outliers : 6.09 % Allowed : 28.68 % Favored : 65.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.57 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.12 (0.34), residues: 589 helix: -2.84 (1.24), residues: 14 sheet: -1.46 (0.35), residues: 217 loop : -2.54 (0.33), residues: 358 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP A 103 HIS 0.006 0.002 HIS B 40 PHE 0.013 0.002 PHE A 1 TYR 0.020 0.002 TYR B 55 ARG 0.002 0.000 ARG B 217 Details of bonding type rmsd hydrogen bonds : bond 0.04266 ( 98) hydrogen bonds : angle 8.10509 ( 213) SS BOND : bond 0.00702 ( 5) SS BOND : angle 1.23825 ( 10) covalent geometry : bond 0.00432 ( 4614) covalent geometry : angle 0.74498 ( 6304) *********************** 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 127 residues out of total 509 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 96 time to evaluate : 0.447 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 38 PHE cc_start: 0.6586 (m-80) cc_final: 0.6319 (m-80) REVERT: C 149 LEU cc_start: 0.8098 (OUTLIER) cc_final: 0.7730 (pp) REVERT: C 217 LYS cc_start: 0.7617 (OUTLIER) cc_final: 0.7320 (tptp) outliers start: 31 outliers final: 13 residues processed: 119 average time/residue: 0.1524 time to fit residues: 23.3339 Evaluate side-chains 110 residues out of total 509 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 95 time to evaluate : 0.437 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 40 THR Chi-restraints excluded: chain A residue 138 ASN 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 192 VAL 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 22 optimal weight: 3.9990 chunk 36 optimal weight: 0.8980 chunk 47 optimal weight: 0.3980 chunk 20 optimal weight: 1.9990 chunk 39 optimal weight: 0.4980 chunk 21 optimal weight: 0.6980 chunk 2 optimal weight: 0.4980 chunk 5 optimal weight: 0.8980 chunk 38 optimal weight: 0.6980 chunk 50 optimal weight: 0.0670 chunk 18 optimal weight: 0.8980 overall best weight: 0.4318 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 11 GLN B 95 GLN ** C 11 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 = 0.4384 r_free = 0.4384 target = 0.189216 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 24)----------------| | r_work = 0.4129 r_free = 0.4129 target = 0.166102 restraints weight = 7051.368| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.4195 r_free = 0.4195 target = 0.171903 restraints weight = 4045.164| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.4239 r_free = 0.4239 target = 0.175816 restraints weight = 2618.719| |-----------------------------------------------------------------------------| r_work (final): 0.4226 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6060 moved from start: 0.1266 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.062 4619 Z= 0.144 Angle : 0.701 7.543 6314 Z= 0.359 Chirality : 0.046 0.207 720 Planarity : 0.005 0.054 800 Dihedral : 5.654 37.532 642 Min Nonbonded Distance : 2.538 Molprobity Statistics. All-atom Clashscore : 16.24 Ramachandran Plot: Outliers : 0.34 % Allowed : 15.62 % Favored : 84.04 % Rotamer: Outliers : 5.89 % Allowed : 29.08 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.09 (0.34), residues: 589 helix: -2.56 (1.37), residues: 14 sheet: -1.44 (0.34), residues: 222 loop : -2.54 (0.33), residues: 353 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP A 103 HIS 0.004 0.002 HIS B 40 PHE 0.014 0.002 PHE A 1 TYR 0.019 0.001 TYR B 55 ARG 0.002 0.000 ARG B 67 Details of bonding type rmsd hydrogen bonds : bond 0.03629 ( 98) hydrogen bonds : angle 7.23851 ( 213) SS BOND : bond 0.00600 ( 5) SS BOND : angle 0.98367 ( 10) covalent geometry : bond 0.00341 ( 4614) covalent geometry : angle 0.70044 ( 6304) *********************** 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: 30 poor density : 95 time to evaluate : 0.441 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 154 TRP cc_start: 0.6469 (m100) cc_final: 0.6149 (m100) REVERT: C 36 ASP cc_start: 0.5909 (OUTLIER) cc_final: 0.5364 (t70) REVERT: C 38 PHE cc_start: 0.6629 (m-80) cc_final: 0.6288 (m-80) REVERT: C 106 ARG cc_start: 0.7066 (mtm180) cc_final: 0.6772 (mtm180) REVERT: C 149 LEU cc_start: 0.8005 (OUTLIER) cc_final: 0.7636 (pp) REVERT: C 159 GLU cc_start: 0.7627 (tp30) cc_final: 0.6976 (tp30) REVERT: C 217 LYS cc_start: 0.7613 (OUTLIER) cc_final: 0.7275 (tptp) outliers start: 30 outliers final: 18 residues processed: 112 average time/residue: 0.1615 time to fit residues: 23.8746 Evaluate side-chains 113 residues out of total 509 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 92 time to evaluate : 0.858 ------------------------------------------------------------------------------- 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 158 THR Chi-restraints excluded: chain B residue 24 VAL Chi-restraints excluded: chain B residue 95 GLN 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 153 VAL Chi-restraints excluded: chain C residue 162 THR 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 24 optimal weight: 1.9990 chunk 51 optimal weight: 3.9990 chunk 40 optimal weight: 2.9990 chunk 45 optimal weight: 0.9980 chunk 10 optimal weight: 0.9980 chunk 37 optimal weight: 0.9980 chunk 33 optimal weight: 1.9990 chunk 30 optimal weight: 2.9990 chunk 17 optimal weight: 3.9990 chunk 8 optimal weight: 1.9990 chunk 39 optimal weight: 0.8980 overall best weight: 1.1782 ------------------------------------------------------------------------------- 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 204 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4305 r_free = 0.4305 target = 0.181159 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.4048 r_free = 0.4048 target = 0.158524 restraints weight = 7047.749| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.4112 r_free = 0.4112 target = 0.163979 restraints weight = 4141.328| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.4154 r_free = 0.4154 target = 0.167689 restraints weight = 2719.582| |-----------------------------------------------------------------------------| r_work (final): 0.4153 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6192 moved from start: 0.1623 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.066 4619 Z= 0.253 Angle : 0.786 11.148 6314 Z= 0.405 Chirality : 0.049 0.231 720 Planarity : 0.006 0.054 800 Dihedral : 5.904 37.137 637 Min Nonbonded Distance : 2.547 Molprobity Statistics. All-atom Clashscore : 21.31 Ramachandran Plot: Outliers : 0.34 % Allowed : 16.13 % Favored : 83.53 % Rotamer: Outliers : 7.47 % Allowed : 27.70 % Favored : 64.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.57 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.32 (0.33), residues: 589 helix: -3.52 (0.77), residues: 26 sheet: -1.25 (0.35), residues: 209 loop : -2.84 (0.32), residues: 354 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.003 TRP A 103 HIS 0.007 0.002 HIS B 40 PHE 0.016 0.002 PHE B 122 TYR 0.019 0.002 TYR B 55 ARG 0.004 0.000 ARG B 217 Details of bonding type rmsd hydrogen bonds : bond 0.04550 ( 98) hydrogen bonds : angle 7.56311 ( 213) SS BOND : bond 0.00748 ( 5) SS BOND : angle 1.36541 ( 10) covalent geometry : bond 0.00542 ( 4614) covalent geometry : angle 0.78446 ( 6304) *********************** 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 137 residues out of total 509 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 99 time to evaluate : 0.486 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 55 TYR cc_start: 0.4836 (p90) cc_final: 0.4559 (p90) REVERT: B 154 TRP cc_start: 0.6717 (m100) cc_final: 0.6316 (m100) REVERT: C 36 ASP cc_start: 0.6063 (OUTLIER) cc_final: 0.5502 (t70) REVERT: C 38 PHE cc_start: 0.6647 (m-80) cc_final: 0.6300 (m-80) REVERT: C 149 LEU cc_start: 0.8204 (OUTLIER) cc_final: 0.7882 (pp) REVERT: C 217 LYS cc_start: 0.7627 (OUTLIER) cc_final: 0.7315 (tptp) outliers start: 38 outliers final: 23 residues processed: 126 average time/residue: 0.1470 time to fit residues: 24.3413 Evaluate side-chains 124 residues out of total 509 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 98 time to evaluate : 0.444 ------------------------------------------------------------------------------- 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 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 0 optimal weight: 7.9990 chunk 18 optimal weight: 0.8980 chunk 56 optimal weight: 0.7980 chunk 38 optimal weight: 1.9990 chunk 9 optimal weight: 1.9990 chunk 24 optimal weight: 1.9990 chunk 11 optimal weight: 0.4980 chunk 26 optimal weight: 1.9990 chunk 50 optimal weight: 2.9990 chunk 28 optimal weight: 0.8980 chunk 41 optimal weight: 0.9980 overall best weight: 0.8180 ------------------------------------------------------------------------------- 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 96 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 = 0.4300 r_free = 0.4300 target = 0.178990 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.4051 r_free = 0.4051 target = 0.157322 restraints weight = 7240.084| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.4111 r_free = 0.4111 target = 0.162448 restraints weight = 4313.469| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 25)----------------| | r_work = 0.4152 r_free = 0.4152 target = 0.165980 restraints weight = 2862.283| |-----------------------------------------------------------------------------| r_work (final): 0.4171 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6156 moved from start: 0.1764 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= 0.199 Angle : 0.771 11.494 6314 Z= 0.392 Chirality : 0.048 0.219 720 Planarity : 0.006 0.052 800 Dihedral : 5.819 37.292 637 Min Nonbonded Distance : 2.547 Molprobity Statistics. All-atom Clashscore : 21.09 Ramachandran Plot: Outliers : 0.34 % Allowed : 15.45 % Favored : 84.21 % Rotamer: Outliers : 6.88 % Allowed : 29.27 % Favored : 63.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.57 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.11 (0.34), residues: 589 helix: -3.33 (0.95), residues: 20 sheet: -1.25 (0.35), residues: 211 loop : -2.62 (0.33), residues: 358 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.002 TRP A 103 HIS 0.008 0.002 HIS B 40 PHE 0.013 0.002 PHE B 122 TYR 0.019 0.002 TYR B 55 ARG 0.002 0.000 ARG B 217 Details of bonding type rmsd hydrogen bonds : bond 0.03877 ( 98) hydrogen bonds : angle 7.36308 ( 213) SS BOND : bond 0.00645 ( 5) SS BOND : angle 1.31797 ( 10) covalent geometry : bond 0.00437 ( 4614) covalent geometry : angle 0.76983 ( 6304) *********************** 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 137 residues out of total 509 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 102 time to evaluate : 0.477 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 92 ARG cc_start: 0.8044 (ttp-170) cc_final: 0.7807 (ttp-170) REVERT: A 141 ASP cc_start: 0.6613 (OUTLIER) cc_final: 0.6193 (t0) REVERT: B 55 TYR cc_start: 0.4737 (p90) cc_final: 0.4524 (p90) REVERT: B 166 GLN cc_start: 0.7120 (tm-30) cc_final: 0.6872 (tm-30) REVERT: C 36 ASP cc_start: 0.6033 (OUTLIER) cc_final: 0.5446 (t70) REVERT: C 38 PHE cc_start: 0.6655 (m-80) cc_final: 0.6352 (m-80) REVERT: C 149 LEU cc_start: 0.8181 (OUTLIER) cc_final: 0.7851 (pp) REVERT: C 159 GLU cc_start: 0.7868 (tp30) cc_final: 0.7610 (tp30) REVERT: C 161 VAL cc_start: 0.8419 (p) cc_final: 0.8115 (m) REVERT: C 217 LYS cc_start: 0.7620 (OUTLIER) cc_final: 0.7257 (tptp) outliers start: 35 outliers final: 22 residues processed: 125 average time/residue: 0.1322 time to fit residues: 21.7898 Evaluate side-chains 125 residues out of total 509 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 99 time to evaluate : 0.464 ------------------------------------------------------------------------------- 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 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 205 GLN 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 153 VAL Chi-restraints excluded: chain C residue 171 THR Chi-restraints excluded: chain C residue 194 THR 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 37 optimal weight: 0.9990 chunk 50 optimal weight: 1.9990 chunk 0 optimal weight: 8.9990 chunk 1 optimal weight: 0.9990 chunk 57 optimal weight: 0.2980 chunk 41 optimal weight: 1.9990 chunk 10 optimal weight: 0.4980 chunk 21 optimal weight: 2.9990 chunk 19 optimal weight: 0.9990 chunk 55 optimal weight: 0.9990 chunk 42 optimal weight: 0.8980 overall best weight: 0.7384 ------------------------------------------------------------------------------- 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 = 0.4307 r_free = 0.4307 target = 0.179228 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.4061 r_free = 0.4061 target = 0.157842 restraints weight = 7095.328| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.4121 r_free = 0.4121 target = 0.162965 restraints weight = 4209.063| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.4162 r_free = 0.4162 target = 0.166444 restraints weight = 2774.461| |-----------------------------------------------------------------------------| r_work (final): 0.4181 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6146 moved from start: 0.1986 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.050 4619 Z= 0.188 Angle : 0.757 12.712 6314 Z= 0.387 Chirality : 0.048 0.172 720 Planarity : 0.005 0.052 800 Dihedral : 5.781 37.175 637 Min Nonbonded Distance : 2.496 Molprobity Statistics. All-atom Clashscore : 20.75 Ramachandran Plot: Outliers : 0.34 % Allowed : 15.62 % Favored : 84.04 % Rotamer: Outliers : 7.86 % Allowed : 29.08 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.14 (0.34), residues: 589 helix: -3.41 (0.91), residues: 20 sheet: -1.30 (0.36), residues: 201 loop : -2.60 (0.32), residues: 368 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.002 TRP A 103 HIS 0.007 0.002 HIS B 195 PHE 0.013 0.002 PHE A 1 TYR 0.017 0.002 TYR B 55 ARG 0.002 0.000 ARG B 217 Details of bonding type rmsd hydrogen bonds : bond 0.03760 ( 98) hydrogen bonds : angle 7.22592 ( 213) SS BOND : bond 0.00606 ( 5) SS BOND : angle 1.12305 ( 10) covalent geometry : bond 0.00420 ( 4614) covalent geometry : angle 0.75664 ( 6304) *********************** 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 139 residues out of total 509 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 99 time to evaluate : 0.431 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 154 TRP cc_start: 0.6721 (m100) cc_final: 0.6410 (m100) REVERT: C 36 ASP cc_start: 0.6039 (OUTLIER) cc_final: 0.5420 (t70) REVERT: C 38 PHE cc_start: 0.6627 (m-80) cc_final: 0.6338 (m-80) REVERT: C 149 LEU cc_start: 0.8164 (OUTLIER) cc_final: 0.7834 (pp) REVERT: C 159 GLU cc_start: 0.7767 (tp30) cc_final: 0.7561 (tp30) REVERT: C 161 VAL cc_start: 0.8418 (p) cc_final: 0.8121 (m) REVERT: C 217 LYS cc_start: 0.7615 (OUTLIER) cc_final: 0.7240 (tptp) REVERT: C 220 LYS cc_start: 0.4727 (OUTLIER) cc_final: 0.3808 (ptpp) outliers start: 40 outliers final: 28 residues processed: 127 average time/residue: 0.1367 time to fit residues: 22.6959 Evaluate side-chains 129 residues out of total 509 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 97 time to evaluate : 0.443 ------------------------------------------------------------------------------- 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 95 GLN Chi-restraints excluded: chain B residue 116 VAL Chi-restraints excluded: chain B residue 121 VAL Chi-restraints excluded: chain B residue 205 GLN 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 171 THR Chi-restraints excluded: chain C residue 194 THR 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 55 optimal weight: 3.9990 chunk 7 optimal weight: 2.9990 chunk 10 optimal weight: 0.6980 chunk 0 optimal weight: 8.9990 chunk 44 optimal weight: 0.9990 chunk 3 optimal weight: 0.0770 chunk 41 optimal weight: 1.9990 chunk 37 optimal weight: 0.9980 chunk 50 optimal weight: 1.9990 chunk 15 optimal weight: 1.9990 chunk 16 optimal weight: 0.4980 overall best weight: 0.6540 ------------------------------------------------------------------------------- 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 = 0.4340 r_free = 0.4340 target = 0.183844 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.4079 r_free = 0.4079 target = 0.161126 restraints weight = 7029.032| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.4141 r_free = 0.4141 target = 0.166446 restraints weight = 4198.830| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.4184 r_free = 0.4184 target = 0.170118 restraints weight = 2803.355| |-----------------------------------------------------------------------------| r_work (final): 0.4180 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6141 moved from start: 0.2019 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 4619 Z= 0.176 Angle : 0.754 12.489 6314 Z= 0.384 Chirality : 0.048 0.221 720 Planarity : 0.005 0.052 800 Dihedral : 5.684 35.867 637 Min Nonbonded Distance : 2.491 Molprobity Statistics. All-atom Clashscore : 19.73 Ramachandran Plot: Outliers : 0.34 % Allowed : 15.62 % Favored : 84.04 % Rotamer: Outliers : 6.68 % Allowed : 29.27 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.15 (0.34), residues: 589 helix: -3.48 (0.89), residues: 20 sheet: -1.23 (0.35), residues: 208 loop : -2.67 (0.32), residues: 361 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP A 103 HIS 0.007 0.002 HIS B 195 PHE 0.013 0.002 PHE A 1 TYR 0.019 0.002 TYR B 55 ARG 0.002 0.000 ARG B 217 Details of bonding type rmsd hydrogen bonds : bond 0.03616 ( 98) hydrogen bonds : angle 7.08669 ( 213) SS BOND : bond 0.00536 ( 5) SS BOND : angle 0.98317 ( 10) covalent geometry : bond 0.00390 ( 4614) covalent geometry : angle 0.75387 ( 6304) *********************** 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 134 residues out of total 509 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 100 time to evaluate : 0.480 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 154 TRP cc_start: 0.6811 (m100) cc_final: 0.6372 (m100) REVERT: C 36 ASP cc_start: 0.6019 (OUTLIER) cc_final: 0.5422 (t70) REVERT: C 38 PHE cc_start: 0.6641 (m-80) cc_final: 0.6367 (m-80) REVERT: C 106 ARG cc_start: 0.7141 (OUTLIER) cc_final: 0.6846 (ttm170) REVERT: C 149 LEU cc_start: 0.8171 (OUTLIER) cc_final: 0.7820 (pp) REVERT: C 161 VAL cc_start: 0.8426 (p) cc_final: 0.8122 (m) REVERT: C 217 LYS cc_start: 0.7606 (OUTLIER) cc_final: 0.7194 (tptp) REVERT: C 220 LYS cc_start: 0.4692 (OUTLIER) cc_final: 0.3819 (ptpp) outliers start: 34 outliers final: 23 residues processed: 122 average time/residue: 0.1383 time to fit residues: 22.1413 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 : 0.476 ------------------------------------------------------------------------------- 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 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 101 CYS Chi-restraints excluded: chain C residue 106 ARG 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 194 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 52 optimal weight: 0.7980 chunk 41 optimal weight: 0.3980 chunk 58 optimal weight: 0.0370 chunk 11 optimal weight: 0.8980 chunk 14 optimal weight: 1.9990 chunk 3 optimal weight: 0.7980 chunk 4 optimal weight: 1.9990 chunk 47 optimal weight: 1.9990 chunk 23 optimal weight: 3.9990 chunk 22 optimal weight: 0.7980 chunk 17 optimal weight: 0.0670 overall best weight: 0.4196 ------------------------------------------------------------------------------- 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 = 0.4342 r_free = 0.4342 target = 0.182556 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.4095 r_free = 0.4095 target = 0.160988 restraints weight = 7136.147| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.4156 r_free = 0.4156 target = 0.166177 restraints weight = 4244.795| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.4198 r_free = 0.4198 target = 0.169760 restraints weight = 2820.785| |-----------------------------------------------------------------------------| r_work (final): 0.4220 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6086 moved from start: 0.2177 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 4619 Z= 0.143 Angle : 0.730 13.660 6314 Z= 0.369 Chirality : 0.047 0.200 720 Planarity : 0.005 0.052 800 Dihedral : 5.488 36.224 637 Min Nonbonded Distance : 2.495 Molprobity Statistics. All-atom Clashscore : 16.58 Ramachandran Plot: Outliers : 0.34 % Allowed : 14.43 % Favored : 85.23 % Rotamer: Outliers : 5.50 % Allowed : 30.65 % Favored : 63.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.57 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.00 (0.34), residues: 589 helix: -2.83 (1.26), residues: 14 sheet: -1.30 (0.36), residues: 208 loop : -2.49 (0.32), residues: 367 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.002 TRP A 103 HIS 0.006 0.002 HIS B 195 PHE 0.012 0.002 PHE A 1 TYR 0.013 0.001 TYR B 55 ARG 0.003 0.000 ARG A 92 Details of bonding type rmsd hydrogen bonds : bond 0.03250 ( 98) hydrogen bonds : angle 6.76224 ( 213) SS BOND : bond 0.00486 ( 5) SS BOND : angle 0.87452 ( 10) covalent geometry : bond 0.00322 ( 4614) covalent geometry : angle 0.72990 ( 6304) *********************** 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 : 0.445 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 77 TYR cc_start: 0.6284 (m-80) cc_final: 0.5878 (m-10) REVERT: B 154 TRP cc_start: 0.6828 (m100) cc_final: 0.6335 (m100) REVERT: C 36 ASP cc_start: 0.5996 (OUTLIER) cc_final: 0.5279 (t70) REVERT: C 38 PHE cc_start: 0.6591 (m-80) cc_final: 0.6363 (m-80) REVERT: C 106 ARG cc_start: 0.6800 (OUTLIER) cc_final: 0.6512 (ttm170) REVERT: C 149 LEU cc_start: 0.8122 (OUTLIER) cc_final: 0.7762 (pp) REVERT: C 161 VAL cc_start: 0.8411 (p) cc_final: 0.8137 (m) REVERT: C 217 LYS cc_start: 0.7578 (OUTLIER) cc_final: 0.7135 (tptp) REVERT: C 220 LYS cc_start: 0.4663 (OUTLIER) cc_final: 0.3817 (ptpp) outliers start: 28 outliers final: 21 residues processed: 119 average time/residue: 0.1336 time to fit residues: 21.0382 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 : 0.484 ------------------------------------------------------------------------------- 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 75 VAL Chi-restraints excluded: chain A residue 105 VAL 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 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 101 CYS Chi-restraints excluded: chain C residue 106 ARG 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=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 59 random chunks: chunk 35 optimal weight: 2.9990 chunk 38 optimal weight: 0.6980 chunk 22 optimal weight: 0.3980 chunk 33 optimal weight: 0.6980 chunk 7 optimal weight: 0.8980 chunk 47 optimal weight: 2.9990 chunk 42 optimal weight: 0.3980 chunk 17 optimal weight: 1.9990 chunk 53 optimal weight: 4.9990 chunk 31 optimal weight: 0.9990 chunk 58 optimal weight: 0.0010 overall best weight: 0.4386 ------------------------------------------------------------------------------- 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 38 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4398 r_free = 0.4398 target = 0.189564 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.4134 r_free = 0.4134 target = 0.166354 restraints weight = 6964.980| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.4202 r_free = 0.4202 target = 0.172195 restraints weight = 4028.293| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.4249 r_free = 0.4249 target = 0.176207 restraints weight = 2610.704| |-----------------------------------------------------------------------------| r_work (final): 0.4240 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6074 moved from start: 0.2300 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 4619 Z= 0.144 Angle : 0.735 14.368 6314 Z= 0.371 Chirality : 0.047 0.194 720 Planarity : 0.006 0.056 800 Dihedral : 5.496 36.747 637 Min Nonbonded Distance : 2.491 Molprobity Statistics. All-atom Clashscore : 16.91 Ramachandran Plot: Outliers : 0.34 % Allowed : 15.28 % Favored : 84.38 % Rotamer: Outliers : 5.30 % Allowed : 31.43 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.90 (0.34), residues: 589 helix: -2.69 (1.31), residues: 14 sheet: -1.23 (0.36), residues: 208 loop : -2.43 (0.32), residues: 367 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP A 103 HIS 0.006 0.002 HIS B 195 PHE 0.012 0.002 PHE B 68 TYR 0.013 0.001 TYR B 77 ARG 0.002 0.000 ARG A 92 Details of bonding type rmsd hydrogen bonds : bond 0.03236 ( 98) hydrogen bonds : angle 6.67407 ( 213) SS BOND : bond 0.00469 ( 5) SS BOND : angle 0.91878 ( 10) covalent geometry : bond 0.00329 ( 4614) covalent geometry : angle 0.73465 ( 6304) *********************** 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 127 residues out of total 509 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 100 time to evaluate : 0.476 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 77 TYR cc_start: 0.6276 (m-80) cc_final: 0.5868 (m-10) REVERT: B 154 TRP cc_start: 0.6860 (m100) cc_final: 0.6625 (m100) REVERT: C 36 ASP cc_start: 0.6062 (OUTLIER) cc_final: 0.5492 (t70) REVERT: C 38 PHE cc_start: 0.6631 (m-80) cc_final: 0.6359 (m-80) REVERT: C 149 LEU cc_start: 0.8113 (OUTLIER) cc_final: 0.7760 (pp) REVERT: C 161 VAL cc_start: 0.8414 (p) cc_final: 0.8103 (m) REVERT: C 217 LYS cc_start: 0.7570 (OUTLIER) cc_final: 0.7077 (tptp) REVERT: C 220 LYS cc_start: 0.4672 (OUTLIER) cc_final: 0.3887 (ptpp) outliers start: 27 outliers final: 21 residues processed: 119 average time/residue: 0.1337 time to fit residues: 21.1204 Evaluate side-chains 120 residues out of total 509 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 95 time to evaluate : 0.439 ------------------------------------------------------------------------------- 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 99 THR Chi-restraints excluded: chain A residue 105 VAL Chi-restraints excluded: chain A residue 158 THR 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 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 59 random chunks: chunk 39 optimal weight: 0.6980 chunk 50 optimal weight: 0.7980 chunk 28 optimal weight: 0.5980 chunk 7 optimal weight: 1.9990 chunk 12 optimal weight: 3.9990 chunk 17 optimal weight: 0.9980 chunk 32 optimal weight: 2.9990 chunk 31 optimal weight: 3.9990 chunk 1 optimal weight: 0.0670 chunk 19 optimal weight: 1.9990 chunk 2 optimal weight: 0.0020 overall best weight: 0.4326 ------------------------------------------------------------------------------- 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 96 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4415 r_free = 0.4415 target = 0.191678 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.4145 r_free = 0.4145 target = 0.167892 restraints weight = 6934.995| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 42)----------------| | r_work = 0.4217 r_free = 0.4217 target = 0.174081 restraints weight = 3881.614| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.4265 r_free = 0.4265 target = 0.178219 restraints weight = 2453.521| |-----------------------------------------------------------------------------| r_work (final): 0.4241 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6065 moved from start: 0.2369 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 4619 Z= 0.143 Angle : 0.758 14.531 6314 Z= 0.376 Chirality : 0.047 0.187 720 Planarity : 0.005 0.053 800 Dihedral : 5.532 37.354 637 Min Nonbonded Distance : 2.489 Molprobity Statistics. All-atom Clashscore : 17.03 Ramachandran Plot: Outliers : 0.34 % Allowed : 14.60 % Favored : 85.06 % Rotamer: Outliers : 4.91 % Allowed : 31.63 % Favored : 63.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.57 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.85 (0.35), residues: 589 helix: -2.53 (1.38), residues: 14 sheet: -1.21 (0.36), residues: 208 loop : -2.39 (0.33), residues: 367 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.002 TRP A 103 HIS 0.007 0.002 HIS B 195 PHE 0.011 0.002 PHE A 1 TYR 0.014 0.001 TYR C 205 ARG 0.003 0.000 ARG A 98 Details of bonding type rmsd hydrogen bonds : bond 0.03208 ( 98) hydrogen bonds : angle 6.63089 ( 213) SS BOND : bond 0.00479 ( 5) SS BOND : angle 0.92172 ( 10) covalent geometry : bond 0.00326 ( 4614) covalent geometry : angle 0.75747 ( 6304) ********************** 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 122 residues out of total 509 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 97 time to evaluate : 0.435 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 77 TYR cc_start: 0.6247 (m-80) cc_final: 0.5990 (m-80) REVERT: B 154 TRP cc_start: 0.6871 (m100) cc_final: 0.6644 (m100) REVERT: C 36 ASP cc_start: 0.6049 (OUTLIER) cc_final: 0.5096 (t70) REVERT: C 38 PHE cc_start: 0.6621 (m-80) cc_final: 0.6392 (m-80) REVERT: C 106 ARG cc_start: 0.6804 (ttm170) cc_final: 0.6369 (ttp-110) REVERT: C 149 LEU cc_start: 0.8106 (OUTLIER) cc_final: 0.7754 (pp) REVERT: C 161 VAL cc_start: 0.8430 (p) cc_final: 0.8103 (m) REVERT: C 217 LYS cc_start: 0.7559 (OUTLIER) cc_final: 0.7035 (tptp) REVERT: C 220 LYS cc_start: 0.4678 (OUTLIER) cc_final: 0.3900 (ptpp) outliers start: 25 outliers final: 21 residues processed: 114 average time/residue: 0.1336 time to fit residues: 20.3216 Evaluate side-chains 121 residues out of total 509 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 96 time to evaluate : 0.510 ------------------------------------------------------------------------------- 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 75 VAL Chi-restraints excluded: chain A residue 105 VAL Chi-restraints excluded: chain A residue 158 THR 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 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 59 random chunks: chunk 25 optimal weight: 0.9980 chunk 32 optimal weight: 0.4980 chunk 16 optimal weight: 2.9990 chunk 4 optimal weight: 2.9990 chunk 52 optimal weight: 0.8980 chunk 15 optimal weight: 0.7980 chunk 3 optimal weight: 0.9980 chunk 57 optimal weight: 0.6980 chunk 9 optimal weight: 1.9990 chunk 5 optimal weight: 0.8980 chunk 0 optimal weight: 0.6980 overall best weight: 0.7180 ------------------------------------------------------------------------------- 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** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4366 r_free = 0.4366 target = 0.186278 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.4099 r_free = 0.4099 target = 0.163342 restraints weight = 6961.321| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.4168 r_free = 0.4168 target = 0.169120 restraints weight = 4035.222| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.4215 r_free = 0.4215 target = 0.173060 restraints weight = 2603.492| |-----------------------------------------------------------------------------| r_work (final): 0.4218 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6117 moved from start: 0.2445 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 4619 Z= 0.180 Angle : 0.783 15.823 6314 Z= 0.391 Chirality : 0.048 0.188 720 Planarity : 0.006 0.055 800 Dihedral : 5.686 38.327 637 Min Nonbonded Distance : 2.476 Molprobity Statistics. All-atom Clashscore : 19.40 Ramachandran Plot: Outliers : 0.34 % Allowed : 15.79 % Favored : 83.87 % Rotamer: Outliers : 5.11 % Allowed : 31.63 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.09 (0.34), residues: 589 helix: -3.11 (1.00), residues: 20 sheet: -1.12 (0.36), residues: 213 loop : -2.72 (0.32), residues: 356 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.002 TRP A 103 HIS 0.007 0.002 HIS B 195 PHE 0.014 0.002 PHE C 34 TYR 0.013 0.002 TYR C 205 ARG 0.006 0.001 ARG A 98 Details of bonding type rmsd hydrogen bonds : bond 0.03638 ( 98) hydrogen bonds : angle 6.80718 ( 213) SS BOND : bond 0.00584 ( 5) SS BOND : angle 1.16640 ( 10) covalent geometry : bond 0.00398 ( 4614) covalent geometry : angle 0.78188 ( 6304) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1826.30 seconds wall clock time: 32 minutes 43.11 seconds (1963.11 seconds total)