Starting phenix.real_space_refine on Tue Jan 13 09:57:47 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7zcg_14630/01_2026/7zcg_14630.cif Found real_map, /net/cci-nas-00/data/ceres_data/7zcg_14630/01_2026/7zcg_14630.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.3 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/7zcg_14630/01_2026/7zcg_14630.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7zcg_14630/01_2026/7zcg_14630.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/7zcg_14630/01_2026/7zcg_14630.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7zcg_14630/01_2026/7zcg_14630.map" } resolution = 3.3 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= 0.000 sd= 0.001 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 31 5.16 5 C 1520 2.51 5 N 453 2.21 5 O 464 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 6 residue(s): 0.00s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5927/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 2468 Number of models: 1 Model: "" Number of chains: 2 Chain: "B" Number of atoms: 1194 Number of conformers: 1 Conformer: "" Number of residues, atoms: 147, 1194 Classifications: {'peptide': 147} Link IDs: {'PTRANS': 2, 'TRANS': 144} Chain: "A" Number of atoms: 1274 Number of conformers: 1 Conformer: "" Number of residues, atoms: 159, 1274 Classifications: {'peptide': 159} Link IDs: {'PTRANS': 2, 'TRANS': 156} Time building chain proxies: 0.69, per 1000 atoms: 0.28 Number of scatterers: 2468 At special positions: 0 Unit cell: (122.032, 139.916, 47.34, 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 31 16.00 O 464 8.00 N 453 7.00 C 1520 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 0.21 Conformation dependent library (CDL) restraints added in 68.9 milliseconds 604 Ramachandran restraints generated. 302 Oldfield, 0 Emsley, 302 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 596 Finding SS restraints... Secondary structure from input PDB file: 7 helices and 0 sheets defined 94.8% alpha, 0.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.04 Creating SS restraints... Processing helix chain 'B' and resid 10 through 54 removed outlier: 3.723A pdb=" N LYS B 52 " --> pdb=" O LYS B 48 " (cutoff:3.500A) removed outlier: 3.801A pdb=" N GLN B 53 " --> pdb=" O LYS B 49 " (cutoff:3.500A) Processing helix chain 'B' and resid 57 through 115 removed outlier: 3.596A pdb=" N LYS B 75 " --> pdb=" O ARG B 71 " (cutoff:3.500A) removed outlier: 3.838A pdb=" N THR B 92 " --> pdb=" O LEU B 88 " (cutoff:3.500A) removed outlier: 3.879A pdb=" N LEU B 93 " --> pdb=" O LYS B 89 " (cutoff:3.500A) removed outlier: 4.154A pdb=" N LYS B 94 " --> pdb=" O ILE B 90 " (cutoff:3.500A) removed outlier: 3.950A pdb=" N SER B 95 " --> pdb=" O GLN B 91 " (cutoff:3.500A) Processing helix chain 'B' and resid 118 through 152 removed outlier: 3.754A pdb=" N ILE B 122 " --> pdb=" O LYS B 118 " (cutoff:3.500A) Processing helix chain 'A' and resid 12 through 54 Processing helix chain 'A' and resid 58 through 116 removed outlier: 4.252A pdb=" N VAL A 62 " --> pdb=" O ASP A 58 " (cutoff:3.500A) removed outlier: 3.574A pdb=" N SER A 70 " --> pdb=" O GLU A 66 " (cutoff:3.500A) removed outlier: 3.647A pdb=" N ARG A 71 " --> pdb=" O MET A 67 " (cutoff:3.500A) Processing helix chain 'A' and resid 119 through 150 removed outlier: 3.599A pdb=" N THR A 126 " --> pdb=" O GLU A 122 " (cutoff:3.500A) removed outlier: 3.526A pdb=" N ILE A 139 " --> pdb=" O MET A 135 " (cutoff:3.500A) Processing helix chain 'A' and resid 153 through 169 removed outlier: 3.867A pdb=" N MET A 157 " --> pdb=" O ASP A 153 " (cutoff:3.500A) removed outlier: 3.529A pdb=" N GLU A 159 " --> pdb=" O GLU A 155 " (cutoff:3.500A) removed outlier: 3.729A pdb=" N GLU A 160 " --> pdb=" O GLU A 156 " (cutoff:3.500A) removed outlier: 3.714A pdb=" N GLU A 162 " --> pdb=" O GLU A 158 " (cutoff:3.500A) 245 hydrogen bonds defined for protein. 735 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: 0.31 Time building geometry restraints manager: 0.27 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: 854 1.34 - 1.46: 341 1.46 - 1.58: 1223 1.58 - 1.70: 0 1.70 - 1.82: 61 Bond restraints: 2479 Sorted by residual: bond pdb=" CB PRO A 11 " pdb=" CG PRO A 11 " ideal model delta sigma weight residual 1.492 1.575 -0.083 5.00e-02 4.00e+02 2.78e+00 bond pdb=" CB MET A 111 " pdb=" CG MET A 111 " ideal model delta sigma weight residual 1.520 1.481 0.039 3.00e-02 1.11e+03 1.70e+00 bond pdb=" CG1 ILE B 44 " pdb=" CD1 ILE B 44 " ideal model delta sigma weight residual 1.513 1.465 0.048 3.90e-02 6.57e+02 1.51e+00 bond pdb=" CB GLN B 84 " pdb=" CG GLN B 84 " ideal model delta sigma weight residual 1.520 1.487 0.033 3.00e-02 1.11e+03 1.23e+00 bond pdb=" CG GLN B 84 " pdb=" CD GLN B 84 " ideal model delta sigma weight residual 1.516 1.490 0.026 2.50e-02 1.60e+03 1.12e+00 ... (remaining 2474 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.14: 3209 2.14 - 4.28: 65 4.28 - 6.42: 10 6.42 - 8.56: 2 8.56 - 10.70: 1 Bond angle restraints: 3287 Sorted by residual: angle pdb=" CB MET A 127 " pdb=" CG MET A 127 " pdb=" SD MET A 127 " ideal model delta sigma weight residual 112.70 123.40 -10.70 3.00e+00 1.11e-01 1.27e+01 angle pdb=" CA MET A 127 " pdb=" CB MET A 127 " pdb=" CG MET A 127 " ideal model delta sigma weight residual 114.10 120.20 -6.10 2.00e+00 2.50e-01 9.30e+00 angle pdb=" CA GLU A 41 " pdb=" CB GLU A 41 " pdb=" CG GLU A 41 " ideal model delta sigma weight residual 114.10 119.78 -5.68 2.00e+00 2.50e-01 8.06e+00 angle pdb=" CB MET A 67 " pdb=" CG MET A 67 " pdb=" SD MET A 67 " ideal model delta sigma weight residual 112.70 121.02 -8.32 3.00e+00 1.11e-01 7.70e+00 angle pdb=" C GLY B 54 " pdb=" N GLN B 55 " pdb=" CA GLN B 55 " ideal model delta sigma weight residual 121.54 126.54 -5.00 1.91e+00 2.74e-01 6.86e+00 ... (remaining 3282 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.95: 1397 17.95 - 35.90: 199 35.90 - 53.84: 39 53.84 - 71.79: 5 71.79 - 89.74: 1 Dihedral angle restraints: 1641 sinusoidal: 739 harmonic: 902 Sorted by residual: dihedral pdb=" CB MET A 157 " pdb=" CG MET A 157 " pdb=" SD MET A 157 " pdb=" CE MET A 157 " ideal model delta sinusoidal sigma weight residual -180.00 -132.07 -47.93 3 1.50e+01 4.44e-03 8.57e+00 dihedral pdb=" CG ARG A 32 " pdb=" CD ARG A 32 " pdb=" NE ARG A 32 " pdb=" CZ ARG A 32 " ideal model delta sinusoidal sigma weight residual -90.00 -129.23 39.23 2 1.50e+01 4.44e-03 8.53e+00 dihedral pdb=" CA LYS A 119 " pdb=" CB LYS A 119 " pdb=" CG LYS A 119 " pdb=" CD LYS A 119 " ideal model delta sinusoidal sigma weight residual 180.00 132.35 47.65 3 1.50e+01 4.44e-03 8.52e+00 ... (remaining 1638 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.028: 233 0.028 - 0.056: 73 0.056 - 0.084: 48 0.084 - 0.113: 13 0.113 - 0.141: 3 Chirality restraints: 370 Sorted by residual: chirality pdb=" CA LYS B 75 " pdb=" N LYS B 75 " pdb=" C LYS B 75 " pdb=" CB LYS B 75 " both_signs ideal model delta sigma weight residual False 2.51 2.37 0.14 2.00e-01 2.50e+01 4.95e-01 chirality pdb=" CA PRO B 120 " pdb=" N PRO B 120 " pdb=" C PRO B 120 " pdb=" CB PRO B 120 " both_signs ideal model delta sigma weight residual False 2.72 2.60 0.12 2.00e-01 2.50e+01 3.56e-01 chirality pdb=" CA ARG B 20 " pdb=" N ARG B 20 " pdb=" C ARG B 20 " pdb=" CB ARG B 20 " both_signs ideal model delta sigma weight residual False 2.51 2.40 0.12 2.00e-01 2.50e+01 3.32e-01 ... (remaining 367 not shown) Planarity restraints: 423 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C THR B 10 " 0.034 5.00e-02 4.00e+02 5.24e-02 4.40e+00 pdb=" N PRO B 11 " -0.091 5.00e-02 4.00e+02 pdb=" CA PRO B 11 " 0.027 5.00e-02 4.00e+02 pdb=" CD PRO B 11 " 0.029 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CG GLU A 41 " 0.008 2.00e-02 2.50e+03 1.59e-02 2.52e+00 pdb=" CD GLU A 41 " -0.027 2.00e-02 2.50e+03 pdb=" OE1 GLU A 41 " 0.010 2.00e-02 2.50e+03 pdb=" OE2 GLU A 41 " 0.010 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TRP A 19 " -0.012 2.00e-02 2.50e+03 7.37e-03 1.36e+00 pdb=" CG TRP A 19 " 0.019 2.00e-02 2.50e+03 pdb=" CD1 TRP A 19 " -0.003 2.00e-02 2.50e+03 pdb=" CD2 TRP A 19 " -0.000 2.00e-02 2.50e+03 pdb=" NE1 TRP A 19 " -0.001 2.00e-02 2.50e+03 pdb=" CE2 TRP A 19 " -0.000 2.00e-02 2.50e+03 pdb=" CE3 TRP A 19 " 0.002 2.00e-02 2.50e+03 pdb=" CZ2 TRP A 19 " -0.003 2.00e-02 2.50e+03 pdb=" CZ3 TRP A 19 " -0.000 2.00e-02 2.50e+03 pdb=" CH2 TRP A 19 " -0.001 2.00e-02 2.50e+03 ... (remaining 420 not shown) Histogram of nonbonded interaction distances: 2.27 - 2.79: 514 2.79 - 3.32: 2722 3.32 - 3.85: 3967 3.85 - 4.37: 4286 4.37 - 4.90: 7082 Nonbonded interactions: 18571 Sorted by model distance: nonbonded pdb=" OD1 ASP A 58 " pdb=" N VAL A 59 " model vdw 2.268 3.120 nonbonded pdb=" OD1 ASP B 30 " pdb=" NH2 ARG B 33 " model vdw 2.282 3.120 nonbonded pdb=" N LYS A 119 " pdb=" OE2 GLU A 122 " model vdw 2.334 3.120 nonbonded pdb=" O GLU B 140 " pdb=" ND2 ASN B 144 " model vdw 2.364 3.120 nonbonded pdb=" O LEU B 66 " pdb=" OG1 THR B 69 " model vdw 2.379 3.040 ... (remaining 18566 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 individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 28.140 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: 0.060 Check model and map are aligned: 0.000 Set scattering table: 0.010 Process input model: 4.240 Find NCS groups from input model: 0.010 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:1.180 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 33.650 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8044 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.083 2479 Z= 0.176 Angle : 0.769 10.705 3287 Z= 0.405 Chirality : 0.039 0.141 370 Planarity : 0.005 0.052 423 Dihedral : 16.047 89.738 1045 Min Nonbonded Distance : 2.268 Molprobity Statistics. All-atom Clashscore : 11.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.98 % Favored : 97.02 % Rotamer: Outliers : 0.00 % Allowed : 0.37 % Favored : 99.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 3.02 (0.49), residues: 302 helix: 2.23 (0.31), residues: 275 sheet: None (None), residues: 0 loop : -0.45 (1.46), residues: 27 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG A 99 TYR 0.002 0.001 TYR A 78 PHE 0.008 0.002 PHE A 148 TRP 0.019 0.004 TRP A 19 HIS 0.000 0.000 HIS A 83 Details of bonding type rmsd covalent geometry : bond 0.00422 ( 2479) covalent geometry : angle 0.76880 ( 3287) hydrogen bonds : bond 0.14509 ( 245) hydrogen bonds : angle 4.43207 ( 735) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 604 Ramachandran restraints generated. 302 Oldfield, 0 Emsley, 302 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 604 Ramachandran restraints generated. 302 Oldfield, 0 Emsley, 302 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 212 residues out of total 272 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 212 time to evaluate : 0.107 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 20 ARG cc_start: 0.8034 (ptm-80) cc_final: 0.7627 (ptt90) REVERT: B 23 ASN cc_start: 0.8763 (m110) cc_final: 0.8532 (m110) REVERT: B 74 ARG cc_start: 0.7758 (tpp80) cc_final: 0.7401 (mmt180) REVERT: B 89 LYS cc_start: 0.8782 (ttmt) cc_final: 0.8100 (tptt) REVERT: B 128 GLU cc_start: 0.7599 (mt-10) cc_final: 0.7300 (mt-10) REVERT: A 25 LYS cc_start: 0.8821 (tptm) cc_final: 0.8554 (tptt) REVERT: A 46 ARG cc_start: 0.8194 (ttp80) cc_final: 0.7861 (mtm110) REVERT: A 81 LYS cc_start: 0.9054 (ttmt) cc_final: 0.8757 (ttpt) REVERT: A 139 ILE cc_start: 0.8848 (pt) cc_final: 0.8612 (pt) outliers start: 0 outliers final: 0 residues processed: 212 average time/residue: 0.0981 time to fit residues: 22.8965 Evaluate side-chains 177 residues out of total 272 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 177 time to evaluate : 0.109 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 29 random chunks: chunk 27 optimal weight: 0.5980 chunk 12 optimal weight: 0.6980 chunk 24 optimal weight: 0.7980 chunk 28 optimal weight: 2.9990 chunk 13 optimal weight: 0.7980 chunk 1 optimal weight: 0.5980 chunk 8 optimal weight: 0.6980 chunk 16 optimal weight: 0.5980 chunk 15 optimal weight: 0.9990 chunk 25 optimal weight: 1.9990 chunk 26 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 17 ASN ** A 93 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 124 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3641 r_free = 0.3641 target = 0.114169 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3475 r_free = 0.3475 target = 0.103677 restraints weight = 4960.380| |-----------------------------------------------------------------------------| r_work (start): 0.3480 rms_B_bonded: 2.31 r_work: 0.3343 rms_B_bonded: 3.14 restraints_weight: 0.5000 r_work (final): 0.3343 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8353 moved from start: 0.3307 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 2479 Z= 0.174 Angle : 0.647 6.065 3287 Z= 0.347 Chirality : 0.039 0.129 370 Planarity : 0.004 0.052 423 Dihedral : 3.443 12.364 332 Min Nonbonded Distance : 2.452 Molprobity Statistics. All-atom Clashscore : 10.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.99 % Favored : 98.01 % Rotamer: Outliers : 1.84 % Allowed : 27.57 % Favored : 70.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 4.02 (0.47), residues: 302 helix: 2.92 (0.29), residues: 276 sheet: None (None), residues: 0 loop : -0.80 (1.57), residues: 26 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG A 39 TYR 0.009 0.002 TYR A 78 PHE 0.005 0.001 PHE B 76 TRP 0.011 0.003 TRP A 19 HIS 0.002 0.001 HIS A 83 Details of bonding type rmsd covalent geometry : bond 0.00402 ( 2479) covalent geometry : angle 0.64721 ( 3287) hydrogen bonds : bond 0.05341 ( 245) hydrogen bonds : angle 3.71947 ( 735) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 604 Ramachandran restraints generated. 302 Oldfield, 0 Emsley, 302 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 604 Ramachandran restraints generated. 302 Oldfield, 0 Emsley, 302 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 189 residues out of total 272 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 184 time to evaluate : 0.091 Fit side-chains revert: symmetry clash REVERT: B 20 ARG cc_start: 0.8405 (ptm-80) cc_final: 0.8101 (ttp80) REVERT: B 23 ASN cc_start: 0.9066 (m110) cc_final: 0.8642 (m110) REVERT: B 28 GLU cc_start: 0.8629 (OUTLIER) cc_final: 0.8393 (pt0) REVERT: B 46 ASP cc_start: 0.8660 (t0) cc_final: 0.8365 (t0) REVERT: B 56 MET cc_start: 0.6733 (mmp) cc_final: 0.6433 (mmp) REVERT: B 89 LYS cc_start: 0.8832 (ttmt) cc_final: 0.8134 (tptt) REVERT: B 125 ILE cc_start: 0.8741 (mt) cc_final: 0.8468 (mt) REVERT: A 25 LYS cc_start: 0.9101 (tptm) cc_final: 0.8834 (tptt) REVERT: A 46 ARG cc_start: 0.8194 (ttp80) cc_final: 0.7964 (mtm110) REVERT: A 85 ASN cc_start: 0.9180 (t0) cc_final: 0.8905 (t0) REVERT: A 114 MET cc_start: 0.8422 (ttm) cc_final: 0.8202 (ttm) outliers start: 5 outliers final: 2 residues processed: 185 average time/residue: 0.0754 time to fit residues: 15.7617 Evaluate side-chains 184 residues out of total 272 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 181 time to evaluate : 0.064 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 28 GLU Chi-restraints excluded: chain B residue 118 LYS Chi-restraints excluded: chain A residue 110 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 29 random chunks: chunk 14 optimal weight: 0.0770 chunk 1 optimal weight: 0.8980 chunk 7 optimal weight: 0.6980 chunk 15 optimal weight: 0.7980 chunk 28 optimal weight: 0.9980 chunk 19 optimal weight: 0.3980 chunk 26 optimal weight: 0.9980 chunk 10 optimal weight: 1.9990 chunk 17 optimal weight: 0.8980 chunk 23 optimal weight: 0.7980 chunk 6 optimal weight: 0.5980 overall best weight: 0.5138 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 93 ASN ** 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 = 0.3649 r_free = 0.3649 target = 0.114546 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3478 r_free = 0.3478 target = 0.103843 restraints weight = 4871.510| |-----------------------------------------------------------------------------| r_work (start): 0.3470 rms_B_bonded: 2.29 r_work: 0.3336 rms_B_bonded: 3.09 restraints_weight: 0.5000 r_work (final): 0.3336 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8359 moved from start: 0.3766 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 2479 Z= 0.148 Angle : 0.570 6.036 3287 Z= 0.313 Chirality : 0.038 0.143 370 Planarity : 0.004 0.055 423 Dihedral : 3.383 13.126 332 Min Nonbonded Distance : 2.457 Molprobity Statistics. All-atom Clashscore : 11.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.99 % Favored : 98.01 % Rotamer: Outliers : 2.94 % Allowed : 30.15 % Favored : 66.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 4.53 (0.47), residues: 302 helix: 3.27 (0.29), residues: 276 sheet: None (None), residues: 0 loop : -0.87 (1.54), residues: 26 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 115 TYR 0.005 0.001 TYR B 72 PHE 0.003 0.001 PHE A 148 TRP 0.009 0.002 TRP A 19 HIS 0.001 0.000 HIS A 83 Details of bonding type rmsd covalent geometry : bond 0.00340 ( 2479) covalent geometry : angle 0.56962 ( 3287) hydrogen bonds : bond 0.04872 ( 245) hydrogen bonds : angle 3.62011 ( 735) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 604 Ramachandran restraints generated. 302 Oldfield, 0 Emsley, 302 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 604 Ramachandran restraints generated. 302 Oldfield, 0 Emsley, 302 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 192 residues out of total 272 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 184 time to evaluate : 0.071 Fit side-chains REVERT: B 14 LEU cc_start: 0.9311 (OUTLIER) cc_final: 0.9023 (tt) REVERT: B 23 ASN cc_start: 0.9166 (m110) cc_final: 0.8646 (m110) REVERT: B 46 ASP cc_start: 0.8610 (t0) cc_final: 0.8175 (t0) REVERT: B 74 ARG cc_start: 0.8152 (tpp80) cc_final: 0.7770 (mmt180) REVERT: B 89 LYS cc_start: 0.8820 (ttmt) cc_final: 0.8453 (tppt) REVERT: B 125 ILE cc_start: 0.8892 (mt) cc_final: 0.8618 (mt) REVERT: A 25 LYS cc_start: 0.9028 (tptm) cc_final: 0.8779 (tptt) REVERT: A 46 ARG cc_start: 0.8139 (ttp80) cc_final: 0.7926 (mtm110) REVERT: A 85 ASN cc_start: 0.9170 (t0) cc_final: 0.8895 (t0) outliers start: 8 outliers final: 4 residues processed: 185 average time/residue: 0.0789 time to fit residues: 16.4683 Evaluate side-chains 185 residues out of total 272 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 180 time to evaluate : 0.110 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 14 LEU Chi-restraints excluded: chain B residue 118 LYS Chi-restraints excluded: chain A residue 14 GLU Chi-restraints excluded: chain A residue 103 SER Chi-restraints excluded: chain A residue 144 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 29 random chunks: chunk 1 optimal weight: 0.8980 chunk 11 optimal weight: 1.9990 chunk 10 optimal weight: 0.9980 chunk 5 optimal weight: 0.8980 chunk 2 optimal weight: 0.1980 chunk 17 optimal weight: 1.9990 chunk 8 optimal weight: 0.0980 chunk 14 optimal weight: 0.0030 chunk 0 optimal weight: 1.9990 chunk 25 optimal weight: 1.9990 chunk 19 optimal weight: 0.6980 overall best weight: 0.3790 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 91 GLN ** A 93 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3636 r_free = 0.3636 target = 0.114227 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3466 r_free = 0.3466 target = 0.103615 restraints weight = 4851.077| |-----------------------------------------------------------------------------| r_work (start): 0.3462 rms_B_bonded: 2.25 r_work: 0.3321 rms_B_bonded: 3.09 restraints_weight: 0.5000 r_work (final): 0.3321 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8352 moved from start: 0.3936 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 2479 Z= 0.139 Angle : 0.586 7.401 3287 Z= 0.311 Chirality : 0.036 0.138 370 Planarity : 0.004 0.061 423 Dihedral : 3.313 13.530 332 Min Nonbonded Distance : 2.449 Molprobity Statistics. All-atom Clashscore : 9.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.32 % Favored : 97.68 % Rotamer: Outliers : 3.31 % Allowed : 30.51 % Favored : 66.18 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 4.87 (0.47), residues: 302 helix: 3.51 (0.29), residues: 273 sheet: None (None), residues: 0 loop : -0.44 (1.50), residues: 29 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B 115 TYR 0.006 0.001 TYR B 72 PHE 0.004 0.001 PHE A 148 TRP 0.007 0.001 TRP A 19 HIS 0.000 0.000 HIS A 83 Details of bonding type rmsd covalent geometry : bond 0.00308 ( 2479) covalent geometry : angle 0.58593 ( 3287) hydrogen bonds : bond 0.04629 ( 245) hydrogen bonds : angle 3.53251 ( 735) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 604 Ramachandran restraints generated. 302 Oldfield, 0 Emsley, 302 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 604 Ramachandran restraints generated. 302 Oldfield, 0 Emsley, 302 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 195 residues out of total 272 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 186 time to evaluate : 0.113 Fit side-chains REVERT: B 14 LEU cc_start: 0.9335 (OUTLIER) cc_final: 0.9037 (tt) REVERT: B 23 ASN cc_start: 0.9208 (m110) cc_final: 0.8692 (m110) REVERT: B 74 ARG cc_start: 0.8293 (tpp80) cc_final: 0.7856 (mmt180) REVERT: B 89 LYS cc_start: 0.8526 (ttmt) cc_final: 0.8277 (tppt) REVERT: B 91 GLN cc_start: 0.9028 (tp-100) cc_final: 0.8775 (tp-100) REVERT: B 121 GLN cc_start: 0.8372 (pm20) cc_final: 0.8082 (pm20) REVERT: B 125 ILE cc_start: 0.8925 (mt) cc_final: 0.8640 (mt) REVERT: A 21 LEU cc_start: 0.9269 (tp) cc_final: 0.9037 (tp) REVERT: A 24 ARG cc_start: 0.8665 (OUTLIER) cc_final: 0.8338 (mtm110) REVERT: A 46 ARG cc_start: 0.8155 (ttp80) cc_final: 0.7939 (mtm110) REVERT: A 85 ASN cc_start: 0.9180 (t0) cc_final: 0.8889 (t0) outliers start: 9 outliers final: 5 residues processed: 187 average time/residue: 0.0752 time to fit residues: 16.1103 Evaluate side-chains 188 residues out of total 272 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 181 time to evaluate : 0.103 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 14 LEU Chi-restraints excluded: chain B residue 15 LEU Chi-restraints excluded: chain B residue 118 LYS Chi-restraints excluded: chain A residue 14 GLU Chi-restraints excluded: chain A residue 24 ARG Chi-restraints excluded: chain A residue 60 CYS Chi-restraints excluded: chain A residue 151 MET Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 29 random chunks: chunk 28 optimal weight: 0.6980 chunk 6 optimal weight: 0.6980 chunk 21 optimal weight: 0.5980 chunk 3 optimal weight: 0.9980 chunk 16 optimal weight: 0.8980 chunk 12 optimal weight: 1.9990 chunk 17 optimal weight: 0.9990 chunk 1 optimal weight: 0.7980 chunk 8 optimal weight: 0.5980 chunk 10 optimal weight: 1.9990 chunk 14 optimal weight: 0.6980 overall best weight: 0.6580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 93 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3634 r_free = 0.3634 target = 0.113444 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3472 r_free = 0.3472 target = 0.103222 restraints weight = 4947.005| |-----------------------------------------------------------------------------| r_work (start): 0.3474 rms_B_bonded: 2.21 r_work: 0.3335 rms_B_bonded: 3.04 restraints_weight: 0.5000 r_work (final): 0.3335 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8362 moved from start: 0.4270 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 2479 Z= 0.156 Angle : 0.636 7.645 3287 Z= 0.335 Chirality : 0.038 0.146 370 Planarity : 0.004 0.059 423 Dihedral : 3.312 14.375 332 Min Nonbonded Distance : 2.429 Molprobity Statistics. All-atom Clashscore : 8.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.32 % Favored : 97.68 % Rotamer: Outliers : 4.04 % Allowed : 31.99 % Favored : 63.97 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 4.99 (0.47), residues: 302 helix: 3.59 (0.29), residues: 273 sheet: None (None), residues: 0 loop : -0.39 (1.45), residues: 29 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG B 115 TYR 0.015 0.002 TYR B 72 PHE 0.003 0.001 PHE A 148 TRP 0.011 0.003 TRP A 19 HIS 0.000 0.000 HIS A 83 Details of bonding type rmsd covalent geometry : bond 0.00365 ( 2479) covalent geometry : angle 0.63598 ( 3287) hydrogen bonds : bond 0.04709 ( 245) hydrogen bonds : angle 3.53200 ( 735) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 604 Ramachandran restraints generated. 302 Oldfield, 0 Emsley, 302 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 604 Ramachandran restraints generated. 302 Oldfield, 0 Emsley, 302 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 200 residues out of total 272 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 189 time to evaluate : 0.169 Fit side-chains REVERT: B 14 LEU cc_start: 0.9339 (OUTLIER) cc_final: 0.9053 (tt) REVERT: B 23 ASN cc_start: 0.9184 (m110) cc_final: 0.8720 (m110) REVERT: B 46 ASP cc_start: 0.8600 (t0) cc_final: 0.8209 (t0) REVERT: B 74 ARG cc_start: 0.8251 (tpp80) cc_final: 0.7920 (tpt170) REVERT: B 82 ASN cc_start: 0.8544 (m-40) cc_final: 0.7991 (m-40) REVERT: B 89 LYS cc_start: 0.8489 (ttmt) cc_final: 0.8251 (tppt) REVERT: B 121 GLN cc_start: 0.8304 (pm20) cc_final: 0.8005 (pm20) REVERT: B 125 ILE cc_start: 0.9028 (mt) cc_final: 0.8708 (mt) REVERT: A 46 ARG cc_start: 0.8181 (ttp80) cc_final: 0.7960 (mtm110) REVERT: A 85 ASN cc_start: 0.9126 (t0) cc_final: 0.8866 (t0) outliers start: 11 outliers final: 5 residues processed: 190 average time/residue: 0.0700 time to fit residues: 15.2272 Evaluate side-chains 187 residues out of total 272 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 181 time to evaluate : 0.118 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 14 LEU Chi-restraints excluded: chain B residue 28 GLU Chi-restraints excluded: chain A residue 14 GLU Chi-restraints excluded: chain A residue 103 SER Chi-restraints excluded: chain A residue 139 ILE Chi-restraints excluded: chain A residue 144 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 29 random chunks: chunk 12 optimal weight: 1.9990 chunk 26 optimal weight: 1.9990 chunk 9 optimal weight: 1.9990 chunk 10 optimal weight: 1.9990 chunk 14 optimal weight: 0.9980 chunk 18 optimal weight: 4.9990 chunk 21 optimal weight: 0.8980 chunk 27 optimal weight: 0.0870 chunk 25 optimal weight: 0.4980 chunk 20 optimal weight: 0.9980 chunk 3 optimal weight: 0.8980 overall best weight: 0.6758 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 53 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3625 r_free = 0.3625 target = 0.112889 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.3466 r_free = 0.3466 target = 0.102715 restraints weight = 4926.694| |-----------------------------------------------------------------------------| r_work (start): 0.3465 rms_B_bonded: 2.20 r_work: 0.3326 rms_B_bonded: 3.01 restraints_weight: 0.5000 r_work (final): 0.3326 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8371 moved from start: 0.4557 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.055 2479 Z= 0.160 Angle : 0.630 7.748 3287 Z= 0.334 Chirality : 0.040 0.156 370 Planarity : 0.004 0.058 423 Dihedral : 3.355 15.006 332 Min Nonbonded Distance : 2.394 Molprobity Statistics. All-atom Clashscore : 9.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.32 % Favored : 97.68 % Rotamer: Outliers : 3.68 % Allowed : 30.88 % Favored : 65.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 5.04 (0.47), residues: 302 helix: 3.62 (0.29), residues: 273 sheet: None (None), residues: 0 loop : -0.28 (1.47), residues: 29 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG B 115 TYR 0.009 0.002 TYR B 72 PHE 0.003 0.001 PHE A 148 TRP 0.008 0.002 TRP A 19 HIS 0.000 0.000 HIS A 83 Details of bonding type rmsd covalent geometry : bond 0.00381 ( 2479) covalent geometry : angle 0.62992 ( 3287) hydrogen bonds : bond 0.04716 ( 245) hydrogen bonds : angle 3.56361 ( 735) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 604 Ramachandran restraints generated. 302 Oldfield, 0 Emsley, 302 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 604 Ramachandran restraints generated. 302 Oldfield, 0 Emsley, 302 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 193 residues out of total 272 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 183 time to evaluate : 0.112 Fit side-chains REVERT: B 23 ASN cc_start: 0.9173 (m110) cc_final: 0.8411 (m110) REVERT: B 74 ARG cc_start: 0.8225 (tpp80) cc_final: 0.7880 (tpt170) REVERT: B 82 ASN cc_start: 0.8482 (m-40) cc_final: 0.7944 (m-40) REVERT: B 89 LYS cc_start: 0.8443 (ttmt) cc_final: 0.8212 (tppt) REVERT: B 121 GLN cc_start: 0.8369 (pm20) cc_final: 0.8095 (pm20) REVERT: B 125 ILE cc_start: 0.8894 (mt) cc_final: 0.8583 (mt) REVERT: A 25 LYS cc_start: 0.7500 (tptt) cc_final: 0.6962 (tttp) REVERT: A 46 ARG cc_start: 0.8186 (ttp80) cc_final: 0.7928 (mtm110) REVERT: A 85 ASN cc_start: 0.9142 (t0) cc_final: 0.8867 (t0) REVERT: A 127 MET cc_start: 0.8501 (mmm) cc_final: 0.8268 (mmm) REVERT: A 128 ARG cc_start: 0.8470 (mtm110) cc_final: 0.8267 (mtm-85) outliers start: 10 outliers final: 5 residues processed: 184 average time/residue: 0.0764 time to fit residues: 15.8691 Evaluate side-chains 184 residues out of total 272 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 179 time to evaluate : 0.076 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 28 GLU Chi-restraints excluded: chain B residue 53 GLN Chi-restraints excluded: chain A residue 15 LEU Chi-restraints excluded: chain A residue 103 SER Chi-restraints excluded: chain A residue 159 GLU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 29 random chunks: chunk 9 optimal weight: 3.9990 chunk 3 optimal weight: 0.6980 chunk 23 optimal weight: 0.7980 chunk 12 optimal weight: 0.8980 chunk 13 optimal weight: 0.6980 chunk 8 optimal weight: 0.9990 chunk 2 optimal weight: 0.7980 chunk 24 optimal weight: 0.8980 chunk 22 optimal weight: 0.9990 chunk 0 optimal weight: 1.9990 chunk 7 optimal weight: 0.5980 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 38 GLN ** A 93 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3607 r_free = 0.3607 target = 0.112280 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3448 r_free = 0.3448 target = 0.102008 restraints weight = 4876.157| |-----------------------------------------------------------------------------| r_work (start): 0.3443 rms_B_bonded: 2.24 r_work: 0.3304 rms_B_bonded: 3.04 restraints_weight: 0.5000 r_work (final): 0.3304 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8379 moved from start: 0.4738 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.054 2479 Z= 0.170 Angle : 0.660 7.713 3287 Z= 0.356 Chirality : 0.040 0.154 370 Planarity : 0.004 0.058 423 Dihedral : 3.336 15.046 332 Min Nonbonded Distance : 2.379 Molprobity Statistics. All-atom Clashscore : 9.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.32 % Favored : 97.68 % Rotamer: Outliers : 2.94 % Allowed : 34.19 % Favored : 62.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 4.94 (0.46), residues: 302 helix: 3.57 (0.28), residues: 273 sheet: None (None), residues: 0 loop : -0.53 (1.39), residues: 29 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG B 115 TYR 0.009 0.002 TYR B 72 PHE 0.005 0.001 PHE A 148 TRP 0.009 0.002 TRP A 19 HIS 0.000 0.000 HIS A 83 Details of bonding type rmsd covalent geometry : bond 0.00411 ( 2479) covalent geometry : angle 0.66045 ( 3287) hydrogen bonds : bond 0.04775 ( 245) hydrogen bonds : angle 3.67612 ( 735) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 604 Ramachandran restraints generated. 302 Oldfield, 0 Emsley, 302 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 604 Ramachandran restraints generated. 302 Oldfield, 0 Emsley, 302 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 189 residues out of total 272 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 181 time to evaluate : 0.083 Fit side-chains REVERT: B 19 GLN cc_start: 0.8612 (tp40) cc_final: 0.8223 (tp-100) REVERT: B 23 ASN cc_start: 0.9104 (m110) cc_final: 0.8462 (m110) REVERT: B 46 ASP cc_start: 0.8560 (t0) cc_final: 0.8320 (t0) REVERT: B 74 ARG cc_start: 0.8284 (tpp80) cc_final: 0.7905 (tpt170) REVERT: B 82 ASN cc_start: 0.8488 (m-40) cc_final: 0.7987 (m-40) REVERT: B 89 LYS cc_start: 0.8394 (ttmt) cc_final: 0.8178 (tppt) REVERT: B 125 ILE cc_start: 0.8902 (mt) cc_final: 0.8582 (mt) REVERT: A 25 LYS cc_start: 0.7551 (tptt) cc_final: 0.7006 (tttp) REVERT: A 46 ARG cc_start: 0.8225 (ttp80) cc_final: 0.7978 (mtm110) REVERT: A 85 ASN cc_start: 0.9171 (t0) cc_final: 0.8882 (t0) outliers start: 8 outliers final: 7 residues processed: 182 average time/residue: 0.0717 time to fit residues: 14.9447 Evaluate side-chains 184 residues out of total 272 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 177 time to evaluate : 0.062 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 28 GLU Chi-restraints excluded: chain B residue 101 GLN Chi-restraints excluded: chain A residue 15 LEU Chi-restraints excluded: chain A residue 24 ARG Chi-restraints excluded: chain A residue 103 SER Chi-restraints excluded: chain A residue 144 LEU Chi-restraints excluded: chain A residue 159 GLU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 29 random chunks: chunk 24 optimal weight: 0.8980 chunk 0 optimal weight: 1.9990 chunk 16 optimal weight: 0.9980 chunk 27 optimal weight: 0.5980 chunk 15 optimal weight: 0.9980 chunk 7 optimal weight: 0.9980 chunk 1 optimal weight: 0.8980 chunk 21 optimal weight: 0.8980 chunk 12 optimal weight: 0.6980 chunk 2 optimal weight: 0.5980 chunk 18 optimal weight: 4.9990 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 53 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 38 GLN ** A 93 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3600 r_free = 0.3600 target = 0.112041 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 24)----------------| | r_work = 0.3440 r_free = 0.3440 target = 0.101687 restraints weight = 4913.985| |-----------------------------------------------------------------------------| r_work (start): 0.3432 rms_B_bonded: 2.28 r_work: 0.3293 rms_B_bonded: 3.06 restraints_weight: 0.5000 r_work (final): 0.3293 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8388 moved from start: 0.4900 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 2479 Z= 0.169 Angle : 0.667 7.525 3287 Z= 0.359 Chirality : 0.041 0.158 370 Planarity : 0.005 0.057 423 Dihedral : 3.464 19.529 332 Min Nonbonded Distance : 2.377 Molprobity Statistics. All-atom Clashscore : 10.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.32 % Favored : 97.68 % Rotamer: Outliers : 2.94 % Allowed : 34.56 % Favored : 62.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 4.85 (0.47), residues: 302 helix: 3.51 (0.29), residues: 273 sheet: None (None), residues: 0 loop : -0.62 (1.38), residues: 29 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG B 115 TYR 0.009 0.002 TYR B 72 PHE 0.004 0.001 PHE A 148 TRP 0.009 0.002 TRP A 19 HIS 0.000 0.000 HIS A 83 Details of bonding type rmsd covalent geometry : bond 0.00402 ( 2479) covalent geometry : angle 0.66660 ( 3287) hydrogen bonds : bond 0.04810 ( 245) hydrogen bonds : angle 3.69723 ( 735) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 604 Ramachandran restraints generated. 302 Oldfield, 0 Emsley, 302 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 604 Ramachandran restraints generated. 302 Oldfield, 0 Emsley, 302 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 192 residues out of total 272 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 184 time to evaluate : 0.076 Fit side-chains REVERT: B 19 GLN cc_start: 0.8778 (tp40) cc_final: 0.8281 (tp-100) REVERT: B 23 ASN cc_start: 0.9124 (m110) cc_final: 0.8451 (m110) REVERT: B 46 ASP cc_start: 0.8578 (t0) cc_final: 0.8321 (t0) REVERT: B 74 ARG cc_start: 0.8360 (tpp80) cc_final: 0.7952 (tpt170) REVERT: B 82 ASN cc_start: 0.8482 (m-40) cc_final: 0.8012 (m-40) REVERT: B 89 LYS cc_start: 0.8362 (ttmt) cc_final: 0.8155 (tppt) REVERT: B 121 GLN cc_start: 0.8386 (pm20) cc_final: 0.8082 (pm20) REVERT: B 125 ILE cc_start: 0.8878 (mt) cc_final: 0.8557 (mt) REVERT: A 46 ARG cc_start: 0.8231 (ttp80) cc_final: 0.7985 (mtm110) REVERT: A 85 ASN cc_start: 0.9168 (t0) cc_final: 0.8891 (t0) REVERT: A 128 ARG cc_start: 0.8527 (mtm110) cc_final: 0.8122 (mtm-85) outliers start: 8 outliers final: 7 residues processed: 184 average time/residue: 0.0709 time to fit residues: 14.7570 Evaluate side-chains 187 residues out of total 272 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 180 time to evaluate : 0.106 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 87 SER Chi-restraints excluded: chain B residue 101 GLN Chi-restraints excluded: chain A residue 14 GLU Chi-restraints excluded: chain A residue 15 LEU Chi-restraints excluded: chain A residue 103 SER Chi-restraints excluded: chain A residue 144 LEU Chi-restraints excluded: chain A residue 159 GLU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 29 random chunks: chunk 18 optimal weight: 3.9990 chunk 17 optimal weight: 0.9980 chunk 9 optimal weight: 0.3980 chunk 11 optimal weight: 0.4980 chunk 25 optimal weight: 0.0670 chunk 26 optimal weight: 0.9980 chunk 7 optimal weight: 1.9990 chunk 1 optimal weight: 0.8980 chunk 24 optimal weight: 0.8980 chunk 13 optimal weight: 0.7980 chunk 22 optimal weight: 0.6980 overall best weight: 0.4918 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 53 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 91 GLN A 38 GLN A 93 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3612 r_free = 0.3612 target = 0.113025 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3453 r_free = 0.3453 target = 0.102598 restraints weight = 4955.166| |-----------------------------------------------------------------------------| r_work (start): 0.3452 rms_B_bonded: 2.31 r_work: 0.3312 rms_B_bonded: 3.10 restraints_weight: 0.5000 r_work (final): 0.3312 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8373 moved from start: 0.4907 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.046 2479 Z= 0.155 Angle : 0.692 7.668 3287 Z= 0.367 Chirality : 0.040 0.159 370 Planarity : 0.004 0.060 423 Dihedral : 3.545 20.719 332 Min Nonbonded Distance : 2.383 Molprobity Statistics. All-atom Clashscore : 9.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.32 % Favored : 97.68 % Rotamer: Outliers : 1.84 % Allowed : 35.66 % Favored : 62.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 4.86 (0.47), residues: 302 helix: 3.53 (0.29), residues: 273 sheet: None (None), residues: 0 loop : -0.70 (1.36), residues: 29 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A 35 TYR 0.008 0.001 TYR B 72 PHE 0.004 0.001 PHE A 148 TRP 0.009 0.002 TRP A 19 HIS 0.000 0.000 HIS A 83 Details of bonding type rmsd covalent geometry : bond 0.00359 ( 2479) covalent geometry : angle 0.69230 ( 3287) hydrogen bonds : bond 0.04682 ( 245) hydrogen bonds : angle 3.68238 ( 735) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 604 Ramachandran restraints generated. 302 Oldfield, 0 Emsley, 302 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 604 Ramachandran restraints generated. 302 Oldfield, 0 Emsley, 302 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 185 residues out of total 272 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 180 time to evaluate : 0.087 Fit side-chains REVERT: B 19 GLN cc_start: 0.8764 (tp40) cc_final: 0.8240 (tp-100) REVERT: B 23 ASN cc_start: 0.9137 (m110) cc_final: 0.8421 (m110) REVERT: B 74 ARG cc_start: 0.8354 (tpp80) cc_final: 0.7969 (tpt170) REVERT: B 82 ASN cc_start: 0.8417 (m-40) cc_final: 0.7956 (m-40) REVERT: B 89 LYS cc_start: 0.8351 (ttmt) cc_final: 0.8140 (tppt) REVERT: B 121 GLN cc_start: 0.8334 (pm20) cc_final: 0.8116 (pm20) REVERT: B 125 ILE cc_start: 0.8766 (mt) cc_final: 0.8436 (mt) REVERT: A 46 ARG cc_start: 0.8254 (ttp80) cc_final: 0.8014 (mtm110) REVERT: A 85 ASN cc_start: 0.9159 (t0) cc_final: 0.8900 (t0) REVERT: A 128 ARG cc_start: 0.8389 (mtm110) cc_final: 0.8098 (mtm-85) outliers start: 5 outliers final: 5 residues processed: 180 average time/residue: 0.0699 time to fit residues: 14.2325 Evaluate side-chains 189 residues out of total 272 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 184 time to evaluate : 0.168 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 87 SER Chi-restraints excluded: chain B residue 101 GLN Chi-restraints excluded: chain A residue 14 GLU Chi-restraints excluded: chain A residue 103 SER Chi-restraints excluded: chain A residue 159 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 29 random chunks: chunk 4 optimal weight: 1.9990 chunk 13 optimal weight: 0.6980 chunk 17 optimal weight: 0.8980 chunk 6 optimal weight: 1.9990 chunk 14 optimal weight: 0.0370 chunk 22 optimal weight: 0.8980 chunk 28 optimal weight: 0.8980 chunk 19 optimal weight: 0.9980 chunk 11 optimal weight: 0.7980 chunk 10 optimal weight: 1.9990 chunk 9 optimal weight: 3.9990 overall best weight: 0.6658 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 53 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 38 GLN A 154 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3606 r_free = 0.3606 target = 0.112425 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3447 r_free = 0.3447 target = 0.102009 restraints weight = 5043.520| |-----------------------------------------------------------------------------| r_work (start): 0.3451 rms_B_bonded: 2.31 r_work: 0.3310 rms_B_bonded: 3.10 restraints_weight: 0.5000 r_work (final): 0.3310 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8390 moved from start: 0.5029 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.050 2479 Z= 0.167 Angle : 0.704 8.391 3287 Z= 0.373 Chirality : 0.041 0.165 370 Planarity : 0.004 0.057 423 Dihedral : 3.569 21.398 332 Min Nonbonded Distance : 2.375 Molprobity Statistics. All-atom Clashscore : 11.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.32 % Favored : 97.68 % Rotamer: Outliers : 2.57 % Allowed : 34.93 % Favored : 62.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 4.77 (0.47), residues: 302 helix: 3.47 (0.29), residues: 273 sheet: None (None), residues: 0 loop : -0.82 (1.33), residues: 29 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG A 35 TYR 0.001 0.001 TYR A 78 PHE 0.005 0.001 PHE A 148 TRP 0.007 0.002 TRP A 19 HIS 0.000 0.000 HIS A 83 Details of bonding type rmsd covalent geometry : bond 0.00401 ( 2479) covalent geometry : angle 0.70430 ( 3287) hydrogen bonds : bond 0.04786 ( 245) hydrogen bonds : angle 3.73859 ( 735) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 604 Ramachandran restraints generated. 302 Oldfield, 0 Emsley, 302 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 604 Ramachandran restraints generated. 302 Oldfield, 0 Emsley, 302 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 193 residues out of total 272 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 186 time to evaluate : 0.068 Fit side-chains REVERT: B 19 GLN cc_start: 0.8795 (tp40) cc_final: 0.8231 (tp-100) REVERT: B 23 ASN cc_start: 0.9146 (m110) cc_final: 0.8435 (m110) REVERT: B 74 ARG cc_start: 0.8369 (tpp80) cc_final: 0.7970 (tpt170) REVERT: B 82 ASN cc_start: 0.8446 (m-40) cc_final: 0.8007 (m-40) REVERT: B 89 LYS cc_start: 0.8367 (ttmt) cc_final: 0.8162 (tppt) REVERT: A 25 LYS cc_start: 0.7573 (tptt) cc_final: 0.7036 (tttp) REVERT: A 46 ARG cc_start: 0.8257 (ttp80) cc_final: 0.8019 (mtm110) REVERT: A 85 ASN cc_start: 0.9128 (t0) cc_final: 0.8921 (t0) REVERT: A 128 ARG cc_start: 0.8415 (mtm110) cc_final: 0.8124 (mtm-85) outliers start: 7 outliers final: 6 residues processed: 187 average time/residue: 0.0777 time to fit residues: 16.4401 Evaluate side-chains 182 residues out of total 272 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 176 time to evaluate : 0.105 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 28 GLU Chi-restraints excluded: chain B residue 87 SER Chi-restraints excluded: chain B residue 101 GLN Chi-restraints excluded: chain B residue 118 LYS Chi-restraints excluded: chain A residue 103 SER Chi-restraints excluded: chain A residue 159 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 29 random chunks: chunk 20 optimal weight: 0.5980 chunk 25 optimal weight: 0.7980 chunk 3 optimal weight: 0.9990 chunk 15 optimal weight: 0.7980 chunk 17 optimal weight: 0.9980 chunk 27 optimal weight: 0.9990 chunk 14 optimal weight: 0.3980 chunk 28 optimal weight: 3.9990 chunk 8 optimal weight: 0.6980 chunk 11 optimal weight: 0.0980 chunk 1 optimal weight: 0.9980 overall best weight: 0.5180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 53 GLN B 91 GLN A 38 GLN A 154 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3611 r_free = 0.3611 target = 0.112670 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3453 r_free = 0.3453 target = 0.102368 restraints weight = 5022.552| |-----------------------------------------------------------------------------| r_work (start): 0.3454 rms_B_bonded: 2.29 r_work: 0.3315 rms_B_bonded: 3.09 restraints_weight: 0.5000 r_work (final): 0.3315 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8374 moved from start: 0.5112 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.053 2479 Z= 0.160 Angle : 0.740 8.170 3287 Z= 0.384 Chirality : 0.041 0.160 370 Planarity : 0.004 0.058 423 Dihedral : 3.588 21.925 332 Min Nonbonded Distance : 2.376 Molprobity Statistics. All-atom Clashscore : 10.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.32 % Favored : 97.68 % Rotamer: Outliers : 2.57 % Allowed : 36.76 % Favored : 60.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 4.76 (0.47), residues: 302 helix: 3.47 (0.29), residues: 273 sheet: None (None), residues: 0 loop : -0.86 (1.33), residues: 29 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG A 35 TYR 0.001 0.000 TYR A 78 PHE 0.004 0.001 PHE A 148 TRP 0.008 0.002 TRP A 19 HIS 0.000 0.000 HIS A 83 Details of bonding type rmsd covalent geometry : bond 0.00375 ( 2479) covalent geometry : angle 0.74002 ( 3287) hydrogen bonds : bond 0.04733 ( 245) hydrogen bonds : angle 3.70705 ( 735) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1389.99 seconds wall clock time: 24 minutes 37.90 seconds (1477.90 seconds total)