Starting phenix.real_space_refine on Wed Jul 1 23:31:36 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9muh_48632/07_2026/9muh_48632.cif Found real_map, /net/cci-nas-00/data/ceres_data/9muh_48632/07_2026/9muh_48632.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.1 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/9muh_48632/07_2026/9muh_48632.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9muh_48632/07_2026/9muh_48632.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9muh_48632/07_2026/9muh_48632.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9muh_48632/07_2026/9muh_48632.map" } resolution = 3.1 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= 0.027 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: 5 Type Number sf(0) Gaussians K 2 8.98 5 S 28 5.16 5 C 2676 2.51 5 N 664 2.21 5 O 692 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 2 residue(s): 0.00s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 4062 Number of models: 1 Model: "" Number of chains: 4 Chain: "A" Number of atoms: 1995 Number of conformers: 1 Conformer: "" Number of residues, atoms: 249, 1995 Classifications: {'peptide': 249} Link IDs: {'PTRANS': 5, 'TRANS': 243} Chain: "B" Number of atoms: 1995 Number of conformers: 1 Conformer: "" Number of residues, atoms: 249, 1995 Classifications: {'peptide': 249} Link IDs: {'PTRANS': 5, 'TRANS': 243} Chain: "A" Number of atoms: 37 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 35 Ad-hoc single atom residues: {' K': 2} Unusual residues: {'Y01': 1} Classifications: {'undetermined': 1} Chain breaks: 2 Chain: "B" Number of atoms: 35 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 35 Unusual residues: {'Y01': 1} Classifications: {'undetermined': 1} Time building chain proxies: 0.94, per 1000 atoms: 0.23 Number of scatterers: 4062 At special positions: 0 Unit cell: (91.176, 71.264, 82.792, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) K 2 19.00 S 28 16.00 O 692 8.00 N 664 7.00 C 2676 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: 0.22 Conformation dependent library (CDL) restraints added in 118.4 milliseconds 988 Ramachandran restraints generated. 494 Oldfield, 0 Emsley, 494 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 920 Finding SS restraints... Secondary structure from input PDB file: 20 helices and 0 sheets defined 85.5% alpha, 0.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.09 Creating SS restraints... Processing helix chain 'A' and resid 2 through 52 removed outlier: 5.545A pdb=" N GLU A 32 " --> pdb=" O ALA A 28 " (cutoff:3.500A) Proline residue: A 33 - end of helix Processing helix chain 'A' and resid 55 through 70 Processing helix chain 'A' and resid 71 through 73 No H-bonds generated for 'chain 'A' and resid 71 through 73' Processing helix chain 'A' and resid 79 through 92 Processing helix chain 'A' and resid 103 through 148 Proline residue: A 119 - end of helix Processing helix chain 'A' and resid 155 through 183 Processing helix chain 'A' and resid 185 through 198 Processing helix chain 'A' and resid 212 through 217 Processing helix chain 'A' and resid 217 through 242 Processing helix chain 'A' and resid 242 through 249 Processing helix chain 'B' and resid 2 through 52 removed outlier: 5.546A pdb=" N GLU B 32 " --> pdb=" O ALA B 28 " (cutoff:3.500A) Proline residue: B 33 - end of helix Processing helix chain 'B' and resid 55 through 70 Processing helix chain 'B' and resid 71 through 73 No H-bonds generated for 'chain 'B' and resid 71 through 73' Processing helix chain 'B' and resid 79 through 92 Processing helix chain 'B' and resid 103 through 148 Proline residue: B 119 - end of helix Processing helix chain 'B' and resid 155 through 183 Processing helix chain 'B' and resid 185 through 198 Processing helix chain 'B' and resid 212 through 217 Processing helix chain 'B' and resid 217 through 242 Processing helix chain 'B' and resid 242 through 249 334 hydrogen bonds defined for protein. 1002 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: 0.62 Time building geometry restraints manager: 0.30 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.32: 606 1.32 - 1.44: 1206 1.44 - 1.56: 2300 1.56 - 1.68: 0 1.68 - 1.81: 46 Bond restraints: 4158 Sorted by residual: bond pdb=" N HIS A 98 " pdb=" CA HIS A 98 " ideal model delta sigma weight residual 1.454 1.488 -0.035 1.23e-02 6.61e+03 7.92e+00 bond pdb=" N HIS B 98 " pdb=" CA HIS B 98 " ideal model delta sigma weight residual 1.454 1.488 -0.034 1.23e-02 6.61e+03 7.65e+00 bond pdb=" N GLN A 77 " pdb=" CA GLN A 77 " ideal model delta sigma weight residual 1.456 1.491 -0.035 1.31e-02 5.83e+03 7.13e+00 bond pdb=" N GLN B 77 " pdb=" CA GLN B 77 " ideal model delta sigma weight residual 1.456 1.491 -0.034 1.31e-02 5.83e+03 6.79e+00 bond pdb=" N ALA A 99 " pdb=" CA ALA A 99 " ideal model delta sigma weight residual 1.453 1.481 -0.028 1.31e-02 5.83e+03 4.61e+00 ... (remaining 4153 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.05: 5375 1.05 - 2.10: 209 2.10 - 3.15: 39 3.15 - 4.20: 8 4.20 - 5.26: 7 Bond angle restraints: 5638 Sorted by residual: angle pdb=" N GLY B 97 " pdb=" CA GLY B 97 " pdb=" C GLY B 97 " ideal model delta sigma weight residual 114.69 110.82 3.87 1.19e+00 7.06e-01 1.06e+01 angle pdb=" CA HIS A 98 " pdb=" CB HIS A 98 " pdb=" CG HIS A 98 " ideal model delta sigma weight residual 113.80 110.68 3.12 1.00e+00 1.00e+00 9.73e+00 angle pdb=" CA ALA A 99 " pdb=" C ALA A 99 " pdb=" O ALA A 99 " ideal model delta sigma weight residual 121.81 118.18 3.63 1.18e+00 7.18e-01 9.46e+00 angle pdb=" CA ALA B 99 " pdb=" C ALA B 99 " pdb=" O ALA B 99 " ideal model delta sigma weight residual 121.81 118.20 3.61 1.18e+00 7.18e-01 9.37e+00 angle pdb=" N GLY A 97 " pdb=" CA GLY A 97 " pdb=" C GLY A 97 " ideal model delta sigma weight residual 114.69 111.07 3.62 1.19e+00 7.06e-01 9.27e+00 ... (remaining 5633 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 13.84: 2307 13.84 - 27.68: 175 27.68 - 41.52: 24 41.52 - 55.36: 6 55.36 - 69.20: 4 Dihedral angle restraints: 2516 sinusoidal: 1070 harmonic: 1446 Sorted by residual: dihedral pdb=" CA TRP B 78 " pdb=" C TRP B 78 " pdb=" N ARG B 79 " pdb=" CA ARG B 79 " ideal model delta harmonic sigma weight residual 180.00 160.75 19.25 0 5.00e+00 4.00e-02 1.48e+01 dihedral pdb=" CA TRP A 78 " pdb=" C TRP A 78 " pdb=" N ARG A 79 " pdb=" CA ARG A 79 " ideal model delta harmonic sigma weight residual 180.00 160.81 19.19 0 5.00e+00 4.00e-02 1.47e+01 dihedral pdb=" N ARG A 142 " pdb=" CA ARG A 142 " pdb=" CB ARG A 142 " pdb=" CG ARG A 142 " ideal model delta sinusoidal sigma weight residual -60.00 -115.61 55.61 3 1.50e+01 4.44e-03 9.36e+00 ... (remaining 2513 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.024: 358 0.024 - 0.047: 148 0.047 - 0.070: 98 0.070 - 0.094: 19 0.094 - 0.117: 19 Chirality restraints: 642 Sorted by residual: chirality pdb=" CA THR B 93 " pdb=" N THR B 93 " pdb=" C THR B 93 " pdb=" CB THR B 93 " both_signs ideal model delta sigma weight residual False 2.53 2.41 0.12 2.00e-01 2.50e+01 3.45e-01 chirality pdb=" CA THR A 93 " pdb=" N THR A 93 " pdb=" C THR A 93 " pdb=" CB THR A 93 " both_signs ideal model delta sigma weight residual False 2.53 2.41 0.12 2.00e-01 2.50e+01 3.42e-01 chirality pdb=" CA VAL B 154 " pdb=" N VAL B 154 " pdb=" C VAL B 154 " pdb=" CB VAL B 154 " both_signs ideal model delta sigma weight residual False 2.44 2.55 -0.11 2.00e-01 2.50e+01 3.18e-01 ... (remaining 639 not shown) Planarity restraints: 690 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C GLU B 32 " 0.017 5.00e-02 4.00e+02 2.60e-02 1.08e+00 pdb=" N PRO B 33 " -0.045 5.00e-02 4.00e+02 pdb=" CA PRO B 33 " 0.013 5.00e-02 4.00e+02 pdb=" CD PRO B 33 " 0.015 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C GLU A 32 " -0.017 5.00e-02 4.00e+02 2.56e-02 1.05e+00 pdb=" N PRO A 33 " 0.044 5.00e-02 4.00e+02 pdb=" CA PRO A 33 " -0.013 5.00e-02 4.00e+02 pdb=" CD PRO A 33 " -0.015 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA ASP A 27 " -0.005 2.00e-02 2.50e+03 9.91e-03 9.82e-01 pdb=" C ASP A 27 " 0.017 2.00e-02 2.50e+03 pdb=" O ASP A 27 " -0.006 2.00e-02 2.50e+03 pdb=" N ALA A 28 " -0.006 2.00e-02 2.50e+03 ... (remaining 687 not shown) Histogram of nonbonded interaction distances: 2.28 - 2.85: 1431 2.85 - 3.43: 4753 3.43 - 4.00: 7894 4.00 - 4.57: 11352 4.57 - 5.14: 15899 Nonbonded interactions: 41329 Sorted by model distance: nonbonded pdb=" O ILE A 88 " pdb=" OG1 THR A 92 " model vdw 2.283 3.040 nonbonded pdb=" O ILE B 88 " pdb=" OG1 THR B 92 " model vdw 2.283 3.040 nonbonded pdb=" O ASP A 211 " pdb=" OG1 THR A 216 " model vdw 2.332 3.040 nonbonded pdb=" O ASP B 211 " pdb=" OG1 THR B 216 " model vdw 2.332 3.040 nonbonded pdb=" O VAL B 76 " pdb=" NE2 GLN B 215 " model vdw 2.373 3.120 ... (remaining 41324 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 Found NCS groups: ncs_group { reference = (chain 'A' and resid 1 through 249) selection = (chain 'B' and resid 1 through 249) } 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: 2.050 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: 0.070 Check model and map are aligned: 0.020 Set scattering table: 0.020 Process input model: 4.910 Find NCS groups from input model: 0.170 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:1.090 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 8.340 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6881 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 4158 Z= 0.180 Angle : 0.511 5.255 5638 Z= 0.299 Chirality : 0.037 0.117 642 Planarity : 0.003 0.026 690 Dihedral : 10.074 69.204 1596 Min Nonbonded Distance : 2.283 Molprobity Statistics. All-atom Clashscore : 3.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.02 % Favored : 97.98 % Rotamer: Outliers : 0.48 % Allowed : 1.20 % Favored : 98.32 % 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: 2.61 (0.35), residues: 494 helix: 2.37 (0.23), residues: 408 sheet: None (None), residues: 0 loop : -1.58 (0.60), residues: 86 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG A 40 TYR 0.010 0.001 TYR A 227 PHE 0.014 0.001 PHE B 223 TRP 0.007 0.001 TRP B 78 HIS 0.004 0.001 HIS A 98 Details of bonding type rmsd/Z covalent geometry : bond 0.00304 / 0.18 ( 4158) covalent geometry : angle 0.51130 / 0.30 ( 5638) hydrogen bonds : bond 0.05282 / 3.86 ( 334) hydrogen bonds : angle 4.07057 / 3.08 ( 1002) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 988 Ramachandran restraints generated. 494 Oldfield, 0 Emsley, 494 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 988 Ramachandran restraints generated. 494 Oldfield, 0 Emsley, 494 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 148 residues out of total 416 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 146 time to evaluate : 0.085 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 240 ASN cc_start: 0.7307 (t0) cc_final: 0.6951 (t0) outliers start: 2 outliers final: 1 residues processed: 148 average time/residue: 0.0718 time to fit residues: 12.5102 Evaluate side-chains 90 residues out of total 416 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 89 time to evaluate : 0.089 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 242 VAL Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 48 random chunks: chunk 24 optimal weight: 0.9990 chunk 26 optimal weight: 0.5980 chunk 2 optimal weight: 1.9990 chunk 16 optimal weight: 1.9990 chunk 32 optimal weight: 0.5980 chunk 31 optimal weight: 0.9980 chunk 25 optimal weight: 0.9980 chunk 19 optimal weight: 0.6980 chunk 30 optimal weight: 0.9980 chunk 22 optimal weight: 0.9990 chunk 37 optimal weight: 0.9990 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 133 ASN B 133 ASN B 217 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4659 r_free = 0.4659 target = 0.222515 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.4395 r_free = 0.4395 target = 0.193169 restraints weight = 4469.352| |-----------------------------------------------------------------------------| r_work (start): 0.4403 rms_B_bonded: 1.62 r_work: 0.4240 rms_B_bonded: 2.65 restraints_weight: 0.5000 r_work: 0.4110 rms_B_bonded: 4.49 restraints_weight: 0.2500 r_work (final): 0.4110 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7424 moved from start: 0.2960 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.030 4158 Z= 0.189 Angle : 0.587 4.973 5638 Z= 0.312 Chirality : 0.041 0.155 642 Planarity : 0.004 0.025 690 Dihedral : 6.252 58.605 703 Min Nonbonded Distance : 2.526 Molprobity Statistics. All-atom Clashscore : 9.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.42 % Favored : 98.58 % Rotamer: Outliers : 2.40 % Allowed : 6.49 % Favored : 91.11 % 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: 3.05 (0.36), residues: 494 helix: 2.69 (0.23), residues: 408 sheet: None (None), residues: 0 loop : -1.54 (0.57), residues: 86 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG A 137 TYR 0.026 0.002 TYR B 18 PHE 0.017 0.002 PHE A 109 TRP 0.005 0.001 TRP B 78 HIS 0.013 0.002 HIS B 98 Details of bonding type rmsd/Z covalent geometry : bond 0.00412 / 0.19 ( 4158) covalent geometry : angle 0.58677 / 0.31 ( 5638) hydrogen bonds : bond 0.04315 / 2.96 ( 334) hydrogen bonds : angle 4.07312 / 3.09 ( 1002) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 988 Ramachandran restraints generated. 494 Oldfield, 0 Emsley, 494 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 988 Ramachandran restraints generated. 494 Oldfield, 0 Emsley, 494 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 114 residues out of total 416 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 104 time to evaluate : 0.089 Fit side-chains revert: symmetry clash REVERT: A 44 ARG cc_start: 0.7599 (ttm-80) cc_final: 0.7341 (ttm170) REVERT: A 249 MET cc_start: 0.3742 (mmt) cc_final: 0.2716 (ptt) REVERT: B 4 GLN cc_start: 0.5066 (mp10) cc_final: 0.4466 (mm-40) outliers start: 10 outliers final: 6 residues processed: 106 average time/residue: 0.0529 time to fit residues: 6.8498 Evaluate side-chains 91 residues out of total 416 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 85 time to evaluate : 0.085 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 212 GLN Chi-restraints excluded: chain A residue 242 VAL Chi-restraints excluded: chain B residue 102 SER Chi-restraints excluded: chain B residue 149 MET Chi-restraints excluded: chain B residue 169 SER Chi-restraints excluded: chain B residue 229 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 48 random chunks: chunk 5 optimal weight: 1.9990 chunk 22 optimal weight: 0.9990 chunk 24 optimal weight: 0.5980 chunk 41 optimal weight: 0.9990 chunk 26 optimal weight: 0.5980 chunk 44 optimal weight: 1.9990 chunk 40 optimal weight: 1.9990 chunk 14 optimal weight: 0.9980 chunk 18 optimal weight: 0.9990 chunk 31 optimal weight: 2.9990 chunk 25 optimal weight: 0.6980 overall best weight: 0.7782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 5 ASN ** A 72 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 133 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 133 ASN B 217 GLN B 240 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4627 r_free = 0.4627 target = 0.216580 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.4359 r_free = 0.4359 target = 0.188706 restraints weight = 4316.007| |-----------------------------------------------------------------------------| r_work (start): 0.4376 rms_B_bonded: 1.55 r_work: 0.4221 rms_B_bonded: 2.50 restraints_weight: 0.5000 r_work: 0.4089 rms_B_bonded: 4.31 restraints_weight: 0.2500 r_work (final): 0.4089 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7489 moved from start: 0.3502 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.032 4158 Z= 0.183 Angle : 0.579 8.405 5638 Z= 0.308 Chirality : 0.040 0.154 642 Planarity : 0.003 0.022 690 Dihedral : 6.038 59.830 703 Min Nonbonded Distance : 2.540 Molprobity Statistics. All-atom Clashscore : 10.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.82 % Favored : 98.18 % Rotamer: Outliers : 2.16 % Allowed : 10.58 % Favored : 87.26 % 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: 2.98 (0.36), residues: 494 helix: 2.65 (0.24), residues: 406 sheet: None (None), residues: 0 loop : -1.47 (0.59), residues: 88 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 49 TYR 0.021 0.002 TYR B 227 PHE 0.014 0.002 PHE A 109 TRP 0.006 0.001 TRP B 78 HIS 0.012 0.002 HIS B 98 Details of bonding type rmsd/Z covalent geometry : bond 0.00397 / 0.18 ( 4158) covalent geometry : angle 0.57950 / 0.31 ( 5638) hydrogen bonds : bond 0.04352 / 2.99 ( 334) hydrogen bonds : angle 4.14106 / 3.14 ( 1002) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 988 Ramachandran restraints generated. 494 Oldfield, 0 Emsley, 494 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 988 Ramachandran restraints generated. 494 Oldfield, 0 Emsley, 494 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 109 residues out of total 416 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 100 time to evaluate : 0.086 Fit side-chains revert: symmetry clash REVERT: A 46 LEU cc_start: 0.7774 (mm) cc_final: 0.7513 (mp) REVERT: A 185 THR cc_start: 0.8573 (p) cc_final: 0.8346 (m) REVERT: A 249 MET cc_start: 0.3913 (mmt) cc_final: 0.2889 (ptt) REVERT: B 186 PHE cc_start: 0.8306 (t80) cc_final: 0.8077 (t80) REVERT: B 217 GLN cc_start: 0.7813 (mt0) cc_final: 0.7589 (mt0) outliers start: 9 outliers final: 4 residues processed: 104 average time/residue: 0.0562 time to fit residues: 7.2012 Evaluate side-chains 92 residues out of total 416 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 88 time to evaluate : 0.104 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 102 SER Chi-restraints excluded: chain B residue 149 MET Chi-restraints excluded: chain B residue 169 SER Chi-restraints excluded: chain B residue 229 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 48 random chunks: chunk 21 optimal weight: 0.6980 chunk 16 optimal weight: 1.9990 chunk 38 optimal weight: 0.9980 chunk 8 optimal weight: 0.9980 chunk 46 optimal weight: 0.6980 chunk 45 optimal weight: 1.9990 chunk 19 optimal weight: 0.9990 chunk 2 optimal weight: 0.9990 chunk 12 optimal weight: 1.9990 chunk 33 optimal weight: 1.9990 chunk 18 optimal weight: 0.1980 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 45 GLN ** A 72 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 133 ASN A 240 ASN B 240 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4621 r_free = 0.4621 target = 0.217630 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.4344 r_free = 0.4344 target = 0.187714 restraints weight = 4416.219| |-----------------------------------------------------------------------------| r_work (start): 0.4355 rms_B_bonded: 1.65 r_work: 0.4197 rms_B_bonded: 2.63 restraints_weight: 0.5000 r_work: 0.4062 rms_B_bonded: 4.52 restraints_weight: 0.2500 r_work (final): 0.4062 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7488 moved from start: 0.3762 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.029 4158 Z= 0.173 Angle : 0.570 8.009 5638 Z= 0.304 Chirality : 0.040 0.149 642 Planarity : 0.003 0.025 690 Dihedral : 5.671 54.352 702 Min Nonbonded Distance : 2.556 Molprobity Statistics. All-atom Clashscore : 8.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.02 % Favored : 97.98 % Rotamer: Outliers : 2.88 % Allowed : 13.46 % Favored : 83.65 % 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: 2.95 (0.35), residues: 494 helix: 2.61 (0.23), residues: 406 sheet: None (None), residues: 0 loop : -1.40 (0.61), residues: 88 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 137 TYR 0.021 0.002 TYR B 192 PHE 0.013 0.002 PHE B 223 TRP 0.005 0.001 TRP B 78 HIS 0.011 0.002 HIS A 98 Details of bonding type rmsd/Z covalent geometry : bond 0.00375 / 0.17 ( 4158) covalent geometry : angle 0.56979 / 0.30 ( 5638) hydrogen bonds : bond 0.04326 / 2.97 ( 334) hydrogen bonds : angle 4.12832 / 3.12 ( 1002) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 988 Ramachandran restraints generated. 494 Oldfield, 0 Emsley, 494 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 988 Ramachandran restraints generated. 494 Oldfield, 0 Emsley, 494 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 107 residues out of total 416 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 95 time to evaluate : 0.146 Fit side-chains REVERT: A 46 LEU cc_start: 0.7914 (mm) cc_final: 0.7500 (mp) REVERT: A 79 ARG cc_start: 0.7459 (ttt-90) cc_final: 0.7099 (ttp80) REVERT: B 4 GLN cc_start: 0.4876 (mp10) cc_final: 0.4479 (mm-40) REVERT: B 18 TYR cc_start: 0.6977 (t80) cc_final: 0.6698 (t80) REVERT: B 186 PHE cc_start: 0.8301 (t80) cc_final: 0.8093 (t80) outliers start: 12 outliers final: 6 residues processed: 102 average time/residue: 0.0543 time to fit residues: 7.1504 Evaluate side-chains 92 residues out of total 416 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 86 time to evaluate : 0.139 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 77 GLN Chi-restraints excluded: chain A residue 132 ILE Chi-restraints excluded: chain B residue 19 LEU Chi-restraints excluded: chain B residue 102 SER Chi-restraints excluded: chain B residue 169 SER Chi-restraints excluded: chain B residue 229 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 48 random chunks: chunk 2 optimal weight: 0.9990 chunk 7 optimal weight: 2.9990 chunk 27 optimal weight: 1.9990 chunk 23 optimal weight: 0.9990 chunk 21 optimal weight: 2.9990 chunk 26 optimal weight: 0.7980 chunk 31 optimal weight: 1.9990 chunk 39 optimal weight: 0.5980 chunk 6 optimal weight: 2.9990 chunk 3 optimal weight: 1.9990 chunk 12 optimal weight: 0.9990 overall best weight: 0.8786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 72 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 141 HIS B 240 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4605 r_free = 0.4605 target = 0.215467 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.4332 r_free = 0.4332 target = 0.186411 restraints weight = 4432.049| |-----------------------------------------------------------------------------| r_work (start): 0.4340 rms_B_bonded: 1.56 r_work: 0.4191 rms_B_bonded: 2.51 restraints_weight: 0.5000 r_work: 0.4052 rms_B_bonded: 4.40 restraints_weight: 0.2500 r_work (final): 0.4052 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7520 moved from start: 0.4165 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.030 4158 Z= 0.198 Angle : 0.595 7.536 5638 Z= 0.318 Chirality : 0.041 0.147 642 Planarity : 0.003 0.024 690 Dihedral : 5.624 44.838 702 Min Nonbonded Distance : 2.556 Molprobity Statistics. All-atom Clashscore : 9.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.02 % Favored : 97.98 % Rotamer: Outliers : 2.40 % Allowed : 15.14 % Favored : 82.45 % 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: 2.75 (0.36), residues: 494 helix: 2.49 (0.23), residues: 406 sheet: None (None), residues: 0 loop : -1.56 (0.61), residues: 88 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG A 145 TYR 0.024 0.002 TYR B 192 PHE 0.013 0.002 PHE B 223 TRP 0.006 0.001 TRP B 78 HIS 0.017 0.003 HIS A 98 Details of bonding type rmsd/Z covalent geometry : bond 0.00439 / 0.20 ( 4158) covalent geometry : angle 0.59542 / 0.32 ( 5638) hydrogen bonds : bond 0.04492 / 3.10 ( 334) hydrogen bonds : angle 4.18390 / 3.17 ( 1002) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 988 Ramachandran restraints generated. 494 Oldfield, 0 Emsley, 494 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 988 Ramachandran restraints generated. 494 Oldfield, 0 Emsley, 494 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 105 residues out of total 416 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 95 time to evaluate : 0.155 Fit side-chains REVERT: A 46 LEU cc_start: 0.7977 (mm) cc_final: 0.7562 (mp) REVERT: A 98 HIS cc_start: 0.6144 (t70) cc_final: 0.5933 (t70) REVERT: B 186 PHE cc_start: 0.8342 (t80) cc_final: 0.8126 (t80) outliers start: 10 outliers final: 4 residues processed: 101 average time/residue: 0.0457 time to fit residues: 5.8811 Evaluate side-chains 91 residues out of total 416 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 87 time to evaluate : 0.136 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 132 ILE Chi-restraints excluded: chain B residue 102 SER Chi-restraints excluded: chain B residue 169 SER Chi-restraints excluded: chain B residue 229 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 48 random chunks: chunk 29 optimal weight: 0.9980 chunk 2 optimal weight: 0.9980 chunk 10 optimal weight: 0.6980 chunk 23 optimal weight: 0.6980 chunk 26 optimal weight: 0.5980 chunk 7 optimal weight: 0.9990 chunk 42 optimal weight: 0.9990 chunk 37 optimal weight: 1.9990 chunk 35 optimal weight: 0.7980 chunk 38 optimal weight: 0.7980 chunk 20 optimal weight: 0.9990 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 39 GLN ** A 72 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 240 ASN B 209 GLN B 240 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4587 r_free = 0.4587 target = 0.211812 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.4325 r_free = 0.4325 target = 0.185520 restraints weight = 4321.833| |-----------------------------------------------------------------------------| r_work (start): 0.4364 rms_B_bonded: 1.46 r_work: 0.4216 rms_B_bonded: 2.38 restraints_weight: 0.5000 r_work: 0.4075 rms_B_bonded: 4.14 restraints_weight: 0.2500 r_work (final): 0.4075 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7519 moved from start: 0.4319 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.031 4158 Z= 0.176 Angle : 0.591 6.941 5638 Z= 0.315 Chirality : 0.040 0.143 642 Planarity : 0.003 0.021 690 Dihedral : 5.564 44.088 702 Min Nonbonded Distance : 2.553 Molprobity Statistics. All-atom Clashscore : 9.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.02 % Favored : 97.98 % Rotamer: Outliers : 1.68 % Allowed : 17.31 % Favored : 81.01 % 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: 2.68 (0.36), residues: 494 helix: 2.42 (0.23), residues: 406 sheet: None (None), residues: 0 loop : -1.47 (0.64), residues: 88 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 137 TYR 0.032 0.002 TYR B 192 PHE 0.037 0.002 PHE B 86 TRP 0.008 0.001 TRP B 78 HIS 0.013 0.002 HIS A 98 Details of bonding type rmsd/Z covalent geometry : bond 0.00387 / 0.18 ( 4158) covalent geometry : angle 0.59061 / 0.32 ( 5638) hydrogen bonds : bond 0.04414 / 3.06 ( 334) hydrogen bonds : angle 4.16017 / 3.14 ( 1002) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 988 Ramachandran restraints generated. 494 Oldfield, 0 Emsley, 494 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 988 Ramachandran restraints generated. 494 Oldfield, 0 Emsley, 494 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 94 residues out of total 416 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 87 time to evaluate : 0.134 Fit side-chains REVERT: A 46 LEU cc_start: 0.7929 (mm) cc_final: 0.7491 (mp) REVERT: A 98 HIS cc_start: 0.6015 (t70) cc_final: 0.5686 (t70) REVERT: A 192 TYR cc_start: 0.8642 (t80) cc_final: 0.8371 (t80) REVERT: A 249 MET cc_start: 0.3502 (mmt) cc_final: 0.2698 (ptt) REVERT: B 4 GLN cc_start: 0.4897 (mp10) cc_final: 0.4519 (mm-40) REVERT: B 18 TYR cc_start: 0.6936 (t80) cc_final: 0.6693 (t80) outliers start: 7 outliers final: 4 residues processed: 90 average time/residue: 0.0543 time to fit residues: 6.1677 Evaluate side-chains 83 residues out of total 416 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 79 time to evaluate : 0.088 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 132 ILE Chi-restraints excluded: chain B residue 102 SER Chi-restraints excluded: chain B residue 169 SER Chi-restraints excluded: chain B residue 229 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 48 random chunks: chunk 32 optimal weight: 0.9980 chunk 22 optimal weight: 0.6980 chunk 13 optimal weight: 1.9990 chunk 37 optimal weight: 0.8980 chunk 1 optimal weight: 0.8980 chunk 8 optimal weight: 1.9990 chunk 30 optimal weight: 0.6980 chunk 0 optimal weight: 3.9990 chunk 35 optimal weight: 0.5980 chunk 15 optimal weight: 0.7980 chunk 44 optimal weight: 1.9990 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 39 GLN ** A 72 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 141 HIS B 209 GLN B 240 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4615 r_free = 0.4615 target = 0.216516 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.4338 r_free = 0.4338 target = 0.188081 restraints weight = 4507.185| |-----------------------------------------------------------------------------| r_work (start): 0.4356 rms_B_bonded: 1.70 r_work: 0.4193 rms_B_bonded: 2.61 restraints_weight: 0.5000 r_work: 0.4068 rms_B_bonded: 4.39 restraints_weight: 0.2500 r_work (final): 0.4068 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7530 moved from start: 0.4428 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.025 4158 Z= 0.178 Angle : 0.597 6.607 5638 Z= 0.318 Chirality : 0.040 0.143 642 Planarity : 0.003 0.021 690 Dihedral : 5.630 44.859 702 Min Nonbonded Distance : 2.544 Molprobity Statistics. All-atom Clashscore : 9.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.23 % Favored : 97.77 % Rotamer: Outliers : 1.44 % Allowed : 18.27 % Favored : 80.29 % 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: 2.67 (0.36), residues: 494 helix: 2.41 (0.23), residues: 406 sheet: None (None), residues: 0 loop : -1.47 (0.63), residues: 88 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 183 TYR 0.019 0.002 TYR B 192 PHE 0.028 0.002 PHE B 86 TRP 0.007 0.001 TRP B 78 HIS 0.013 0.002 HIS A 98 Details of bonding type rmsd/Z covalent geometry : bond 0.00389 / 0.18 ( 4158) covalent geometry : angle 0.59748 / 0.32 ( 5638) hydrogen bonds : bond 0.04392 / 3.05 ( 334) hydrogen bonds : angle 4.17526 / 3.16 ( 1002) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 988 Ramachandran restraints generated. 494 Oldfield, 0 Emsley, 494 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 988 Ramachandran restraints generated. 494 Oldfield, 0 Emsley, 494 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 89 residues out of total 416 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 83 time to evaluate : 0.140 Fit side-chains REVERT: A 46 LEU cc_start: 0.7900 (mm) cc_final: 0.7447 (mp) REVERT: A 98 HIS cc_start: 0.6049 (t70) cc_final: 0.5752 (t70) REVERT: A 192 TYR cc_start: 0.8696 (t80) cc_final: 0.8363 (t80) REVERT: A 249 MET cc_start: 0.3746 (mmt) cc_final: 0.2901 (ptt) REVERT: B 4 GLN cc_start: 0.4960 (mp10) cc_final: 0.4588 (mm-40) REVERT: B 18 TYR cc_start: 0.7022 (t80) cc_final: 0.6723 (t80) outliers start: 6 outliers final: 4 residues processed: 86 average time/residue: 0.0509 time to fit residues: 5.5985 Evaluate side-chains 81 residues out of total 416 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 77 time to evaluate : 0.084 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 132 ILE Chi-restraints excluded: chain B residue 102 SER Chi-restraints excluded: chain B residue 169 SER Chi-restraints excluded: chain B residue 229 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 48 random chunks: chunk 39 optimal weight: 1.9990 chunk 18 optimal weight: 0.5980 chunk 35 optimal weight: 0.6980 chunk 16 optimal weight: 1.9990 chunk 11 optimal weight: 0.6980 chunk 37 optimal weight: 0.7980 chunk 6 optimal weight: 2.9990 chunk 24 optimal weight: 0.6980 chunk 26 optimal weight: 0.6980 chunk 25 optimal weight: 0.6980 chunk 22 optimal weight: 0.5980 overall best weight: 0.6580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 72 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 209 GLN B 240 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4620 r_free = 0.4620 target = 0.217086 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.4339 r_free = 0.4339 target = 0.187294 restraints weight = 4428.559| |-----------------------------------------------------------------------------| r_work (start): 0.4345 rms_B_bonded: 1.67 r_work: 0.4186 rms_B_bonded: 2.69 restraints_weight: 0.5000 r_work: 0.4051 rms_B_bonded: 4.63 restraints_weight: 0.2500 r_work (final): 0.4051 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7524 moved from start: 0.4482 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.022 4158 Z= 0.168 Angle : 0.601 6.847 5638 Z= 0.324 Chirality : 0.040 0.143 642 Planarity : 0.003 0.022 690 Dihedral : 5.670 45.082 702 Min Nonbonded Distance : 2.540 Molprobity Statistics. All-atom Clashscore : 9.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.02 % Favored : 97.98 % Rotamer: Outliers : 1.68 % Allowed : 18.27 % Favored : 80.05 % 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: 2.59 (0.35), residues: 494 helix: 2.36 (0.23), residues: 408 sheet: None (None), residues: 0 loop : -1.64 (0.60), residues: 86 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 183 TYR 0.016 0.002 TYR A 192 PHE 0.025 0.002 PHE B 86 TRP 0.007 0.001 TRP B 78 HIS 0.012 0.002 HIS A 98 Details of bonding type rmsd/Z covalent geometry : bond 0.00359 / 0.17 ( 4158) covalent geometry : angle 0.60118 / 0.32 ( 5638) hydrogen bonds : bond 0.04380 / 3.06 ( 334) hydrogen bonds : angle 4.17521 / 3.15 ( 1002) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 988 Ramachandran restraints generated. 494 Oldfield, 0 Emsley, 494 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 988 Ramachandran restraints generated. 494 Oldfield, 0 Emsley, 494 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 86 residues out of total 416 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 79 time to evaluate : 0.137 Fit side-chains revert: symmetry clash REVERT: A 98 HIS cc_start: 0.6131 (t70) cc_final: 0.5826 (t70) REVERT: A 249 MET cc_start: 0.3938 (mmt) cc_final: 0.3129 (ptt) REVERT: B 4 GLN cc_start: 0.4968 (mp10) cc_final: 0.4572 (mm-40) outliers start: 7 outliers final: 4 residues processed: 84 average time/residue: 0.0533 time to fit residues: 5.6790 Evaluate side-chains 86 residues out of total 416 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 82 time to evaluate : 0.137 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 132 ILE Chi-restraints excluded: chain B residue 102 SER Chi-restraints excluded: chain B residue 169 SER Chi-restraints excluded: chain B residue 229 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 48 random chunks: chunk 42 optimal weight: 0.4980 chunk 41 optimal weight: 0.7980 chunk 2 optimal weight: 0.9980 chunk 28 optimal weight: 0.9980 chunk 26 optimal weight: 0.9990 chunk 17 optimal weight: 0.5980 chunk 3 optimal weight: 1.9990 chunk 36 optimal weight: 0.5980 chunk 37 optimal weight: 0.5980 chunk 8 optimal weight: 0.6980 chunk 45 optimal weight: 0.5980 overall best weight: 0.5780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 39 GLN ** A 72 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 209 GLN B 240 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4626 r_free = 0.4626 target = 0.217850 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.4357 r_free = 0.4357 target = 0.189214 restraints weight = 4516.717| |-----------------------------------------------------------------------------| r_work (start): 0.4367 rms_B_bonded: 1.62 r_work: 0.4197 rms_B_bonded: 2.69 restraints_weight: 0.5000 r_work: 0.4070 rms_B_bonded: 4.57 restraints_weight: 0.2500 r_work (final): 0.4070 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7507 moved from start: 0.4539 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 4158 Z= 0.159 Angle : 0.597 6.925 5638 Z= 0.323 Chirality : 0.040 0.141 642 Planarity : 0.003 0.021 690 Dihedral : 5.673 45.053 702 Min Nonbonded Distance : 2.529 Molprobity Statistics. All-atom Clashscore : 9.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.02 % Favored : 97.98 % Rotamer: Outliers : 1.20 % Allowed : 18.99 % Favored : 79.81 % 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: 2.65 (0.36), residues: 494 helix: 2.38 (0.23), residues: 406 sheet: None (None), residues: 0 loop : -1.40 (0.64), residues: 88 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 183 TYR 0.020 0.002 TYR A 18 PHE 0.022 0.002 PHE B 86 TRP 0.007 0.001 TRP B 78 HIS 0.011 0.002 HIS A 98 Details of bonding type rmsd/Z covalent geometry : bond 0.00337 / 0.16 ( 4158) covalent geometry : angle 0.59713 / 0.32 ( 5638) hydrogen bonds : bond 0.04314 / 3.02 ( 334) hydrogen bonds : angle 4.13925 / 3.12 ( 1002) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 988 Ramachandran restraints generated. 494 Oldfield, 0 Emsley, 494 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 988 Ramachandran restraints generated. 494 Oldfield, 0 Emsley, 494 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 85 residues out of total 416 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 80 time to evaluate : 0.086 Fit side-chains REVERT: A 98 HIS cc_start: 0.6093 (t70) cc_final: 0.5749 (t70) REVERT: A 249 MET cc_start: 0.3924 (mmt) cc_final: 0.3177 (ptt) REVERT: B 18 TYR cc_start: 0.6851 (t80) cc_final: 0.6582 (t80) REVERT: B 249 MET cc_start: 0.2793 (tpp) cc_final: 0.2399 (tpt) outliers start: 5 outliers final: 3 residues processed: 84 average time/residue: 0.0544 time to fit residues: 5.7080 Evaluate side-chains 81 residues out of total 416 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 78 time to evaluate : 0.138 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 185 THR Chi-restraints excluded: chain B residue 102 SER Chi-restraints excluded: chain B residue 169 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 48 random chunks: chunk 38 optimal weight: 0.4980 chunk 28 optimal weight: 0.8980 chunk 29 optimal weight: 0.9990 chunk 4 optimal weight: 0.7980 chunk 37 optimal weight: 0.7980 chunk 35 optimal weight: 0.2980 chunk 13 optimal weight: 0.6980 chunk 6 optimal weight: 0.7980 chunk 9 optimal weight: 0.0470 chunk 22 optimal weight: 0.7980 chunk 43 optimal weight: 0.9990 overall best weight: 0.4678 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 39 GLN ** A 72 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 240 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4639 r_free = 0.4639 target = 0.219120 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.4372 r_free = 0.4372 target = 0.191043 restraints weight = 4406.673| |-----------------------------------------------------------------------------| r_work (start): 0.4390 rms_B_bonded: 1.56 r_work: 0.4228 rms_B_bonded: 2.56 restraints_weight: 0.5000 r_work: 0.4099 rms_B_bonded: 4.38 restraints_weight: 0.2500 r_work (final): 0.4099 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7486 moved from start: 0.4623 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 4158 Z= 0.149 Angle : 0.598 7.111 5638 Z= 0.324 Chirality : 0.039 0.140 642 Planarity : 0.003 0.021 690 Dihedral : 5.635 45.114 702 Min Nonbonded Distance : 2.527 Molprobity Statistics. All-atom Clashscore : 9.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.23 % Favored : 97.77 % Rotamer: Outliers : 1.44 % Allowed : 19.47 % Favored : 79.09 % 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: 2.64 (0.35), residues: 494 helix: 2.39 (0.23), residues: 408 sheet: None (None), residues: 0 loop : -1.62 (0.60), residues: 86 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 183 TYR 0.024 0.002 TYR B 192 PHE 0.022 0.002 PHE B 86 TRP 0.008 0.001 TRP B 78 HIS 0.010 0.002 HIS A 98 Details of bonding type rmsd/Z covalent geometry : bond 0.00314 / 0.15 ( 4158) covalent geometry : angle 0.59787 / 0.32 ( 5638) hydrogen bonds : bond 0.04215 / 2.95 ( 334) hydrogen bonds : angle 4.10069 / 3.08 ( 1002) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 988 Ramachandran restraints generated. 494 Oldfield, 0 Emsley, 494 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 988 Ramachandran restraints generated. 494 Oldfield, 0 Emsley, 494 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 85 residues out of total 416 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 79 time to evaluate : 0.086 Fit side-chains REVERT: A 249 MET cc_start: 0.4052 (mmt) cc_final: 0.3404 (ptt) REVERT: B 18 TYR cc_start: 0.6982 (t80) cc_final: 0.6673 (t80) REVERT: B 249 MET cc_start: 0.2213 (tpp) cc_final: 0.1873 (tpt) outliers start: 6 outliers final: 5 residues processed: 83 average time/residue: 0.0510 time to fit residues: 5.4102 Evaluate side-chains 81 residues out of total 416 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 76 time to evaluate : 0.139 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 149 MET Chi-restraints excluded: chain A residue 185 THR Chi-restraints excluded: chain B residue 102 SER Chi-restraints excluded: chain B residue 169 SER Chi-restraints excluded: chain B residue 229 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 48 random chunks: chunk 16 optimal weight: 2.9990 chunk 3 optimal weight: 1.9990 chunk 32 optimal weight: 0.5980 chunk 29 optimal weight: 1.9990 chunk 11 optimal weight: 0.7980 chunk 8 optimal weight: 1.9990 chunk 24 optimal weight: 0.8980 chunk 17 optimal weight: 0.6980 chunk 39 optimal weight: 0.6980 chunk 43 optimal weight: 0.5980 chunk 36 optimal weight: 0.7980 overall best weight: 0.6780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 72 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 4 GLN B 240 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4624 r_free = 0.4624 target = 0.218012 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.4340 r_free = 0.4340 target = 0.187653 restraints weight = 4400.857| |-----------------------------------------------------------------------------| r_work (start): 0.4351 rms_B_bonded: 1.70 r_work: 0.4190 rms_B_bonded: 2.74 restraints_weight: 0.5000 r_work: 0.4050 rms_B_bonded: 4.74 restraints_weight: 0.2500 r_work (final): 0.4050 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7526 moved from start: 0.4659 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 4158 Z= 0.173 Angle : 0.619 7.266 5638 Z= 0.332 Chirality : 0.041 0.141 642 Planarity : 0.003 0.021 690 Dihedral : 5.757 46.619 702 Min Nonbonded Distance : 2.541 Molprobity Statistics. All-atom Clashscore : 9.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.43 % Favored : 97.57 % Rotamer: Outliers : 1.20 % Allowed : 19.95 % Favored : 78.85 % 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: 2.69 (0.36), residues: 494 helix: 2.40 (0.23), residues: 406 sheet: None (None), residues: 0 loop : -1.31 (0.65), residues: 88 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 183 TYR 0.022 0.002 TYR A 18 PHE 0.021 0.002 PHE B 86 TRP 0.006 0.001 TRP B 78 HIS 0.011 0.002 HIS A 98 Details of bonding type rmsd/Z covalent geometry : bond 0.00378 / 0.17 ( 4158) covalent geometry : angle 0.61874 / 0.33 ( 5638) hydrogen bonds : bond 0.04361 / 3.06 ( 334) hydrogen bonds : angle 4.16066 / 3.13 ( 1002) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1052.09 seconds wall clock time: 18 minutes 39.82 seconds (1119.82 seconds total)