Starting phenix.real_space_refine on Fri Aug 22 14:35:02 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8do3_27589/08_2025/8do3_27589_trim.cif Found real_map, /net/cci-nas-00/data/ceres_data/8do3_27589/08_2025/8do3_27589.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.22 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8do3_27589/08_2025/8do3_27589.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8do3_27589/08_2025/8do3_27589.map" model { file = "/net/cci-nas-00/data/ceres_data/8do3_27589/08_2025/8do3_27589_trim.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8do3_27589/08_2025/8do3_27589_trim.cif" } resolution = 3.22 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= 0.004 sd= 0.041 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 S 26 5.16 5 Cl 2 4.86 5 C 2765 2.51 5 N 676 2.21 5 O 716 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 4185 Number of models: 1 Model: "" Number of chains: 4 Chain: "B" Number of atoms: 467 Number of conformers: 1 Conformer: "" Number of residues, atoms: 60, 467 Classifications: {'peptide': 60} Incomplete info: {'truncation_to_alanine': 4} Link IDs: {'PTRANS': 3, 'TRANS': 56} Unresolved non-hydrogen bonds: 19 Unresolved non-hydrogen angles: 24 Unresolved non-hydrogen dihedrals: 16 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'PHE:plan': 1, 'GLU:plan': 1, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 15 Chain: "C" Number of atoms: 244 Number of conformers: 1 Conformer: "" Number of residues, atoms: 31, 244 Classifications: {'peptide': 31} Link IDs: {'PTRANS': 2, 'TRANS': 28} Chain: "A" Number of atoms: 3431 Number of conformers: 1 Conformer: "" Number of residues, atoms: 443, 3431 Classifications: {'peptide': 443} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 19, 'TRANS': 423} Chain breaks: 3 Unresolved non-hydrogen bonds: 7 Unresolved non-hydrogen angles: 9 Unresolved non-hydrogen dihedrals: 7 Planarities with less than four sites: {'PHE:plan': 1} Unresolved non-hydrogen planarities: 6 Chain: "A" Number of atoms: 43 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 43 Unusual residues: {'SWR': 1} Classifications: {'undetermined': 1} Time building chain proxies: 1.28, per 1000 atoms: 0.31 Number of scatterers: 4185 At special positions: 0 Unit cell: (86.1, 76.65, 81.9, 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) Cl 2 17.00 S 26 16.00 O 716 8.00 N 676 7.00 C 2765 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: 0.41 Conformation dependent library (CDL) restraints added in 166.1 milliseconds Enol-peptide restraints added in 1.2 microseconds 1044 Ramachandran restraints generated. 522 Oldfield, 0 Emsley, 522 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 978 Finding SS restraints... Secondary structure from input PDB file: 24 helices and 4 sheets defined 76.6% alpha, 4.7% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.08 Creating SS restraints... Processing helix chain 'B' and resid 7 through 25 removed outlier: 3.560A pdb=" N SER B 11 " --> pdb=" O PHE B 7 " (cutoff:3.500A) Processing helix chain 'B' and resid 29 through 66 Proline residue: B 60 - end of helix Processing helix chain 'C' and resid 69 through 95 Processing helix chain 'A' and resid 8 through 14 removed outlier: 4.257A pdb=" N PHE A 12 " --> pdb=" O VAL A 8 " (cutoff:3.500A) Processing helix chain 'A' and resid 27 through 47 Processing helix chain 'A' and resid 75 through 79 removed outlier: 4.600A pdb=" N LEU A 79 " --> pdb=" O LEU A 76 " (cutoff:3.500A) Processing helix chain 'A' and resid 81 through 97 Processing helix chain 'A' and resid 107 through 134 Processing helix chain 'A' and resid 139 through 144 removed outlier: 3.789A pdb=" N GLY A 144 " --> pdb=" O PRO A 140 " (cutoff:3.500A) Processing helix chain 'A' and resid 144 through 172 Processing helix chain 'A' and resid 177 through 197 Processing helix chain 'A' and resid 211 through 223 Processing helix chain 'A' and resid 228 through 235 Processing helix chain 'A' and resid 241 through 260 Processing helix chain 'A' and resid 288 through 312 Processing helix chain 'A' and resid 315 through 322 Processing helix chain 'A' and resid 340 through 345 Processing helix chain 'A' and resid 350 through 357 Processing helix chain 'A' and resid 357 through 384 removed outlier: 4.018A pdb=" N GLY A 384 " --> pdb=" O ILE A 380 " (cutoff:3.500A) Processing helix chain 'A' and resid 386 through 398 Processing helix chain 'A' and resid 405 through 408 Processing helix chain 'A' and resid 409 through 415 Processing helix chain 'A' and resid 416 through 439 Processing helix chain 'A' and resid 442 through 468 removed outlier: 3.539A pdb=" N GLY A 446 " --> pdb=" O GLY A 442 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'C' and resid 67 through 68 Processing sheet with id=AA2, first strand: chain 'A' and resid 200 through 202 Processing sheet with id=AA3, first strand: chain 'A' and resid 277 through 282 Processing sheet with id=AA4, first strand: chain 'A' and resid 323 through 325 removed outlier: 3.632A pdb=" N GLY A 339 " --> pdb=" O THR A 323 " (cutoff:3.500A) removed outlier: 5.973A pdb=" N SER A 325 " --> pdb=" O PRO A 337 " (cutoff:3.500A) 318 hydrogen bonds defined for protein. 942 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: 0.55 Time building geometry restraints manager: 0.55 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.33: 1056 1.33 - 1.45: 765 1.45 - 1.57: 2409 1.57 - 1.69: 1 1.69 - 1.81: 45 Bond restraints: 4276 Sorted by residual: bond pdb=" C2 SWR A 501 " pdb=" N5 SWR A 501 " ideal model delta sigma weight residual 1.463 1.526 -0.063 2.00e-02 2.50e+03 9.91e+00 bond pdb=" C6 SWR A 501 " pdb=" C7 SWR A 501 " ideal model delta sigma weight residual 1.433 1.395 0.038 2.00e-02 2.50e+03 3.68e+00 bond pdb=" CA ALA A 440 " pdb=" C ALA A 440 " ideal model delta sigma weight residual 1.523 1.502 0.021 1.30e-02 5.92e+03 2.60e+00 bond pdb=" CA THR A 445 " pdb=" C THR A 445 " ideal model delta sigma weight residual 1.524 1.504 0.020 1.24e-02 6.50e+03 2.55e+00 bond pdb=" CA TYR A 63 " pdb=" C TYR A 63 " ideal model delta sigma weight residual 1.522 1.500 0.022 1.38e-02 5.25e+03 2.51e+00 ... (remaining 4271 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.60: 5631 1.60 - 3.20: 118 3.20 - 4.79: 32 4.79 - 6.39: 7 6.39 - 7.99: 2 Bond angle restraints: 5790 Sorted by residual: angle pdb=" N ILE A 441 " pdb=" CA ILE A 441 " pdb=" C ILE A 441 " ideal model delta sigma weight residual 109.58 105.73 3.85 1.29e+00 6.01e-01 8.91e+00 angle pdb=" N SWR A 501 " pdb=" C2 SWR A 501 " pdb=" N5 SWR A 501 " ideal model delta sigma weight residual 110.48 118.47 -7.99 3.00e+00 1.11e-01 7.10e+00 angle pdb=" C19 SWR A 501 " pdb=" N5 SWR A 501 " pdb=" C2 SWR A 501 " ideal model delta sigma weight residual 125.55 117.82 7.73 3.00e+00 1.11e-01 6.65e+00 angle pdb=" C LYS A 171 " pdb=" N GLY A 172 " pdb=" CA GLY A 172 " ideal model delta sigma weight residual 121.41 117.18 4.23 1.96e+00 2.60e-01 4.65e+00 angle pdb=" C25 SWR A 501 " pdb=" C20 SWR A 501 " pdb=" N6 SWR A 501 " ideal model delta sigma weight residual 123.71 117.45 6.26 3.00e+00 1.11e-01 4.35e+00 ... (remaining 5785 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.42: 2282 16.42 - 32.84: 204 32.84 - 49.26: 31 49.26 - 65.68: 11 65.68 - 82.10: 4 Dihedral angle restraints: 2532 sinusoidal: 1008 harmonic: 1524 Sorted by residual: dihedral pdb=" CA ASN A 300 " pdb=" CB ASN A 300 " pdb=" CG ASN A 300 " pdb=" OD1 ASN A 300 " ideal model delta sinusoidal sigma weight residual 120.00 -173.50 -66.50 2 2.00e+01 2.50e-03 1.01e+01 dihedral pdb=" CA ILE A 401 " pdb=" C ILE A 401 " pdb=" N ASN A 402 " pdb=" CA ASN A 402 " ideal model delta harmonic sigma weight residual -180.00 -164.96 -15.04 0 5.00e+00 4.00e-02 9.05e+00 dihedral pdb=" CB GLU A 264 " pdb=" CG GLU A 264 " pdb=" CD GLU A 264 " pdb=" OE1 GLU A 264 " ideal model delta sinusoidal sigma weight residual 0.00 -80.48 80.48 1 3.00e+01 1.11e-03 8.90e+00 ... (remaining 2529 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.031: 421 0.031 - 0.061: 175 0.061 - 0.092: 64 0.092 - 0.123: 14 0.123 - 0.154: 3 Chirality restraints: 677 Sorted by residual: chirality pdb=" CA ILE A 441 " pdb=" N ILE A 441 " pdb=" C ILE A 441 " pdb=" CB ILE A 441 " both_signs ideal model delta sigma weight residual False 2.43 2.59 -0.15 2.00e-01 2.50e+01 5.89e-01 chirality pdb=" C2 SWR A 501 " pdb=" N SWR A 501 " pdb=" C1 SWR A 501 " pdb=" N5 SWR A 501 " both_signs ideal model delta sigma weight residual False -2.47 -2.60 0.14 2.00e-01 2.50e+01 4.74e-01 chirality pdb=" CA ILE A 48 " pdb=" N ILE A 48 " pdb=" C ILE A 48 " pdb=" CB ILE A 48 " both_signs ideal model delta sigma weight residual False 2.43 2.56 -0.12 2.00e-01 2.50e+01 3.78e-01 ... (remaining 674 not shown) Planarity restraints: 709 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C19 SWR A 501 " 0.205 2.00e-02 2.50e+03 6.09e-01 6.49e+03 pdb=" C2 SWR A 501 " 0.224 2.00e-02 2.50e+03 pdb=" C20 SWR A 501 " -0.290 2.00e-02 2.50e+03 pdb=" N5 SWR A 501 " -0.354 2.00e-02 2.50e+03 pdb=" N6 SWR A 501 " -0.481 2.00e-02 2.50e+03 pdb=" O5 SWR A 501 " 1.302 2.00e-02 2.50e+03 pdb=" O6 SWR A 501 " -0.605 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" N SWR A 501 " 0.059 2.00e-02 2.50e+03 2.13e-01 9.11e+02 pdb=" O SWR A 501 " -0.212 2.00e-02 2.50e+03 pdb=" C1 SWR A 501 " -0.381 2.00e-02 2.50e+03 pdb=" C13 SWR A 501 " 0.117 2.00e-02 2.50e+03 pdb=" C2 SWR A 501 " 0.190 2.00e-02 2.50e+03 pdb=" C3 SWR A 501 " -0.079 2.00e-02 2.50e+03 pdb=" C4 SWR A 501 " 0.338 2.00e-02 2.50e+03 pdb=" N1 SWR A 501 " -0.032 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C20 SWR A 501 " -0.027 2.00e-02 2.50e+03 5.54e-02 6.14e+01 pdb=" C21 SWR A 501 " -0.038 2.00e-02 2.50e+03 pdb=" C22 SWR A 501 " -0.032 2.00e-02 2.50e+03 pdb=" C23 SWR A 501 " -0.015 2.00e-02 2.50e+03 pdb=" C24 SWR A 501 " -0.034 2.00e-02 2.50e+03 pdb=" C25 SWR A 501 " -0.043 2.00e-02 2.50e+03 pdb=" N6 SWR A 501 " 0.104 2.00e-02 2.50e+03 pdb="CL1 SWR A 501 " 0.085 2.00e-02 2.50e+03 ... (remaining 706 not shown) Histogram of nonbonded interaction distances: 2.45 - 2.94: 1840 2.94 - 3.43: 4518 3.43 - 3.92: 7024 3.92 - 4.41: 7554 4.41 - 4.90: 13088 Nonbonded interactions: 34024 Sorted by model distance: nonbonded pdb=" O THR A 124 " pdb=" OG SER A 128 " model vdw 2.452 3.040 nonbonded pdb=" O LEU A 181 " pdb=" OG1 THR A 185 " model vdw 2.461 3.040 nonbonded pdb=" O GLN A 20 " pdb=" OH TYR A 173 " model vdw 2.464 3.040 nonbonded pdb=" NH2 ARG B 20 " pdb=" O LYS A 415 " model vdw 2.523 3.120 nonbonded pdb=" O VAL B 8 " pdb=" OG SER B 11 " model vdw 2.538 3.040 ... (remaining 34019 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: 1.010 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.050 Check model and map are aligned: 0.010 Set scattering table: 0.010 Process input model: 5.240 Find NCS groups from input model: 0.010 Set up NCS constraints: 0.000 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.230 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 7.570 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7524 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 0.063 4276 Z= 0.204 Angle : 0.621 7.992 5790 Z= 0.313 Chirality : 0.039 0.154 677 Planarity : 0.025 0.609 709 Dihedral : 13.224 82.100 1554 Min Nonbonded Distance : 2.452 Molprobity Statistics. All-atom Clashscore : 6.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.30 % Favored : 97.70 % Rotamer: Outliers : 0.00 % Allowed : 0.22 % Favored : 99.78 % 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 aren not related in a simple way. whole: 2.39 (0.37), residues: 522 helix: 2.48 (0.26), residues: 393 sheet: -1.48 (1.46), residues: 14 loop : -1.34 (0.52), residues: 115 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 405 TYR 0.006 0.001 TYR A 131 PHE 0.011 0.001 PHE A 252 TRP 0.012 0.001 TRP A 64 HIS 0.002 0.001 HIS B 58 Details of bonding type rmsd covalent geometry : bond 0.00409 ( 4276) covalent geometry : angle 0.62114 ( 5790) hydrogen bonds : bond 0.12969 ( 318) hydrogen bonds : angle 4.91748 ( 942) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1044 Ramachandran restraints generated. 522 Oldfield, 0 Emsley, 522 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1044 Ramachandran restraints generated. 522 Oldfield, 0 Emsley, 522 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 60 residues out of total 453 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 60 time to evaluate : 0.152 Fit side-chains REVERT: B 30 ARG cc_start: 0.7320 (tpp80) cc_final: 0.6345 (mmm160) REVERT: A 82 SER cc_start: 0.8718 (t) cc_final: 0.8456 (t) outliers start: 0 outliers final: 0 residues processed: 60 average time/residue: 0.1018 time to fit residues: 7.2588 Evaluate side-chains 53 residues out of total 453 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 53 time to evaluate : 0.164 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 53 random chunks: chunk 24 optimal weight: 1.9990 chunk 48 optimal weight: 0.5980 chunk 26 optimal weight: 0.8980 chunk 2 optimal weight: 2.9990 chunk 16 optimal weight: 0.9980 chunk 32 optimal weight: 0.7980 chunk 31 optimal weight: 2.9990 chunk 25 optimal weight: 0.7980 chunk 50 optimal weight: 0.6980 chunk 19 optimal weight: 3.9990 chunk 30 optimal weight: 0.9990 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3738 r_free = 0.3738 target = 0.150360 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3397 r_free = 0.3397 target = 0.120659 restraints weight = 4713.378| |-----------------------------------------------------------------------------| r_work (start): 0.3276 rms_B_bonded: 2.00 r_work: 0.3130 rms_B_bonded: 2.82 restraints_weight: 0.5000 r_work: 0.2972 rms_B_bonded: 4.57 restraints_weight: 0.2500 r_work (final): 0.2972 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7424 moved from start: 0.0820 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 4276 Z= 0.162 Angle : 0.568 6.067 5790 Z= 0.281 Chirality : 0.039 0.145 677 Planarity : 0.004 0.039 709 Dihedral : 5.200 33.077 594 Min Nonbonded Distance : 2.611 Molprobity Statistics. All-atom Clashscore : 6.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.11 % Favored : 97.89 % Rotamer: Outliers : 1.12 % Allowed : 4.24 % Favored : 94.64 % 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 aren not related in a simple way. whole: 2.61 (0.37), residues: 522 helix: 2.58 (0.26), residues: 395 sheet: -1.72 (1.43), residues: 14 loop : -1.04 (0.55), residues: 113 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 24 TYR 0.007 0.001 TYR A 63 PHE 0.008 0.001 PHE A 252 TRP 0.008 0.001 TRP A 64 HIS 0.002 0.001 HIS B 58 Details of bonding type rmsd covalent geometry : bond 0.00381 ( 4276) covalent geometry : angle 0.56793 ( 5790) hydrogen bonds : bond 0.04207 ( 318) hydrogen bonds : angle 4.08001 ( 942) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1044 Ramachandran restraints generated. 522 Oldfield, 0 Emsley, 522 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1044 Ramachandran restraints generated. 522 Oldfield, 0 Emsley, 522 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 60 residues out of total 453 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 55 time to evaluate : 0.159 Fit side-chains REVERT: B 30 ARG cc_start: 0.7442 (tpp80) cc_final: 0.6019 (mmm160) REVERT: B 55 LYS cc_start: 0.8027 (tttt) cc_final: 0.7675 (tttp) REVERT: A 24 ARG cc_start: 0.5868 (OUTLIER) cc_final: 0.4833 (mmt180) REVERT: A 82 SER cc_start: 0.8870 (t) cc_final: 0.8641 (t) REVERT: A 91 MET cc_start: 0.7646 (mmm) cc_final: 0.7342 (mmm) outliers start: 5 outliers final: 4 residues processed: 58 average time/residue: 0.0917 time to fit residues: 6.4181 Evaluate side-chains 59 residues out of total 453 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 54 time to evaluate : 0.108 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 68 VAL Chi-restraints excluded: chain A residue 24 ARG Chi-restraints excluded: chain A residue 67 VAL Chi-restraints excluded: chain A residue 163 LEU Chi-restraints excluded: chain A residue 463 LYS Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 53 random chunks: chunk 39 optimal weight: 3.9990 chunk 2 optimal weight: 0.9980 chunk 9 optimal weight: 7.9990 chunk 38 optimal weight: 0.8980 chunk 10 optimal weight: 2.9990 chunk 30 optimal weight: 0.9990 chunk 41 optimal weight: 2.9990 chunk 5 optimal weight: 0.8980 chunk 37 optimal weight: 0.5980 chunk 8 optimal weight: 1.9990 chunk 1 optimal weight: 0.6980 overall best weight: 0.8180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3731 r_free = 0.3731 target = 0.149593 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3378 r_free = 0.3378 target = 0.119036 restraints weight = 4757.737| |-----------------------------------------------------------------------------| r_work (start): 0.3365 rms_B_bonded: 2.13 r_work: 0.3215 rms_B_bonded: 3.01 restraints_weight: 0.5000 r_work: 0.3064 rms_B_bonded: 4.83 restraints_weight: 0.2500 r_work (final): 0.3064 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7803 moved from start: 0.1128 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 4276 Z= 0.158 Angle : 0.550 6.279 5790 Z= 0.274 Chirality : 0.039 0.128 677 Planarity : 0.004 0.040 709 Dihedral : 5.024 27.634 594 Min Nonbonded Distance : 2.611 Molprobity Statistics. All-atom Clashscore : 6.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.49 % Favored : 97.51 % Rotamer: Outliers : 1.56 % Allowed : 6.70 % Favored : 91.74 % 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 aren not related in a simple way. whole: 2.64 (0.37), residues: 522 helix: 2.58 (0.26), residues: 396 sheet: -2.11 (1.34), residues: 14 loop : -0.85 (0.57), residues: 112 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 24 TYR 0.007 0.001 TYR A 137 PHE 0.009 0.001 PHE A 252 TRP 0.006 0.001 TRP A 34 HIS 0.002 0.001 HIS B 58 Details of bonding type rmsd covalent geometry : bond 0.00381 ( 4276) covalent geometry : angle 0.55018 ( 5790) hydrogen bonds : bond 0.03864 ( 318) hydrogen bonds : angle 3.94637 ( 942) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1044 Ramachandran restraints generated. 522 Oldfield, 0 Emsley, 522 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1044 Ramachandran restraints generated. 522 Oldfield, 0 Emsley, 522 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 59 residues out of total 453 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 52 time to evaluate : 0.167 Fit side-chains REVERT: B 30 ARG cc_start: 0.7681 (tpp80) cc_final: 0.6216 (mmm160) REVERT: B 55 LYS cc_start: 0.8388 (tttt) cc_final: 0.8053 (tttp) REVERT: A 24 ARG cc_start: 0.6282 (OUTLIER) cc_final: 0.5146 (mmt180) REVERT: A 77 MET cc_start: 0.8680 (mmt) cc_final: 0.8346 (mmt) REVERT: A 82 SER cc_start: 0.9094 (t) cc_final: 0.8857 (t) REVERT: A 91 MET cc_start: 0.7859 (mmm) cc_final: 0.7519 (mmm) REVERT: A 368 MET cc_start: 0.7700 (tpt) cc_final: 0.7488 (tpt) outliers start: 7 outliers final: 5 residues processed: 57 average time/residue: 0.1023 time to fit residues: 7.0381 Evaluate side-chains 57 residues out of total 453 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 51 time to evaluate : 0.164 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 68 VAL Chi-restraints excluded: chain A residue 24 ARG Chi-restraints excluded: chain A residue 67 VAL Chi-restraints excluded: chain A residue 163 LEU Chi-restraints excluded: chain A residue 362 VAL Chi-restraints excluded: chain A residue 463 LYS Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 53 random chunks: chunk 2 optimal weight: 0.6980 chunk 21 optimal weight: 0.0000 chunk 22 optimal weight: 0.9990 chunk 49 optimal weight: 1.9990 chunk 30 optimal weight: 0.9990 chunk 19 optimal weight: 0.7980 chunk 50 optimal weight: 0.8980 chunk 36 optimal weight: 0.9990 chunk 20 optimal weight: 0.9990 chunk 5 optimal weight: 0.9990 chunk 40 optimal weight: 3.9990 overall best weight: 0.6786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3737 r_free = 0.3737 target = 0.149874 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3393 r_free = 0.3393 target = 0.120041 restraints weight = 4707.274| |-----------------------------------------------------------------------------| r_work (start): 0.3363 rms_B_bonded: 2.05 r_work: 0.3223 rms_B_bonded: 2.85 restraints_weight: 0.5000 r_work: 0.3071 rms_B_bonded: 4.65 restraints_weight: 0.2500 r_work (final): 0.3071 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7775 moved from start: 0.1237 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 4276 Z= 0.142 Angle : 0.532 6.198 5790 Z= 0.264 Chirality : 0.038 0.128 677 Planarity : 0.004 0.040 709 Dihedral : 5.107 29.013 594 Min Nonbonded Distance : 2.611 Molprobity Statistics. All-atom Clashscore : 5.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.11 % Favored : 97.89 % Rotamer: Outliers : 1.79 % Allowed : 7.81 % Favored : 90.40 % 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 aren not related in a simple way. whole: 2.71 (0.37), residues: 522 helix: 2.61 (0.26), residues: 396 sheet: -1.87 (1.34), residues: 14 loop : -0.81 (0.56), residues: 112 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 24 TYR 0.006 0.001 TYR A 137 PHE 0.008 0.001 PHE A 252 TRP 0.007 0.001 TRP A 34 HIS 0.003 0.001 HIS A 360 Details of bonding type rmsd covalent geometry : bond 0.00339 ( 4276) covalent geometry : angle 0.53161 ( 5790) hydrogen bonds : bond 0.03670 ( 318) hydrogen bonds : angle 3.87819 ( 942) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1044 Ramachandran restraints generated. 522 Oldfield, 0 Emsley, 522 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1044 Ramachandran restraints generated. 522 Oldfield, 0 Emsley, 522 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 62 residues out of total 453 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 54 time to evaluate : 0.093 Fit side-chains REVERT: B 30 ARG cc_start: 0.7654 (tpp80) cc_final: 0.6179 (mmm160) REVERT: B 55 LYS cc_start: 0.8387 (tttt) cc_final: 0.8049 (tttp) REVERT: A 24 ARG cc_start: 0.6229 (OUTLIER) cc_final: 0.5092 (mmt180) REVERT: A 77 MET cc_start: 0.8665 (mmt) cc_final: 0.8315 (mmt) REVERT: A 82 SER cc_start: 0.9109 (t) cc_final: 0.8861 (t) outliers start: 8 outliers final: 6 residues processed: 59 average time/residue: 0.0956 time to fit residues: 6.7333 Evaluate side-chains 60 residues out of total 453 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 53 time to evaluate : 0.135 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 66 VAL Chi-restraints excluded: chain C residue 68 VAL Chi-restraints excluded: chain A residue 24 ARG Chi-restraints excluded: chain A residue 67 VAL Chi-restraints excluded: chain A residue 163 LEU Chi-restraints excluded: chain A residue 362 VAL Chi-restraints excluded: chain A residue 463 LYS Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 53 random chunks: chunk 47 optimal weight: 1.9990 chunk 41 optimal weight: 0.9990 chunk 26 optimal weight: 0.6980 chunk 4 optimal weight: 0.9980 chunk 40 optimal weight: 0.2980 chunk 35 optimal weight: 1.9990 chunk 51 optimal weight: 1.9990 chunk 32 optimal weight: 0.5980 chunk 24 optimal weight: 3.9990 chunk 23 optimal weight: 0.7980 chunk 39 optimal weight: 0.3980 overall best weight: 0.5580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3745 r_free = 0.3745 target = 0.150875 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3399 r_free = 0.3399 target = 0.120658 restraints weight = 4732.125| |-----------------------------------------------------------------------------| r_work (start): 0.3371 rms_B_bonded: 2.10 r_work: 0.3226 rms_B_bonded: 2.95 restraints_weight: 0.5000 r_work: 0.3072 rms_B_bonded: 4.81 restraints_weight: 0.2500 r_work (final): 0.3072 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7766 moved from start: 0.1347 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 4276 Z= 0.129 Angle : 0.533 6.170 5790 Z= 0.263 Chirality : 0.038 0.128 677 Planarity : 0.004 0.039 709 Dihedral : 5.023 26.917 594 Min Nonbonded Distance : 2.616 Molprobity Statistics. All-atom Clashscore : 6.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.49 % Favored : 97.51 % Rotamer: Outliers : 1.56 % Allowed : 11.38 % Favored : 87.05 % 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 aren not related in a simple way. whole: 2.76 (0.37), residues: 522 helix: 2.64 (0.26), residues: 396 sheet: -1.57 (1.35), residues: 14 loop : -0.79 (0.56), residues: 112 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 24 TYR 0.019 0.001 TYR A 336 PHE 0.007 0.001 PHE A 252 TRP 0.007 0.001 TRP A 34 HIS 0.002 0.001 HIS A 360 Details of bonding type rmsd covalent geometry : bond 0.00305 ( 4276) covalent geometry : angle 0.53253 ( 5790) hydrogen bonds : bond 0.03528 ( 318) hydrogen bonds : angle 3.83348 ( 942) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1044 Ramachandran restraints generated. 522 Oldfield, 0 Emsley, 522 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1044 Ramachandran restraints generated. 522 Oldfield, 0 Emsley, 522 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 59 residues out of total 453 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 52 time to evaluate : 0.162 Fit side-chains REVERT: B 30 ARG cc_start: 0.7685 (tpp80) cc_final: 0.6206 (mmm160) REVERT: B 55 LYS cc_start: 0.8370 (tttt) cc_final: 0.8032 (tttp) REVERT: A 77 MET cc_start: 0.8622 (mmt) cc_final: 0.8293 (mmt) REVERT: A 82 SER cc_start: 0.9134 (t) cc_final: 0.8869 (t) REVERT: A 91 MET cc_start: 0.7918 (mmm) cc_final: 0.7522 (mmm) outliers start: 7 outliers final: 6 residues processed: 56 average time/residue: 0.0940 time to fit residues: 6.4270 Evaluate side-chains 57 residues out of total 453 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 51 time to evaluate : 0.180 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 66 VAL Chi-restraints excluded: chain C residue 68 VAL Chi-restraints excluded: chain A residue 67 VAL Chi-restraints excluded: chain A residue 163 LEU Chi-restraints excluded: chain A residue 362 VAL Chi-restraints excluded: chain A residue 463 LYS Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 53 random chunks: chunk 11 optimal weight: 0.6980 chunk 32 optimal weight: 0.6980 chunk 44 optimal weight: 0.0470 chunk 16 optimal weight: 0.8980 chunk 28 optimal weight: 2.9990 chunk 47 optimal weight: 1.9990 chunk 6 optimal weight: 0.2980 chunk 4 optimal weight: 1.9990 chunk 29 optimal weight: 0.6980 chunk 22 optimal weight: 0.5980 chunk 18 optimal weight: 0.0010 overall best weight: 0.3284 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3767 r_free = 0.3767 target = 0.152723 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3429 r_free = 0.3429 target = 0.122916 restraints weight = 4747.827| |-----------------------------------------------------------------------------| r_work (start): 0.3426 rms_B_bonded: 2.08 r_work: 0.3274 rms_B_bonded: 2.98 restraints_weight: 0.5000 r_work: 0.3118 rms_B_bonded: 4.87 restraints_weight: 0.2500 r_work (final): 0.3118 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7749 moved from start: 0.1450 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.036 4276 Z= 0.109 Angle : 0.517 7.338 5790 Z= 0.253 Chirality : 0.038 0.127 677 Planarity : 0.004 0.039 709 Dihedral : 5.036 26.607 594 Min Nonbonded Distance : 2.616 Molprobity Statistics. All-atom Clashscore : 6.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.11 % Favored : 97.89 % Rotamer: Outliers : 0.67 % Allowed : 12.05 % Favored : 87.28 % 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 aren not related in a simple way. whole: 2.90 (0.37), residues: 522 helix: 2.73 (0.26), residues: 395 sheet: -1.25 (1.38), residues: 14 loop : -0.72 (0.55), residues: 113 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 24 TYR 0.019 0.001 TYR A 336 PHE 0.006 0.001 PHE A 156 TRP 0.006 0.001 TRP A 34 HIS 0.001 0.001 HIS A 360 Details of bonding type rmsd covalent geometry : bond 0.00248 ( 4276) covalent geometry : angle 0.51688 ( 5790) hydrogen bonds : bond 0.03316 ( 318) hydrogen bonds : angle 3.76540 ( 942) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1044 Ramachandran restraints generated. 522 Oldfield, 0 Emsley, 522 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1044 Ramachandran restraints generated. 522 Oldfield, 0 Emsley, 522 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 54 residues out of total 453 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 51 time to evaluate : 0.157 Fit side-chains REVERT: B 30 ARG cc_start: 0.7715 (tpp80) cc_final: 0.6191 (mmm160) REVERT: A 77 MET cc_start: 0.8572 (mmt) cc_final: 0.8258 (mmt) REVERT: A 82 SER cc_start: 0.9134 (t) cc_final: 0.8871 (t) outliers start: 3 outliers final: 2 residues processed: 53 average time/residue: 0.0905 time to fit residues: 5.9769 Evaluate side-chains 52 residues out of total 453 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 50 time to evaluate : 0.179 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 66 VAL Chi-restraints excluded: chain A residue 163 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 53 random chunks: chunk 23 optimal weight: 1.9990 chunk 42 optimal weight: 0.8980 chunk 46 optimal weight: 2.9990 chunk 14 optimal weight: 0.0980 chunk 19 optimal weight: 0.5980 chunk 10 optimal weight: 7.9990 chunk 31 optimal weight: 2.9990 chunk 9 optimal weight: 0.0670 chunk 0 optimal weight: 4.9990 chunk 51 optimal weight: 0.5980 chunk 12 optimal weight: 0.8980 overall best weight: 0.4518 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3733 r_free = 0.3733 target = 0.150137 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3394 r_free = 0.3394 target = 0.120263 restraints weight = 4767.063| |-----------------------------------------------------------------------------| r_work (start): 0.3421 rms_B_bonded: 2.06 r_work: 0.3273 rms_B_bonded: 2.96 restraints_weight: 0.5000 r_work: 0.3116 rms_B_bonded: 4.83 restraints_weight: 0.2500 r_work (final): 0.3116 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7752 moved from start: 0.1518 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 4276 Z= 0.116 Angle : 0.523 8.102 5790 Z= 0.254 Chirality : 0.038 0.129 677 Planarity : 0.004 0.039 709 Dihedral : 5.092 26.480 594 Min Nonbonded Distance : 2.615 Molprobity Statistics. All-atom Clashscore : 7.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.30 % Favored : 97.70 % Rotamer: Outliers : 1.56 % Allowed : 11.83 % Favored : 86.61 % 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 aren not related in a simple way. whole: 2.93 (0.37), residues: 522 helix: 2.76 (0.26), residues: 395 sheet: -1.29 (1.37), residues: 14 loop : -0.72 (0.55), residues: 113 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 24 TYR 0.018 0.001 TYR A 336 PHE 0.006 0.001 PHE A 252 TRP 0.007 0.001 TRP A 34 HIS 0.002 0.001 HIS A 360 Details of bonding type rmsd covalent geometry : bond 0.00267 ( 4276) covalent geometry : angle 0.52272 ( 5790) hydrogen bonds : bond 0.03314 ( 318) hydrogen bonds : angle 3.73182 ( 942) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1044 Ramachandran restraints generated. 522 Oldfield, 0 Emsley, 522 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1044 Ramachandran restraints generated. 522 Oldfield, 0 Emsley, 522 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 61 residues out of total 453 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 54 time to evaluate : 0.125 Fit side-chains REVERT: B 30 ARG cc_start: 0.7724 (tpp80) cc_final: 0.6191 (mmm160) REVERT: A 77 MET cc_start: 0.8580 (mmt) cc_final: 0.8241 (mmt) REVERT: A 82 SER cc_start: 0.9151 (t) cc_final: 0.8879 (t) REVERT: A 91 MET cc_start: 0.7865 (mmm) cc_final: 0.7542 (mmm) REVERT: A 311 ARG cc_start: 0.6060 (mtm180) cc_final: 0.5770 (mtp180) outliers start: 7 outliers final: 5 residues processed: 59 average time/residue: 0.0873 time to fit residues: 6.3101 Evaluate side-chains 58 residues out of total 453 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 53 time to evaluate : 0.155 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 66 VAL Chi-restraints excluded: chain A residue 67 VAL Chi-restraints excluded: chain A residue 141 SER Chi-restraints excluded: chain A residue 163 LEU Chi-restraints excluded: chain A residue 463 LYS Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 53 random chunks: chunk 2 optimal weight: 0.1980 chunk 45 optimal weight: 0.5980 chunk 15 optimal weight: 2.9990 chunk 17 optimal weight: 3.9990 chunk 38 optimal weight: 4.9990 chunk 21 optimal weight: 0.2980 chunk 25 optimal weight: 3.9990 chunk 36 optimal weight: 0.9990 chunk 6 optimal weight: 0.5980 chunk 46 optimal weight: 0.6980 chunk 18 optimal weight: 0.2980 overall best weight: 0.3980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3717 r_free = 0.3717 target = 0.149809 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3359 r_free = 0.3359 target = 0.118284 restraints weight = 4764.355| |-----------------------------------------------------------------------------| r_work (start): 0.3374 rms_B_bonded: 2.15 r_work: 0.3228 rms_B_bonded: 3.02 restraints_weight: 0.5000 r_work: 0.3072 rms_B_bonded: 4.91 restraints_weight: 0.2500 r_work (final): 0.3072 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7732 moved from start: 0.1598 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.056 4276 Z= 0.116 Angle : 0.540 8.805 5790 Z= 0.261 Chirality : 0.038 0.157 677 Planarity : 0.004 0.039 709 Dihedral : 5.375 30.254 594 Min Nonbonded Distance : 2.614 Molprobity Statistics. All-atom Clashscore : 7.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.11 % Favored : 97.89 % Rotamer: Outliers : 1.34 % Allowed : 12.72 % Favored : 85.94 % 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 aren not related in a simple way. whole: 2.92 (0.37), residues: 522 helix: 2.75 (0.26), residues: 395 sheet: -1.22 (1.36), residues: 14 loop : -0.74 (0.54), residues: 113 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 24 TYR 0.017 0.001 TYR A 336 PHE 0.007 0.001 PHE A 156 TRP 0.006 0.001 TRP A 34 HIS 0.002 0.001 HIS A 360 Details of bonding type rmsd covalent geometry : bond 0.00271 ( 4276) covalent geometry : angle 0.53957 ( 5790) hydrogen bonds : bond 0.03277 ( 318) hydrogen bonds : angle 3.74704 ( 942) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1044 Ramachandran restraints generated. 522 Oldfield, 0 Emsley, 522 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1044 Ramachandran restraints generated. 522 Oldfield, 0 Emsley, 522 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 62 residues out of total 453 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 56 time to evaluate : 0.161 Fit side-chains REVERT: B 30 ARG cc_start: 0.7703 (tpp80) cc_final: 0.6150 (mmm160) REVERT: A 20 GLN cc_start: 0.7617 (tm-30) cc_final: 0.7127 (tm-30) REVERT: A 77 MET cc_start: 0.8550 (mmt) cc_final: 0.8251 (mmt) REVERT: A 82 SER cc_start: 0.9119 (t) cc_final: 0.8865 (t) REVERT: A 91 MET cc_start: 0.7868 (mmm) cc_final: 0.7515 (mmm) REVERT: A 92 GLN cc_start: 0.7658 (mm-40) cc_final: 0.6466 (tt0) REVERT: A 311 ARG cc_start: 0.6159 (mtm180) cc_final: 0.5910 (mtp180) REVERT: A 408 SER cc_start: 0.8369 (m) cc_final: 0.7847 (p) outliers start: 6 outliers final: 5 residues processed: 60 average time/residue: 0.0741 time to fit residues: 5.5180 Evaluate side-chains 61 residues out of total 453 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 56 time to evaluate : 0.156 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 66 VAL Chi-restraints excluded: chain C residue 68 VAL Chi-restraints excluded: chain A residue 141 SER Chi-restraints excluded: chain A residue 163 LEU Chi-restraints excluded: chain A residue 362 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 53 random chunks: chunk 23 optimal weight: 0.9980 chunk 2 optimal weight: 0.0980 chunk 40 optimal weight: 0.7980 chunk 6 optimal weight: 0.7980 chunk 48 optimal weight: 0.9990 chunk 14 optimal weight: 0.2980 chunk 13 optimal weight: 0.3980 chunk 20 optimal weight: 0.8980 chunk 16 optimal weight: 0.7980 chunk 8 optimal weight: 0.9980 chunk 46 optimal weight: 0.6980 overall best weight: 0.4580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3765 r_free = 0.3765 target = 0.153454 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3409 r_free = 0.3409 target = 0.121817 restraints weight = 4804.576| |-----------------------------------------------------------------------------| r_work (start): 0.3407 rms_B_bonded: 2.18 r_work: 0.3268 rms_B_bonded: 2.97 restraints_weight: 0.5000 r_work: 0.3117 rms_B_bonded: 4.84 restraints_weight: 0.2500 r_work (final): 0.3117 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7758 moved from start: 0.1651 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 4276 Z= 0.120 Angle : 0.548 9.071 5790 Z= 0.265 Chirality : 0.038 0.156 677 Planarity : 0.004 0.039 709 Dihedral : 5.279 31.370 594 Min Nonbonded Distance : 2.615 Molprobity Statistics. All-atom Clashscore : 7.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.11 % Favored : 97.89 % Rotamer: Outliers : 1.34 % Allowed : 13.17 % Favored : 85.49 % 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 aren not related in a simple way. whole: 2.92 (0.37), residues: 522 helix: 2.75 (0.26), residues: 395 sheet: -1.27 (1.35), residues: 14 loop : -0.73 (0.55), residues: 113 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 24 TYR 0.016 0.001 TYR A 336 PHE 0.006 0.001 PHE A 252 TRP 0.006 0.001 TRP A 34 HIS 0.002 0.001 HIS A 360 Details of bonding type rmsd covalent geometry : bond 0.00279 ( 4276) covalent geometry : angle 0.54788 ( 5790) hydrogen bonds : bond 0.03282 ( 318) hydrogen bonds : angle 3.74239 ( 942) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1044 Ramachandran restraints generated. 522 Oldfield, 0 Emsley, 522 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1044 Ramachandran restraints generated. 522 Oldfield, 0 Emsley, 522 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 62 residues out of total 453 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 56 time to evaluate : 0.096 Fit side-chains REVERT: B 30 ARG cc_start: 0.7757 (tpp80) cc_final: 0.6254 (mmm160) REVERT: A 20 GLN cc_start: 0.7661 (tm-30) cc_final: 0.7144 (tm-30) REVERT: A 77 MET cc_start: 0.8547 (mmt) cc_final: 0.8247 (mmt) REVERT: A 82 SER cc_start: 0.9152 (t) cc_final: 0.8887 (t) REVERT: A 92 GLN cc_start: 0.7662 (mm-40) cc_final: 0.6493 (tt0) REVERT: A 231 ARG cc_start: 0.7884 (tmt170) cc_final: 0.7580 (tmt170) REVERT: A 311 ARG cc_start: 0.5969 (mtm180) cc_final: 0.5756 (mtp180) REVERT: A 408 SER cc_start: 0.8391 (m) cc_final: 0.7888 (p) outliers start: 6 outliers final: 5 residues processed: 61 average time/residue: 0.0745 time to fit residues: 5.6042 Evaluate side-chains 60 residues out of total 453 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 55 time to evaluate : 0.148 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 66 VAL Chi-restraints excluded: chain C residue 68 VAL Chi-restraints excluded: chain A residue 67 VAL Chi-restraints excluded: chain A residue 141 SER Chi-restraints excluded: chain A residue 362 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 53 random chunks: chunk 20 optimal weight: 1.9990 chunk 2 optimal weight: 0.1980 chunk 25 optimal weight: 0.8980 chunk 29 optimal weight: 1.9990 chunk 50 optimal weight: 2.9990 chunk 18 optimal weight: 0.8980 chunk 38 optimal weight: 3.9990 chunk 42 optimal weight: 1.9990 chunk 13 optimal weight: 0.9990 chunk 51 optimal weight: 0.5980 chunk 9 optimal weight: 4.9990 overall best weight: 0.7182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 27 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3754 r_free = 0.3754 target = 0.152229 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3401 r_free = 0.3401 target = 0.121216 restraints weight = 4772.919| |-----------------------------------------------------------------------------| r_work (start): 0.3400 rms_B_bonded: 2.08 r_work: 0.3254 rms_B_bonded: 2.93 restraints_weight: 0.5000 r_work: 0.3101 rms_B_bonded: 4.76 restraints_weight: 0.2500 r_work (final): 0.3101 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7772 moved from start: 0.1641 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 4276 Z= 0.143 Angle : 0.566 9.056 5790 Z= 0.275 Chirality : 0.039 0.141 677 Planarity : 0.004 0.038 709 Dihedral : 5.500 34.194 594 Min Nonbonded Distance : 2.608 Molprobity Statistics. All-atom Clashscore : 7.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.30 % Favored : 97.70 % Rotamer: Outliers : 1.34 % Allowed : 13.62 % Favored : 85.04 % 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 aren not related in a simple way. whole: 2.86 (0.37), residues: 522 helix: 2.71 (0.26), residues: 395 sheet: -1.32 (1.38), residues: 14 loop : -0.75 (0.55), residues: 113 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 24 TYR 0.016 0.001 TYR A 336 PHE 0.009 0.001 PHE A 252 TRP 0.006 0.001 TRP A 34 HIS 0.002 0.001 HIS A 360 Details of bonding type rmsd covalent geometry : bond 0.00343 ( 4276) covalent geometry : angle 0.56578 ( 5790) hydrogen bonds : bond 0.03450 ( 318) hydrogen bonds : angle 3.77189 ( 942) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1044 Ramachandran restraints generated. 522 Oldfield, 0 Emsley, 522 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1044 Ramachandran restraints generated. 522 Oldfield, 0 Emsley, 522 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 61 residues out of total 453 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 55 time to evaluate : 0.110 Fit side-chains REVERT: B 30 ARG cc_start: 0.7739 (tpp80) cc_final: 0.6187 (mmm160) REVERT: B 55 LYS cc_start: 0.8348 (tttt) cc_final: 0.8010 (tttp) REVERT: A 20 GLN cc_start: 0.7628 (tm-30) cc_final: 0.7119 (tm-30) REVERT: A 65 MET cc_start: 0.8433 (mmt) cc_final: 0.8172 (mmt) REVERT: A 77 MET cc_start: 0.8589 (mmt) cc_final: 0.8266 (mmt) REVERT: A 82 SER cc_start: 0.9158 (t) cc_final: 0.8892 (t) REVERT: A 92 GLN cc_start: 0.7661 (mm-40) cc_final: 0.6485 (tt0) REVERT: A 231 ARG cc_start: 0.7868 (tmt170) cc_final: 0.7533 (tmt170) REVERT: A 243 MET cc_start: 0.8539 (mmt) cc_final: 0.8293 (mmt) REVERT: A 311 ARG cc_start: 0.6033 (mtm180) cc_final: 0.5784 (mtp180) outliers start: 6 outliers final: 5 residues processed: 58 average time/residue: 0.0897 time to fit residues: 6.2544 Evaluate side-chains 60 residues out of total 453 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 55 time to evaluate : 0.116 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 66 VAL Chi-restraints excluded: chain C residue 68 VAL Chi-restraints excluded: chain A residue 67 VAL Chi-restraints excluded: chain A residue 362 VAL Chi-restraints excluded: chain A residue 463 LYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 53 random chunks: chunk 47 optimal weight: 0.9990 chunk 32 optimal weight: 0.5980 chunk 7 optimal weight: 1.9990 chunk 21 optimal weight: 0.0870 chunk 19 optimal weight: 3.9990 chunk 11 optimal weight: 0.6980 chunk 40 optimal weight: 0.6980 chunk 48 optimal weight: 0.0050 chunk 5 optimal weight: 1.9990 chunk 51 optimal weight: 0.6980 chunk 0 optimal weight: 3.9990 overall best weight: 0.4172 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 27 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3754 r_free = 0.3754 target = 0.152275 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3404 r_free = 0.3404 target = 0.121155 restraints weight = 4726.084| |-----------------------------------------------------------------------------| r_work (start): 0.3399 rms_B_bonded: 2.16 r_work: 0.3249 rms_B_bonded: 3.06 restraints_weight: 0.5000 r_work: 0.3096 rms_B_bonded: 4.93 restraints_weight: 0.2500 r_work (final): 0.3096 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7758 moved from start: 0.1693 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.052 4276 Z= 0.116 Angle : 0.547 8.953 5790 Z= 0.267 Chirality : 0.038 0.143 677 Planarity : 0.004 0.039 709 Dihedral : 5.554 36.795 594 Min Nonbonded Distance : 2.612 Molprobity Statistics. All-atom Clashscore : 7.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.49 % Favored : 97.51 % Rotamer: Outliers : 1.12 % Allowed : 13.84 % Favored : 85.04 % 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 aren not related in a simple way. whole: 2.93 (0.37), residues: 522 helix: 2.75 (0.26), residues: 395 sheet: -1.21 (1.38), residues: 14 loop : -0.68 (0.55), residues: 113 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 24 TYR 0.015 0.001 TYR A 336 PHE 0.006 0.001 PHE A 156 TRP 0.006 0.001 TRP A 64 HIS 0.002 0.001 HIS A 360 Details of bonding type rmsd covalent geometry : bond 0.00271 ( 4276) covalent geometry : angle 0.54745 ( 5790) hydrogen bonds : bond 0.03278 ( 318) hydrogen bonds : angle 3.74471 ( 942) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1157.90 seconds wall clock time: 20 minutes 25.93 seconds (1225.93 seconds total)