Starting phenix.real_space_refine on Wed Sep 17 03:55:54 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9irx_60824/09_2025/9irx_60824.cif Found real_map, /net/cci-nas-00/data/ceres_data/9irx_60824/09_2025/9irx_60824.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.0 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/9irx_60824/09_2025/9irx_60824.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9irx_60824/09_2025/9irx_60824.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9irx_60824/09_2025/9irx_60824.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9irx_60824/09_2025/9irx_60824.map" } resolution = 3.0 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= -0.002 sd= 0.143 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 Br 2 7.06 5 S 27 5.16 5 C 2305 2.51 5 N 586 2.21 5 O 589 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 1 residue(s): 0.00s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5805/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 3509 Number of models: 1 Model: "" Number of chains: 2 Chain: "A" Number of atoms: 3487 Number of conformers: 1 Conformer: "" Number of residues, atoms: 469, 3487 Classifications: {'peptide': 469} Incomplete info: {'truncation_to_alanine': 15} Link IDs: {'PTRANS': 26, 'TRANS': 442} Chain breaks: 5 Unresolved non-hydrogen bonds: 63 Unresolved non-hydrogen angles: 78 Unresolved non-hydrogen dihedrals: 48 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'GLU:plan': 5, 'ARG:plan': 4, 'ASP:plan': 2, 'GLN:plan1': 2} Unresolved non-hydrogen planarities: 54 Chain: "A" Number of atoms: 22 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 22 Unusual residues: {'R75': 1} Classifications: {'undetermined': 1} Time building chain proxies: 0.94, per 1000 atoms: 0.27 Number of scatterers: 3509 At special positions: 0 Unit cell: (106.7, 55.484, 66.154, 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) Br 2 34.99 S 27 16.00 O 589 8.00 N 586 7.00 C 2305 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=2, symmetry=0 Simple disulfide: pdb=" SG CYS A 49 " - pdb=" SG CYS A 116 " distance=2.03 Simple disulfide: pdb=" SG CYS A 88 " - pdb=" SG CYS A 139 " distance=2.02 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: 0.25 Conformation dependent library (CDL) restraints added in 128.3 milliseconds Enol-peptide restraints added in 476.8 nanoseconds 914 Ramachandran restraints generated. 457 Oldfield, 0 Emsley, 457 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 856 Finding SS restraints... Secondary structure from input PDB file: 26 helices and 2 sheets defined 82.1% alpha, 1.3% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.10 Creating SS restraints... Processing helix chain 'A' and resid 3 through 11 Processing helix chain 'A' and resid 14 through 37 Processing helix chain 'A' and resid 37 through 42 Processing helix chain 'A' and resid 68 through 77 Processing helix chain 'A' and resid 130 through 136 Processing helix chain 'A' and resid 138 through 142 removed outlier: 3.504A pdb=" N SER A 141 " --> pdb=" O VAL A 138 " (cutoff:3.500A) Processing helix chain 'A' and resid 143 through 170 removed outlier: 3.626A pdb=" N LEU A 157 " --> pdb=" O LEU A 153 " (cutoff:3.500A) Proline residue: A 165 - end of helix Processing helix chain 'A' and resid 171 through 192 Processing helix chain 'A' and resid 195 through 223 removed outlier: 3.603A pdb=" N GLY A 212 " --> pdb=" O PHE A 208 " (cutoff:3.500A) Processing helix chain 'A' and resid 226 through 228 No H-bonds generated for 'chain 'A' and resid 226 through 228' Processing helix chain 'A' and resid 229 through 255 removed outlier: 3.506A pdb=" N PHE A 241 " --> pdb=" O ASN A 237 " (cutoff:3.500A) removed outlier: 3.808A pdb=" N GLY A 246 " --> pdb=" O SER A 242 " (cutoff:3.500A) Processing helix chain 'A' and resid 257 through 267 Processing helix chain 'A' and resid 267 through 276 removed outlier: 4.034A pdb=" N LEU A 271 " --> pdb=" O VAL A 267 " (cutoff:3.500A) Processing helix chain 'A' and resid 277 through 279 No H-bonds generated for 'chain 'A' and resid 277 through 279' Processing helix chain 'A' and resid 282 through 290 Processing helix chain 'A' and resid 291 through 305 Processing helix chain 'A' and resid 316 through 324 removed outlier: 3.549A pdb=" N LEU A 320 " --> pdb=" O THR A 316 " (cutoff:3.500A) Processing helix chain 'A' and resid 336 through 343 Processing helix chain 'A' and resid 346 through 368 Processing helix chain 'A' and resid 377 through 403 removed outlier: 3.733A pdb=" N GLY A 386 " --> pdb=" O GLN A 382 " (cutoff:3.500A) Proline residue: A 391 - end of helix removed outlier: 4.011A pdb=" N SER A 401 " --> pdb=" O LEU A 397 " (cutoff:3.500A) removed outlier: 3.643A pdb=" N ARG A 402 " --> pdb=" O LEU A 398 " (cutoff:3.500A) Processing helix chain 'A' and resid 405 through 426 Processing helix chain 'A' and resid 430 through 456 Processing helix chain 'A' and resid 464 through 486 Proline residue: A 484 - end of helix Processing helix chain 'A' and resid 487 through 492 removed outlier: 3.563A pdb=" N VAL A 491 " --> pdb=" O LEU A 488 " (cutoff:3.500A) Processing helix chain 'A' and resid 494 through 512 removed outlier: 4.199A pdb=" N LEU A 498 " --> pdb=" O PRO A 494 " (cutoff:3.500A) Proline residue: A 505 - end of helix Processing helix chain 'A' and resid 513 through 515 No H-bonds generated for 'chain 'A' and resid 513 through 515' Processing sheet with id=AA1, first strand: chain 'A' and resid 47 through 49 Processing sheet with id=AA2, first strand: chain 'A' and resid 90 through 91 266 hydrogen bonds defined for protein. 786 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: 0.54 Time building geometry restraints manager: 0.32 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.18 - 1.33: 803 1.33 - 1.48: 1220 1.48 - 1.64: 1526 1.64 - 1.79: 0 1.79 - 1.94: 44 Bond restraints: 3593 Sorted by residual: bond pdb=" CAO R75 A 601 " pdb=" CAS R75 A 601 " ideal model delta sigma weight residual 1.382 1.571 -0.189 2.00e-02 2.50e+03 8.96e+01 bond pdb=" CAP R75 A 601 " pdb=" CAV R75 A 601 " ideal model delta sigma weight residual 1.396 1.569 -0.173 2.00e-02 2.50e+03 7.49e+01 bond pdb=" CAD R75 A 601 " pdb=" CAE R75 A 601 " ideal model delta sigma weight residual 1.382 1.528 -0.146 2.00e-02 2.50e+03 5.31e+01 bond pdb=" CAA R75 A 601 " pdb=" CAB R75 A 601 " ideal model delta sigma weight residual 1.378 1.519 -0.141 2.00e-02 2.50e+03 4.98e+01 bond pdb=" CAC R75 A 601 " pdb=" CAD R75 A 601 " ideal model delta sigma weight residual 1.400 1.533 -0.133 2.00e-02 2.50e+03 4.46e+01 ... (remaining 3588 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.56: 4808 1.56 - 3.12: 61 3.12 - 4.68: 28 4.68 - 6.24: 4 6.24 - 7.80: 5 Bond angle restraints: 4906 Sorted by residual: angle pdb=" CAJ R75 A 601 " pdb=" CAL R75 A 601 " pdb=" CAP R75 A 601 " ideal model delta sigma weight residual 129.37 121.57 7.80 3.00e+00 1.11e-01 6.76e+00 angle pdb=" CAQ R75 A 601 " pdb=" CAM R75 A 601 " pdb=" OAN R75 A 601 " ideal model delta sigma weight residual 116.30 124.01 -7.71 3.00e+00 1.11e-01 6.61e+00 angle pdb=" C VAL A 162 " pdb=" CA VAL A 162 " pdb=" CB VAL A 162 " ideal model delta sigma weight residual 111.94 108.87 3.07 1.26e+00 6.30e-01 5.92e+00 angle pdb=" CAS R75 A 601 " pdb=" CAO R75 A 601 " pdb=" OAN R75 A 601 " ideal model delta sigma weight residual 125.82 132.61 -6.79 3.00e+00 1.11e-01 5.13e+00 angle pdb=" CA TYR A 275 " pdb=" CB TYR A 275 " pdb=" CG TYR A 275 " ideal model delta sigma weight residual 113.90 117.90 -4.00 1.80e+00 3.09e-01 4.95e+00 ... (remaining 4901 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 27.60: 2043 27.60 - 55.19: 37 55.19 - 82.79: 4 82.79 - 110.39: 0 110.39 - 137.99: 1 Dihedral angle restraints: 2085 sinusoidal: 758 harmonic: 1327 Sorted by residual: dihedral pdb=" CAL R75 A 601 " pdb=" CAM R75 A 601 " pdb=" CAQ R75 A 601 " pdb=" CAR R75 A 601 " ideal model delta sinusoidal sigma weight residual 263.96 125.97 137.99 1 3.00e+01 1.11e-03 1.86e+01 dihedral pdb=" SG CYS A 49 " pdb=" CB CYS A 116 " pdb=" SG CYS A 116 " pdb=" CA CYS A 116 " ideal model delta sinusoidal sigma weight residual 79.00 26.30 52.70 1 2.00e+01 2.50e-03 9.46e+00 dihedral pdb=" N LEU A 437 " pdb=" CA LEU A 437 " pdb=" CB LEU A 437 " pdb=" CG LEU A 437 " ideal model delta sinusoidal sigma weight residual -60.00 -110.18 50.18 3 1.50e+01 4.44e-03 8.87e+00 ... (remaining 2082 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.026: 381 0.026 - 0.051: 137 0.051 - 0.077: 42 0.077 - 0.102: 25 0.102 - 0.128: 8 Chirality restraints: 593 Sorted by residual: chirality pdb=" CA ILE A 77 " pdb=" N ILE A 77 " pdb=" C ILE A 77 " pdb=" CB ILE A 77 " both_signs ideal model delta sigma weight residual False 2.43 2.56 -0.13 2.00e-01 2.50e+01 4.09e-01 chirality pdb=" CB VAL A 210 " pdb=" CA VAL A 210 " pdb=" CG1 VAL A 210 " pdb=" CG2 VAL A 210 " both_signs ideal model delta sigma weight residual False -2.63 -2.51 -0.12 2.00e-01 2.50e+01 3.63e-01 chirality pdb=" CA VAL A 121 " pdb=" N VAL A 121 " pdb=" C VAL A 121 " pdb=" CB VAL A 121 " both_signs ideal model delta sigma weight residual False 2.44 2.56 -0.12 2.00e-01 2.50e+01 3.63e-01 ... (remaining 590 not shown) Planarity restraints: 598 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TYR A 275 " 0.008 2.00e-02 2.50e+03 7.55e-03 1.14e+00 pdb=" CG TYR A 275 " -0.018 2.00e-02 2.50e+03 pdb=" CD1 TYR A 275 " 0.006 2.00e-02 2.50e+03 pdb=" CD2 TYR A 275 " 0.001 2.00e-02 2.50e+03 pdb=" CE1 TYR A 275 " -0.001 2.00e-02 2.50e+03 pdb=" CE2 TYR A 275 " 0.004 2.00e-02 2.50e+03 pdb=" CZ TYR A 275 " 0.000 2.00e-02 2.50e+03 pdb=" OH TYR A 275 " 0.000 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C ALA A 51 " -0.017 5.00e-02 4.00e+02 2.62e-02 1.10e+00 pdb=" N PRO A 52 " 0.045 5.00e-02 4.00e+02 pdb=" CA PRO A 52 " -0.013 5.00e-02 4.00e+02 pdb=" CD PRO A 52 " -0.015 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C VAL A 44 " -0.016 5.00e-02 4.00e+02 2.47e-02 9.79e-01 pdb=" N PRO A 45 " 0.043 5.00e-02 4.00e+02 pdb=" CA PRO A 45 " -0.013 5.00e-02 4.00e+02 pdb=" CD PRO A 45 " -0.014 5.00e-02 4.00e+02 ... (remaining 595 not shown) Histogram of nonbonded interaction distances: 2.20 - 2.74: 371 2.74 - 3.28: 3735 3.28 - 3.82: 6332 3.82 - 4.36: 7404 4.36 - 4.90: 12697 Nonbonded interactions: 30539 Sorted by model distance: nonbonded pdb=" OE1 GLN A 149 " pdb=" NH2 ARG A 487 " model vdw 2.197 3.120 nonbonded pdb=" NH2 ARG A 349 " pdb=" O LEU A 459 " model vdw 2.237 3.120 nonbonded pdb=" O ALA A 335 " pdb=" OG1 THR A 467 " model vdw 2.259 3.040 nonbonded pdb=" NH1 ARG A 173 " pdb=" O LEU A 279 " model vdw 2.282 3.120 nonbonded pdb=" N GLU A 281 " pdb=" OE2 GLU A 298 " model vdw 2.285 3.120 ... (remaining 30534 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model ========== 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: 1.120 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: 0.050 Check model and map are aligned: 0.010 Set scattering table: 0.010 Process input model: 4.870 Find NCS groups from input model: 0.020 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:6.430 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 12.510 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7834 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 : 0.009 0.189 3595 Z= 0.428 Angle : 0.583 7.803 4910 Z= 0.275 Chirality : 0.035 0.128 593 Planarity : 0.003 0.026 598 Dihedral : 11.281 137.986 1223 Min Nonbonded Distance : 2.197 Molprobity Statistics. All-atom Clashscore : 7.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.41 % Favored : 97.59 % Rotamer: Outliers : 0.56 % Allowed : 3.89 % Favored : 95.56 % 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: 2.29 (0.40), residues: 457 helix: 1.76 (0.28), residues: 348 sheet: None (None), residues: 0 loop : 0.96 (0.64), residues: 109 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 300 TYR 0.018 0.002 TYR A 275 PHE 0.012 0.001 PHE A 360 TRP 0.007 0.001 TRP A 357 HIS 0.002 0.001 HIS A 47 Details of bonding type rmsd covalent geometry : bond 0.00866 ( 3593) covalent geometry : angle 0.58119 ( 4906) SS BOND : bond 0.00688 ( 2) SS BOND : angle 1.71300 ( 4) hydrogen bonds : bond 0.11788 ( 266) hydrogen bonds : angle 5.49077 ( 786) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 914 Ramachandran restraints generated. 457 Oldfield, 0 Emsley, 457 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 914 Ramachandran restraints generated. 457 Oldfield, 0 Emsley, 457 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 61 residues out of total 375 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 59 time to evaluate : 0.125 Fit side-chains REVERT: A 37 LEU cc_start: 0.8658 (OUTLIER) cc_final: 0.8256 (tp) outliers start: 2 outliers final: 1 residues processed: 60 average time/residue: 0.4541 time to fit residues: 28.2978 Evaluate side-chains 47 residues out of total 375 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 45 time to evaluate : 0.137 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 37 LEU Chi-restraints excluded: chain A residue 210 VAL Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 46 random chunks: chunk 24 optimal weight: 1.9990 chunk 26 optimal weight: 3.9990 chunk 2 optimal weight: 0.9990 chunk 16 optimal weight: 0.0470 chunk 32 optimal weight: 3.9990 chunk 31 optimal weight: 0.6980 chunk 25 optimal weight: 0.7980 chunk 19 optimal weight: 1.9990 chunk 30 optimal weight: 0.7980 chunk 22 optimal weight: 1.9990 chunk 37 optimal weight: 0.9980 overall best weight: 0.6678 ------------------------------------------------------------------------------- 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 = 0.3591 r_free = 0.3591 target = 0.144087 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3255 r_free = 0.3255 target = 0.116143 restraints weight = 3053.732| |-----------------------------------------------------------------------------| r_work (start): 0.3175 rms_B_bonded: 1.40 r_work: 0.3067 rms_B_bonded: 1.96 restraints_weight: 0.5000 r_work: 0.2937 rms_B_bonded: 3.32 restraints_weight: 0.2500 r_work (final): 0.2937 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7904 moved from start: 0.1100 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.062 3595 Z= 0.177 Angle : 0.624 6.368 4910 Z= 0.300 Chirality : 0.040 0.212 593 Planarity : 0.004 0.031 598 Dihedral : 7.998 118.121 501 Min Nonbonded Distance : 2.635 Molprobity Statistics. All-atom Clashscore : 6.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.75 % Favored : 98.25 % Rotamer: Outliers : 4.17 % Allowed : 8.33 % Favored : 87.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 2.35 (0.40), residues: 457 helix: 1.73 (0.28), residues: 352 sheet: None (None), residues: 0 loop : 1.28 (0.65), residues: 105 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG A 300 TYR 0.016 0.002 TYR A 275 PHE 0.015 0.002 PHE A 360 TRP 0.011 0.001 TRP A 357 HIS 0.002 0.001 HIS A 245 Details of bonding type rmsd covalent geometry : bond 0.00433 ( 3593) covalent geometry : angle 0.62303 ( 4906) SS BOND : bond 0.00779 ( 2) SS BOND : angle 1.41249 ( 4) hydrogen bonds : bond 0.04557 ( 266) hydrogen bonds : angle 4.51735 ( 786) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 914 Ramachandran restraints generated. 457 Oldfield, 0 Emsley, 457 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 914 Ramachandran restraints generated. 457 Oldfield, 0 Emsley, 457 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 69 residues out of total 375 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 54 time to evaluate : 0.141 Fit side-chains REVERT: A 37 LEU cc_start: 0.8803 (OUTLIER) cc_final: 0.8173 (tp) REVERT: A 222 MET cc_start: 0.7016 (mmt) cc_final: 0.6798 (mmt) REVERT: A 430 MET cc_start: 0.6539 (OUTLIER) cc_final: 0.5764 (mmt) outliers start: 15 outliers final: 4 residues processed: 62 average time/residue: 0.4550 time to fit residues: 29.2917 Evaluate side-chains 50 residues out of total 375 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 44 time to evaluate : 0.129 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 37 LEU Chi-restraints excluded: chain A residue 210 VAL Chi-restraints excluded: chain A residue 387 VAL Chi-restraints excluded: chain A residue 403 LEU Chi-restraints excluded: chain A residue 430 MET Chi-restraints excluded: chain A residue 463 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 46 random chunks: chunk 24 optimal weight: 1.9990 chunk 35 optimal weight: 0.9980 chunk 8 optimal weight: 0.6980 chunk 45 optimal weight: 0.5980 chunk 34 optimal weight: 0.8980 chunk 36 optimal weight: 0.8980 chunk 9 optimal weight: 0.9990 chunk 41 optimal weight: 0.0980 chunk 2 optimal weight: 0.5980 chunk 19 optimal weight: 0.3980 chunk 39 optimal weight: 1.9990 overall best weight: 0.4780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 473 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3524 r_free = 0.3524 target = 0.139451 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3176 r_free = 0.3176 target = 0.110803 restraints weight = 3149.633| |-----------------------------------------------------------------------------| r_work (start): 0.3159 rms_B_bonded: 1.46 r_work: 0.3046 rms_B_bonded: 2.06 restraints_weight: 0.5000 r_work: 0.2914 rms_B_bonded: 3.48 restraints_weight: 0.2500 r_work (final): 0.2914 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7862 moved from start: 0.1371 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 3595 Z= 0.147 Angle : 0.584 6.518 4910 Z= 0.279 Chirality : 0.039 0.182 593 Planarity : 0.004 0.030 598 Dihedral : 7.654 104.086 501 Min Nonbonded Distance : 2.633 Molprobity Statistics. All-atom Clashscore : 7.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.97 % Favored : 98.03 % Rotamer: Outliers : 3.61 % Allowed : 10.00 % Favored : 86.39 % 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: 2.19 (0.40), residues: 457 helix: 1.62 (0.27), residues: 354 sheet: None (None), residues: 0 loop : 1.16 (0.66), residues: 103 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG A 300 TYR 0.016 0.002 TYR A 275 PHE 0.014 0.002 PHE A 360 TRP 0.011 0.001 TRP A 357 HIS 0.002 0.001 HIS A 245 Details of bonding type rmsd covalent geometry : bond 0.00350 ( 3593) covalent geometry : angle 0.58275 ( 4906) SS BOND : bond 0.00599 ( 2) SS BOND : angle 1.20927 ( 4) hydrogen bonds : bond 0.04122 ( 266) hydrogen bonds : angle 4.31991 ( 786) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 914 Ramachandran restraints generated. 457 Oldfield, 0 Emsley, 457 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 914 Ramachandran restraints generated. 457 Oldfield, 0 Emsley, 457 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 64 residues out of total 375 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 51 time to evaluate : 0.128 Fit side-chains REVERT: A 430 MET cc_start: 0.6453 (OUTLIER) cc_final: 0.5706 (mmt) outliers start: 13 outliers final: 3 residues processed: 58 average time/residue: 0.4311 time to fit residues: 26.0188 Evaluate side-chains 49 residues out of total 375 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 45 time to evaluate : 0.120 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 37 LEU Chi-restraints excluded: chain A residue 403 LEU Chi-restraints excluded: chain A residue 430 MET Chi-restraints excluded: chain A residue 463 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 46 random chunks: chunk 6 optimal weight: 0.6980 chunk 28 optimal weight: 3.9990 chunk 12 optimal weight: 0.9990 chunk 22 optimal weight: 3.9990 chunk 38 optimal weight: 3.9990 chunk 20 optimal weight: 0.8980 chunk 21 optimal weight: 0.5980 chunk 45 optimal weight: 0.5980 chunk 44 optimal weight: 0.8980 chunk 39 optimal weight: 0.8980 chunk 1 optimal weight: 1.9990 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 34 GLN A 262 GLN A 473 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3515 r_free = 0.3515 target = 0.138289 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3173 r_free = 0.3173 target = 0.110156 restraints weight = 3127.001| |-----------------------------------------------------------------------------| r_work (start): 0.3136 rms_B_bonded: 1.43 r_work: 0.3024 rms_B_bonded: 2.03 restraints_weight: 0.5000 r_work: 0.2896 rms_B_bonded: 3.39 restraints_weight: 0.2500 r_work (final): 0.2896 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7900 moved from start: 0.1544 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.054 3595 Z= 0.181 Angle : 0.605 6.227 4910 Z= 0.290 Chirality : 0.040 0.223 593 Planarity : 0.005 0.053 598 Dihedral : 7.511 98.280 500 Min Nonbonded Distance : 2.618 Molprobity Statistics. All-atom Clashscore : 7.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.75 % Favored : 98.25 % Rotamer: Outliers : 4.44 % Allowed : 11.94 % Favored : 83.61 % 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: 2.14 (0.40), residues: 457 helix: 1.53 (0.27), residues: 358 sheet: None (None), residues: 0 loop : 1.36 (0.68), residues: 99 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.001 ARG A 300 TYR 0.018 0.002 TYR A 275 PHE 0.014 0.002 PHE A 360 TRP 0.010 0.001 TRP A 357 HIS 0.002 0.001 HIS A 245 Details of bonding type rmsd covalent geometry : bond 0.00440 ( 3593) covalent geometry : angle 0.60420 ( 4906) SS BOND : bond 0.00793 ( 2) SS BOND : angle 1.21356 ( 4) hydrogen bonds : bond 0.04294 ( 266) hydrogen bonds : angle 4.39397 ( 786) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 914 Ramachandran restraints generated. 457 Oldfield, 0 Emsley, 457 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 914 Ramachandran restraints generated. 457 Oldfield, 0 Emsley, 457 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 64 residues out of total 375 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 48 time to evaluate : 0.144 Fit side-chains REVERT: A 430 MET cc_start: 0.6511 (OUTLIER) cc_final: 0.6304 (mmm) outliers start: 16 outliers final: 7 residues processed: 57 average time/residue: 0.3948 time to fit residues: 23.4814 Evaluate side-chains 54 residues out of total 375 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 46 time to evaluate : 0.137 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 37 LEU Chi-restraints excluded: chain A residue 387 VAL Chi-restraints excluded: chain A residue 389 ASP Chi-restraints excluded: chain A residue 397 LEU Chi-restraints excluded: chain A residue 403 LEU Chi-restraints excluded: chain A residue 424 THR Chi-restraints excluded: chain A residue 430 MET Chi-restraints excluded: chain A residue 463 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 46 random chunks: chunk 15 optimal weight: 0.9980 chunk 8 optimal weight: 0.6980 chunk 39 optimal weight: 0.5980 chunk 31 optimal weight: 0.1980 chunk 13 optimal weight: 0.0170 chunk 35 optimal weight: 0.8980 chunk 42 optimal weight: 0.9990 chunk 3 optimal weight: 0.9980 chunk 30 optimal weight: 1.9990 chunk 2 optimal weight: 0.5980 chunk 1 optimal weight: 0.7980 overall best weight: 0.4218 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 473 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3533 r_free = 0.3533 target = 0.140080 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3193 r_free = 0.3193 target = 0.111729 restraints weight = 3131.099| |-----------------------------------------------------------------------------| r_work (start): 0.3181 rms_B_bonded: 1.45 r_work: 0.3069 rms_B_bonded: 2.05 restraints_weight: 0.5000 r_work: 0.2940 rms_B_bonded: 3.44 restraints_weight: 0.2500 r_work (final): 0.2940 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7869 moved from start: 0.1668 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 3595 Z= 0.137 Angle : 0.578 8.281 4910 Z= 0.273 Chirality : 0.039 0.253 593 Planarity : 0.004 0.059 598 Dihedral : 7.267 86.152 500 Min Nonbonded Distance : 2.594 Molprobity Statistics. All-atom Clashscore : 7.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.97 % Favored : 98.03 % Rotamer: Outliers : 4.17 % Allowed : 14.44 % Favored : 81.39 % 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: 2.30 (0.40), residues: 457 helix: 1.67 (0.27), residues: 358 sheet: None (None), residues: 0 loop : 1.33 (0.69), residues: 99 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.001 ARG A 300 TYR 0.014 0.001 TYR A 275 PHE 0.013 0.002 PHE A 360 TRP 0.012 0.001 TRP A 357 HIS 0.002 0.001 HIS A 245 Details of bonding type rmsd covalent geometry : bond 0.00320 ( 3593) covalent geometry : angle 0.57708 ( 4906) SS BOND : bond 0.00577 ( 2) SS BOND : angle 1.05809 ( 4) hydrogen bonds : bond 0.03956 ( 266) hydrogen bonds : angle 4.25585 ( 786) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 914 Ramachandran restraints generated. 457 Oldfield, 0 Emsley, 457 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 914 Ramachandran restraints generated. 457 Oldfield, 0 Emsley, 457 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 67 residues out of total 375 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 52 time to evaluate : 0.131 Fit side-chains REVERT: A 388 VAL cc_start: 0.8382 (p) cc_final: 0.8021 (t) outliers start: 15 outliers final: 7 residues processed: 60 average time/residue: 0.4053 time to fit residues: 25.3213 Evaluate side-chains 52 residues out of total 375 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 45 time to evaluate : 0.105 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 37 LEU Chi-restraints excluded: chain A residue 387 VAL Chi-restraints excluded: chain A residue 389 ASP Chi-restraints excluded: chain A residue 397 LEU Chi-restraints excluded: chain A residue 403 LEU Chi-restraints excluded: chain A residue 424 THR Chi-restraints excluded: chain A residue 463 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 46 random chunks: chunk 2 optimal weight: 0.5980 chunk 27 optimal weight: 0.9990 chunk 0 optimal weight: 3.9990 chunk 32 optimal weight: 0.0770 chunk 38 optimal weight: 0.9980 chunk 39 optimal weight: 0.9980 chunk 3 optimal weight: 0.6980 chunk 14 optimal weight: 0.8980 chunk 18 optimal weight: 0.6980 chunk 40 optimal weight: 0.9990 chunk 13 optimal weight: 1.9990 overall best weight: 0.5938 ------------------------------------------------------------------------------- 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 = 0.3532 r_free = 0.3532 target = 0.139962 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3191 r_free = 0.3191 target = 0.111571 restraints weight = 3167.613| |-----------------------------------------------------------------------------| r_work (start): 0.3167 rms_B_bonded: 1.45 r_work: 0.3053 rms_B_bonded: 2.06 restraints_weight: 0.5000 r_work: 0.2927 rms_B_bonded: 3.44 restraints_weight: 0.2500 r_work (final): 0.2927 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7892 moved from start: 0.1766 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.046 3595 Z= 0.157 Angle : 0.588 7.913 4910 Z= 0.279 Chirality : 0.039 0.194 593 Planarity : 0.005 0.066 598 Dihedral : 7.051 78.214 500 Min Nonbonded Distance : 2.600 Molprobity Statistics. All-atom Clashscore : 7.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.97 % Favored : 98.03 % Rotamer: Outliers : 3.06 % Allowed : 16.94 % Favored : 80.00 % 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: 2.24 (0.40), residues: 457 helix: 1.62 (0.27), residues: 360 sheet: None (None), residues: 0 loop : 1.32 (0.71), residues: 97 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.015 0.001 ARG A 300 TYR 0.018 0.002 TYR A 275 PHE 0.013 0.002 PHE A 360 TRP 0.010 0.001 TRP A 357 HIS 0.002 0.001 HIS A 245 Details of bonding type rmsd covalent geometry : bond 0.00379 ( 3593) covalent geometry : angle 0.58737 ( 4906) SS BOND : bond 0.00677 ( 2) SS BOND : angle 1.08075 ( 4) hydrogen bonds : bond 0.04100 ( 266) hydrogen bonds : angle 4.29461 ( 786) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 914 Ramachandran restraints generated. 457 Oldfield, 0 Emsley, 457 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 914 Ramachandran restraints generated. 457 Oldfield, 0 Emsley, 457 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 61 residues out of total 375 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 50 time to evaluate : 0.125 Fit side-chains REVERT: A 172 ARG cc_start: 0.7303 (mtt-85) cc_final: 0.7033 (ttm170) REVERT: A 388 VAL cc_start: 0.8446 (p) cc_final: 0.8096 (t) outliers start: 11 outliers final: 6 residues processed: 56 average time/residue: 0.4254 time to fit residues: 24.7782 Evaluate side-chains 52 residues out of total 375 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 46 time to evaluate : 0.121 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 37 LEU Chi-restraints excluded: chain A residue 387 VAL Chi-restraints excluded: chain A residue 389 ASP Chi-restraints excluded: chain A residue 403 LEU Chi-restraints excluded: chain A residue 424 THR Chi-restraints excluded: chain A residue 463 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 46 random chunks: chunk 36 optimal weight: 0.9980 chunk 35 optimal weight: 1.9990 chunk 18 optimal weight: 0.6980 chunk 33 optimal weight: 0.5980 chunk 29 optimal weight: 0.9980 chunk 25 optimal weight: 0.9990 chunk 0 optimal weight: 3.9990 chunk 8 optimal weight: 0.9990 chunk 14 optimal weight: 0.8980 chunk 13 optimal weight: 0.7980 chunk 30 optimal weight: 0.9990 overall best weight: 0.7980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 473 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3517 r_free = 0.3517 target = 0.138626 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3173 r_free = 0.3173 target = 0.110271 restraints weight = 3169.567| |-----------------------------------------------------------------------------| r_work (start): 0.3153 rms_B_bonded: 1.44 r_work: 0.3041 rms_B_bonded: 2.03 restraints_weight: 0.5000 r_work: 0.2913 rms_B_bonded: 3.41 restraints_weight: 0.2500 r_work (final): 0.2913 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7918 moved from start: 0.1805 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.054 3595 Z= 0.187 Angle : 0.616 6.368 4910 Z= 0.295 Chirality : 0.041 0.229 593 Planarity : 0.005 0.066 598 Dihedral : 6.793 71.390 500 Min Nonbonded Distance : 2.613 Molprobity Statistics. All-atom Clashscore : 7.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.97 % Favored : 98.03 % Rotamer: Outliers : 3.61 % Allowed : 16.94 % Favored : 79.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 2.12 (0.40), residues: 457 helix: 1.57 (0.27), residues: 358 sheet: -1.76 (1.97), residues: 10 loop : 1.49 (0.73), residues: 89 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.016 0.001 ARG A 300 TYR 0.016 0.002 TYR A 275 PHE 0.014 0.002 PHE A 360 TRP 0.009 0.001 TRP A 357 HIS 0.002 0.001 HIS A 245 Details of bonding type rmsd covalent geometry : bond 0.00459 ( 3593) covalent geometry : angle 0.61531 ( 4906) SS BOND : bond 0.00859 ( 2) SS BOND : angle 1.18377 ( 4) hydrogen bonds : bond 0.04340 ( 266) hydrogen bonds : angle 4.38053 ( 786) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 914 Ramachandran restraints generated. 457 Oldfield, 0 Emsley, 457 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 914 Ramachandran restraints generated. 457 Oldfield, 0 Emsley, 457 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 61 residues out of total 375 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 48 time to evaluate : 0.155 Fit side-chains REVERT: A 388 VAL cc_start: 0.8543 (p) cc_final: 0.8214 (t) outliers start: 13 outliers final: 7 residues processed: 55 average time/residue: 0.4142 time to fit residues: 23.7581 Evaluate side-chains 53 residues out of total 375 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 46 time to evaluate : 0.074 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 37 LEU Chi-restraints excluded: chain A residue 387 VAL Chi-restraints excluded: chain A residue 389 ASP Chi-restraints excluded: chain A residue 403 LEU Chi-restraints excluded: chain A residue 424 THR Chi-restraints excluded: chain A residue 463 VAL Chi-restraints excluded: chain A residue 482 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 46 random chunks: chunk 7 optimal weight: 1.9990 chunk 34 optimal weight: 0.5980 chunk 43 optimal weight: 1.9990 chunk 9 optimal weight: 0.7980 chunk 39 optimal weight: 0.7980 chunk 25 optimal weight: 0.6980 chunk 32 optimal weight: 0.6980 chunk 6 optimal weight: 0.9990 chunk 14 optimal weight: 0.9980 chunk 33 optimal weight: 0.4980 chunk 16 optimal weight: 0.8980 overall best weight: 0.6580 ------------------------------------------------------------------------------- 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 = 0.3490 r_free = 0.3490 target = 0.136973 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3140 r_free = 0.3140 target = 0.108257 restraints weight = 3157.969| |-----------------------------------------------------------------------------| r_work (start): 0.3151 rms_B_bonded: 1.46 r_work: 0.3038 rms_B_bonded: 2.07 restraints_weight: 0.5000 r_work: 0.2910 rms_B_bonded: 3.46 restraints_weight: 0.2500 r_work (final): 0.2910 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7887 moved from start: 0.1853 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.049 3595 Z= 0.168 Angle : 0.641 11.591 4910 Z= 0.298 Chirality : 0.041 0.287 593 Planarity : 0.005 0.071 598 Dihedral : 6.635 68.061 500 Min Nonbonded Distance : 2.630 Molprobity Statistics. All-atom Clashscore : 7.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.19 % Favored : 97.81 % Rotamer: Outliers : 2.78 % Allowed : 18.06 % Favored : 79.17 % 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: 2.13 (0.40), residues: 457 helix: 1.59 (0.27), residues: 358 sheet: -1.72 (1.96), residues: 10 loop : 1.45 (0.73), residues: 89 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.016 0.001 ARG A 300 TYR 0.018 0.002 TYR A 275 PHE 0.013 0.002 PHE A 360 TRP 0.011 0.001 TRP A 357 HIS 0.002 0.001 HIS A 245 Details of bonding type rmsd covalent geometry : bond 0.00406 ( 3593) covalent geometry : angle 0.64021 ( 4906) SS BOND : bond 0.00738 ( 2) SS BOND : angle 1.09488 ( 4) hydrogen bonds : bond 0.04214 ( 266) hydrogen bonds : angle 4.35307 ( 786) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 914 Ramachandran restraints generated. 457 Oldfield, 0 Emsley, 457 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 914 Ramachandran restraints generated. 457 Oldfield, 0 Emsley, 457 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 57 residues out of total 375 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 47 time to evaluate : 0.135 Fit side-chains REVERT: A 37 LEU cc_start: 0.8950 (OUTLIER) cc_final: 0.8642 (pt) REVERT: A 388 VAL cc_start: 0.8464 (p) cc_final: 0.8130 (t) outliers start: 10 outliers final: 6 residues processed: 52 average time/residue: 0.4096 time to fit residues: 22.2200 Evaluate side-chains 53 residues out of total 375 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 46 time to evaluate : 0.124 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 37 LEU Chi-restraints excluded: chain A residue 387 VAL Chi-restraints excluded: chain A residue 389 ASP Chi-restraints excluded: chain A residue 403 LEU Chi-restraints excluded: chain A residue 424 THR Chi-restraints excluded: chain A residue 463 VAL Chi-restraints excluded: chain A residue 482 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 46 random chunks: chunk 43 optimal weight: 0.2980 chunk 4 optimal weight: 0.7980 chunk 24 optimal weight: 0.9980 chunk 45 optimal weight: 0.5980 chunk 25 optimal weight: 0.9990 chunk 5 optimal weight: 7.9990 chunk 31 optimal weight: 0.2980 chunk 32 optimal weight: 0.1980 chunk 35 optimal weight: 0.8980 chunk 11 optimal weight: 0.6980 chunk 0 optimal weight: 3.9990 overall best weight: 0.4180 ------------------------------------------------------------------------------- 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 = 0.3601 r_free = 0.3601 target = 0.145129 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3271 r_free = 0.3271 target = 0.117332 restraints weight = 3117.516| |-----------------------------------------------------------------------------| r_work (start): 0.3194 rms_B_bonded: 1.42 r_work: 0.3085 rms_B_bonded: 2.02 restraints_weight: 0.5000 r_work: 0.2959 rms_B_bonded: 3.40 restraints_weight: 0.2500 r_work (final): 0.2959 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7888 moved from start: 0.1913 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 3595 Z= 0.137 Angle : 0.598 10.123 4910 Z= 0.279 Chirality : 0.039 0.243 593 Planarity : 0.005 0.073 598 Dihedral : 6.451 69.018 500 Min Nonbonded Distance : 2.639 Molprobity Statistics. All-atom Clashscore : 7.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.19 % Favored : 97.81 % Rotamer: Outliers : 1.94 % Allowed : 19.17 % Favored : 78.89 % 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: 2.19 (0.40), residues: 457 helix: 1.62 (0.27), residues: 361 sheet: -1.68 (1.98), residues: 10 loop : 1.50 (0.75), residues: 86 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.017 0.001 ARG A 300 TYR 0.014 0.001 TYR A 275 PHE 0.013 0.002 PHE A 360 TRP 0.012 0.001 TRP A 357 HIS 0.001 0.001 HIS A 245 Details of bonding type rmsd covalent geometry : bond 0.00318 ( 3593) covalent geometry : angle 0.59775 ( 4906) SS BOND : bond 0.00568 ( 2) SS BOND : angle 1.02221 ( 4) hydrogen bonds : bond 0.04009 ( 266) hydrogen bonds : angle 4.24846 ( 786) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 914 Ramachandran restraints generated. 457 Oldfield, 0 Emsley, 457 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 914 Ramachandran restraints generated. 457 Oldfield, 0 Emsley, 457 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 55 residues out of total 375 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 48 time to evaluate : 0.103 Fit side-chains REVERT: A 37 LEU cc_start: 0.8948 (OUTLIER) cc_final: 0.8628 (pt) REVERT: A 278 TRP cc_start: 0.8081 (m100) cc_final: 0.7786 (m100) REVERT: A 388 VAL cc_start: 0.8560 (p) cc_final: 0.8190 (t) outliers start: 7 outliers final: 6 residues processed: 52 average time/residue: 0.4096 time to fit residues: 22.1585 Evaluate side-chains 53 residues out of total 375 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 46 time to evaluate : 0.131 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 37 LEU Chi-restraints excluded: chain A residue 387 VAL Chi-restraints excluded: chain A residue 403 LEU Chi-restraints excluded: chain A residue 424 THR Chi-restraints excluded: chain A residue 442 LEU Chi-restraints excluded: chain A residue 463 VAL Chi-restraints excluded: chain A residue 482 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 46 random chunks: chunk 33 optimal weight: 0.6980 chunk 8 optimal weight: 0.9990 chunk 31 optimal weight: 0.2980 chunk 28 optimal weight: 2.9990 chunk 45 optimal weight: 0.8980 chunk 23 optimal weight: 0.0040 chunk 39 optimal weight: 0.6980 chunk 1 optimal weight: 0.9990 chunk 32 optimal weight: 0.9990 chunk 44 optimal weight: 0.5980 chunk 18 optimal weight: 0.7980 overall best weight: 0.4592 ------------------------------------------------------------------------------- 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 = 0.3516 r_free = 0.3516 target = 0.139191 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3169 r_free = 0.3169 target = 0.110441 restraints weight = 3231.934| |-----------------------------------------------------------------------------| r_work (start): 0.3158 rms_B_bonded: 1.48 r_work: 0.3046 rms_B_bonded: 2.10 restraints_weight: 0.5000 r_work: 0.2918 rms_B_bonded: 3.52 restraints_weight: 0.2500 r_work (final): 0.2918 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7857 moved from start: 0.1977 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 3595 Z= 0.144 Angle : 0.644 12.184 4910 Z= 0.294 Chirality : 0.040 0.264 593 Planarity : 0.005 0.076 598 Dihedral : 6.382 69.534 500 Min Nonbonded Distance : 2.640 Molprobity Statistics. All-atom Clashscore : 7.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.75 % Favored : 98.25 % Rotamer: Outliers : 1.94 % Allowed : 19.72 % Favored : 78.33 % 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: 2.20 (0.40), residues: 457 helix: 1.66 (0.27), residues: 359 sheet: -1.67 (1.97), residues: 10 loop : 1.33 (0.74), residues: 88 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.018 0.001 ARG A 300 TYR 0.020 0.002 TYR A 275 PHE 0.013 0.002 PHE A 360 TRP 0.011 0.001 TRP A 357 HIS 0.001 0.001 HIS A 245 Details of bonding type rmsd covalent geometry : bond 0.00338 ( 3593) covalent geometry : angle 0.64357 ( 4906) SS BOND : bond 0.00583 ( 2) SS BOND : angle 0.99054 ( 4) hydrogen bonds : bond 0.04043 ( 266) hydrogen bonds : angle 4.28940 ( 786) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 914 Ramachandran restraints generated. 457 Oldfield, 0 Emsley, 457 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 914 Ramachandran restraints generated. 457 Oldfield, 0 Emsley, 457 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 58 residues out of total 375 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 51 time to evaluate : 0.133 Fit side-chains REVERT: A 4 SER cc_start: 0.7809 (m) cc_final: 0.7259 (p) REVERT: A 37 LEU cc_start: 0.8929 (OUTLIER) cc_final: 0.8647 (pt) REVERT: A 278 TRP cc_start: 0.8112 (m100) cc_final: 0.7802 (m100) REVERT: A 388 VAL cc_start: 0.8522 (p) cc_final: 0.8153 (t) outliers start: 7 outliers final: 5 residues processed: 55 average time/residue: 0.4055 time to fit residues: 23.2856 Evaluate side-chains 52 residues out of total 375 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 46 time to evaluate : 0.126 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 37 LEU Chi-restraints excluded: chain A residue 387 VAL Chi-restraints excluded: chain A residue 403 LEU Chi-restraints excluded: chain A residue 424 THR Chi-restraints excluded: chain A residue 463 VAL Chi-restraints excluded: chain A residue 482 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 46 random chunks: chunk 41 optimal weight: 0.8980 chunk 15 optimal weight: 0.6980 chunk 24 optimal weight: 0.9980 chunk 11 optimal weight: 0.0000 chunk 14 optimal weight: 0.9990 chunk 39 optimal weight: 0.9990 chunk 12 optimal weight: 0.9990 chunk 18 optimal weight: 0.6980 chunk 36 optimal weight: 0.6980 chunk 22 optimal weight: 0.9990 chunk 40 optimal weight: 0.8980 overall best weight: 0.5984 ------------------------------------------------------------------------------- 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 = 0.3513 r_free = 0.3513 target = 0.138733 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3168 r_free = 0.3168 target = 0.110329 restraints weight = 3174.583| |-----------------------------------------------------------------------------| r_work (start): 0.3164 rms_B_bonded: 1.47 r_work: 0.3051 rms_B_bonded: 2.09 restraints_weight: 0.5000 r_work: 0.2922 rms_B_bonded: 3.49 restraints_weight: 0.2500 r_work (final): 0.2922 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7858 moved from start: 0.1968 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 3595 Z= 0.161 Angle : 0.643 12.935 4910 Z= 0.299 Chirality : 0.041 0.239 593 Planarity : 0.005 0.061 598 Dihedral : 6.311 69.308 500 Min Nonbonded Distance : 2.639 Molprobity Statistics. All-atom Clashscore : 7.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.75 % Favored : 98.25 % Rotamer: Outliers : 2.22 % Allowed : 20.00 % Favored : 77.78 % 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: 2.18 (0.41), residues: 457 helix: 1.63 (0.28), residues: 360 sheet: -1.67 (1.96), residues: 10 loop : 1.41 (0.75), residues: 87 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.001 ARG A 300 TYR 0.014 0.002 TYR A 275 PHE 0.014 0.002 PHE A 360 TRP 0.010 0.001 TRP A 357 HIS 0.001 0.001 HIS A 245 Details of bonding type rmsd covalent geometry : bond 0.00386 ( 3593) covalent geometry : angle 0.64237 ( 4906) SS BOND : bond 0.00680 ( 2) SS BOND : angle 1.01405 ( 4) hydrogen bonds : bond 0.04205 ( 266) hydrogen bonds : angle 4.31537 ( 786) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1333.40 seconds wall clock time: 23 minutes 33.52 seconds (1413.52 seconds total)