Starting phenix.real_space_refine on Wed Jul 1 23:56:15 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/7y7v_33671/07_2026/7y7v_33671.cif Found real_map, /net/cci-nas-00/data/ceres_data/7y7v_33671/07_2026/7y7v_33671.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.2 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/7y7v_33671/07_2026/7y7v_33671.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7y7v_33671/07_2026/7y7v_33671.cif" restraint_files = "/net/cci-nas-00/data/ceres_data/7y7v_33671/07_2026/7y7v_33671.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/7y7v_33671/07_2026/7y7v_33671.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/7y7v_33671/07_2026/7y7v_33671.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7y7v_33671/07_2026/7y7v_33671.map" } resolution = 2.2 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= -0.001 sd= 0.111 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 34 5.16 5 Cl 1 4.86 5 C 2861 2.51 5 N 659 2.21 5 O 786 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 4 residue(s): 0.00s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 4341 Number of models: 1 Model: "" Number of chains: 2 Chain: "A" Number of atoms: 4240 Number of conformers: 1 Conformer: "" Number of residues, atoms: 532, 4240 Classifications: {'peptide': 532} Link IDs: {'PTRANS': 22, 'TRANS': 509} Chain: "A" Number of atoms: 101 Number of conformers: 1 Conformer: "" Number of residues, atoms: 62, 101 Unusual residues: {' CL': 1, 'NAG': 3} Classifications: {'undetermined': 4, 'water': 58} Link IDs: {None: 61} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen chiralities: 3 Time building chain proxies: 1.12, per 1000 atoms: 0.26 Number of scatterers: 4341 At special positions: 0 Unit cell: (69.28, 71.445, 97.425, 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 1 17.00 S 34 16.00 O 786 8.00 N 659 7.00 C 2861 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=1, symmetry=0 Simple disulfide: pdb=" SG CYS A 164 " - pdb=" SG CYS A 173 " distance=2.04 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 Links applied NAG-ASN " NAG A 701 " - " ASN A 181 " " NAG A 702 " - " ASN A 176 " " NAG A 703 " - " ASN A 184 " Time building additional restraints: 0.45 Conformation dependent library (CDL) restraints added in 187.5 milliseconds 1060 Ramachandran restraints generated. 530 Oldfield, 0 Emsley, 530 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 972 Finding SS restraints... Secondary structure from input PDB file: 32 helices and 1 sheets defined 82.1% alpha, 0.4% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.08 Creating SS restraints... Processing helix chain 'A' and resid 46 through 57 Processing helix chain 'A' and resid 63 through 68 removed outlier: 3.531A pdb=" N VAL A 67 " --> pdb=" O GLY A 63 " (cutoff:3.500A) Processing helix chain 'A' and resid 68 through 77 removed outlier: 3.702A pdb=" N TYR A 72 " --> pdb=" O TRP A 68 " (cutoff:3.500A) Processing helix chain 'A' and resid 78 through 81 removed outlier: 4.763A pdb=" N ALA A 81 " --> pdb=" O GLY A 78 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 78 through 81' Processing helix chain 'A' and resid 82 through 93 Processing helix chain 'A' and resid 93 through 109 Processing helix chain 'A' and resid 113 through 118 removed outlier: 3.798A pdb=" N TRP A 116 " --> pdb=" O LEU A 113 " (cutoff:3.500A) removed outlier: 3.707A pdb=" N LYS A 117 " --> pdb=" O GLY A 114 " (cutoff:3.500A) Processing helix chain 'A' and resid 119 through 121 No H-bonds generated for 'chain 'A' and resid 119 through 121' Processing helix chain 'A' and resid 122 through 154 removed outlier: 4.031A pdb=" N GLY A 126 " --> pdb=" O PHE A 122 " (cutoff:3.500A) removed outlier: 4.061A pdb=" N ILE A 141 " --> pdb=" O ASN A 137 " (cutoff:3.500A) removed outlier: 3.809A pdb=" N VAL A 142 " --> pdb=" O ILE A 138 " (cutoff:3.500A) removed outlier: 3.711A pdb=" N ILE A 143 " --> pdb=" O TYR A 139 " (cutoff:3.500A) removed outlier: 3.666A pdb=" N ILE A 144 " --> pdb=" O TYR A 140 " (cutoff:3.500A) Processing helix chain 'A' and resid 187 through 196 Processing helix chain 'A' and resid 211 through 230 Processing helix chain 'A' and resid 233 through 238 removed outlier: 3.599A pdb=" N THR A 236 " --> pdb=" O VAL A 233 " (cutoff:3.500A) Processing helix chain 'A' and resid 239 through 259 Proline residue: A 247 - end of helix Processing helix chain 'A' and resid 263 through 273 Processing helix chain 'A' and resid 275 through 280 removed outlier: 3.709A pdb=" N SER A 280 " --> pdb=" O ARG A 277 " (cutoff:3.500A) Processing helix chain 'A' and resid 281 through 297 removed outlier: 3.996A pdb=" N TRP A 285 " --> pdb=" O ASP A 281 " (cutoff:3.500A) Processing helix chain 'A' and resid 301 through 310 removed outlier: 3.615A pdb=" N TYR A 309 " --> pdb=" O ALA A 305 " (cutoff:3.500A) removed outlier: 3.947A pdb=" N ASN A 310 " --> pdb=" O LEU A 306 " (cutoff:3.500A) Processing helix chain 'A' and resid 315 through 350 removed outlier: 3.664A pdb=" N ASP A 319 " --> pdb=" O ASN A 315 " (cutoff:3.500A) Processing helix chain 'A' and resid 352 through 358 Processing helix chain 'A' and resid 363 through 374 Proline residue: A 369 - end of helix Processing helix chain 'A' and resid 377 through 412 removed outlier: 3.727A pdb=" N TRP A 381 " --> pdb=" O ILE A 377 " (cutoff:3.500A) Processing helix chain 'A' and resid 412 through 417 Processing helix chain 'A' and resid 419 through 436 Processing helix chain 'A' and resid 437 through 439 No H-bonds generated for 'chain 'A' and resid 437 through 439' Processing helix chain 'A' and resid 442 through 454 removed outlier: 3.900A pdb=" N VAL A 446 " --> pdb=" O GLY A 442 " (cutoff:3.500A) Processing helix chain 'A' and resid 456 through 473 removed outlier: 3.775A pdb=" N ILE A 471 " --> pdb=" O GLU A 467 " (cutoff:3.500A) Processing helix chain 'A' and resid 476 through 489 Processing helix chain 'A' and resid 493 through 502 removed outlier: 4.262A pdb=" N LYS A 497 " --> pdb=" O CYS A 493 " (cutoff:3.500A) Processing helix chain 'A' and resid 502 through 519 Processing helix chain 'A' and resid 530 through 546 removed outlier: 4.004A pdb=" N SER A 544 " --> pdb=" O MET A 540 " (cutoff:3.500A) Processing helix chain 'A' and resid 546 through 559 Processing helix chain 'A' and resid 562 through 572 Processing sheet with id=AA1, first strand: chain 'A' and resid 523 through 524 290 hydrogen bonds defined for protein. 852 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: 0.45 Time building geometry restraints manager: 0.60 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.19 - 1.33: 717 1.33 - 1.46: 1744 1.46 - 1.59: 1904 1.59 - 1.73: 0 1.73 - 1.86: 54 Bond restraints: 4419 Sorted by residual: bond pdb=" C ARG A 172 " pdb=" O ARG A 172 " ideal model delta sigma weight residual 1.235 1.194 0.042 1.33e-02 5.65e+03 9.84e+00 bond pdb=" C ASP A 171 " pdb=" N ARG A 172 " ideal model delta sigma weight residual 1.331 1.305 0.026 1.43e-02 4.89e+03 3.40e+00 bond pdb=" C1 NAG A 702 " pdb=" O5 NAG A 702 " ideal model delta sigma weight residual 1.406 1.442 -0.036 2.00e-02 2.50e+03 3.16e+00 bond pdb=" C1 NAG A 703 " pdb=" O5 NAG A 703 " ideal model delta sigma weight residual 1.406 1.441 -0.035 2.00e-02 2.50e+03 3.01e+00 bond pdb=" C1 NAG A 701 " pdb=" O5 NAG A 701 " ideal model delta sigma weight residual 1.406 1.440 -0.034 2.00e-02 2.50e+03 2.90e+00 ... (remaining 4414 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.26: 5911 2.26 - 4.52: 96 4.52 - 6.78: 11 6.78 - 9.04: 1 9.04 - 11.30: 1 Bond angle restraints: 6020 Sorted by residual: angle pdb=" OG1 THR A 406 " pdb=" CB THR A 406 " pdb=" CG2 THR A 406 " ideal model delta sigma weight residual 109.30 120.60 -11.30 2.00e+00 2.50e-01 3.19e+01 angle pdb=" CA THR A 406 " pdb=" CB THR A 406 " pdb=" CG2 THR A 406 " ideal model delta sigma weight residual 110.50 118.65 -8.15 1.70e+00 3.46e-01 2.30e+01 angle pdb=" CA THR A 406 " pdb=" CB THR A 406 " pdb=" OG1 THR A 406 " ideal model delta sigma weight residual 109.60 115.67 -6.07 1.50e+00 4.44e-01 1.64e+01 angle pdb=" CA ARG A 172 " pdb=" C ARG A 172 " pdb=" O ARG A 172 " ideal model delta sigma weight residual 119.43 114.55 4.88 1.21e+00 6.83e-01 1.63e+01 angle pdb=" N ASP A 52 " pdb=" CA ASP A 52 " pdb=" C ASP A 52 " ideal model delta sigma weight residual 111.28 115.47 -4.19 1.09e+00 8.42e-01 1.48e+01 ... (remaining 6015 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.28: 2103 16.28 - 32.57: 258 32.57 - 48.85: 83 48.85 - 65.14: 19 65.14 - 81.42: 5 Dihedral angle restraints: 2468 sinusoidal: 936 harmonic: 1532 Sorted by residual: dihedral pdb=" CA GLY A 111 " pdb=" C GLY A 111 " pdb=" N GLY A 112 " pdb=" CA GLY A 112 " ideal model delta harmonic sigma weight residual 180.00 -159.61 -20.39 0 5.00e+00 4.00e-02 1.66e+01 dihedral pdb=" CA GLN A 199 " pdb=" C GLN A 199 " pdb=" N MET A 200 " pdb=" CA MET A 200 " ideal model delta harmonic sigma weight residual 180.00 -159.74 -20.26 0 5.00e+00 4.00e-02 1.64e+01 dihedral pdb=" CA TYR A 453 " pdb=" C TYR A 453 " pdb=" N SER A 454 " pdb=" CA SER A 454 " ideal model delta harmonic sigma weight residual 180.00 -159.98 -20.02 0 5.00e+00 4.00e-02 1.60e+01 ... (remaining 2465 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.283: 667 0.283 - 0.565: 2 0.565 - 0.848: 0 0.848 - 1.131: 0 1.131 - 1.413: 1 Chirality restraints: 670 Sorted by residual: chirality pdb=" CB THR A 406 " pdb=" CA THR A 406 " pdb=" OG1 THR A 406 " pdb=" CG2 THR A 406 " both_signs ideal model delta sigma weight residual False 2.55 1.14 1.41 2.00e-01 2.50e+01 4.99e+01 chirality pdb=" CA ASP A 52 " pdb=" N ASP A 52 " pdb=" C ASP A 52 " pdb=" CB ASP A 52 " both_signs ideal model delta sigma weight residual False 2.51 2.14 0.37 2.00e-01 2.50e+01 3.52e+00 chirality pdb=" C1 NAG A 702 " pdb=" ND2 ASN A 176 " pdb=" C2 NAG A 702 " pdb=" O5 NAG A 702 " both_signs ideal model delta sigma weight residual False -2.40 -2.75 0.35 2.00e-01 2.50e+01 3.00e+00 ... (remaining 667 not shown) Planarity restraints: 731 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB ASN A 184 " 0.157 2.00e-02 2.50e+03 1.65e-01 3.38e+02 pdb=" CG ASN A 184 " -0.059 2.00e-02 2.50e+03 pdb=" OD1 ASN A 184 " -0.059 2.00e-02 2.50e+03 pdb=" ND2 ASN A 184 " -0.246 2.00e-02 2.50e+03 pdb=" C1 NAG A 703 " 0.207 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB ASN A 181 " -0.031 2.00e-02 2.50e+03 3.38e-02 1.42e+01 pdb=" CG ASN A 181 " 0.011 2.00e-02 2.50e+03 pdb=" OD1 ASN A 181 " 0.004 2.00e-02 2.50e+03 pdb=" ND2 ASN A 181 " 0.055 2.00e-02 2.50e+03 pdb=" C1 NAG A 701 " -0.039 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB ASN A 176 " 0.024 2.00e-02 2.50e+03 2.51e-02 7.87e+00 pdb=" CG ASN A 176 " -0.006 2.00e-02 2.50e+03 pdb=" OD1 ASN A 176 " -0.011 2.00e-02 2.50e+03 pdb=" ND2 ASN A 176 " -0.038 2.00e-02 2.50e+03 pdb=" C1 NAG A 702 " 0.031 2.00e-02 2.50e+03 ... (remaining 728 not shown) Histogram of nonbonded interaction distances: 2.08 - 2.64: 50 2.64 - 3.21: 4207 3.21 - 3.77: 7211 3.77 - 4.34: 10093 4.34 - 4.90: 15768 Nonbonded interactions: 37329 Sorted by model distance: nonbonded pdb=" O SER A 243 " pdb=" O HOH A 801 " model vdw 2.078 3.040 nonbonded pdb=" OH TYR A 140 " pdb=" O HOH A 802 " model vdw 2.079 3.040 nonbonded pdb=" O MET A 570 " pdb=" O HOH A 803 " model vdw 2.151 3.040 nonbonded pdb=" OD1 ASN A 184 " pdb=" O5 NAG A 703 " model vdw 2.209 3.040 nonbonded pdb=" O LYS A 564 " pdb=" OE1 GLN A 568 " model vdw 2.252 3.040 ... (remaining 37324 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: 0.500 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.000 Extract box with map and model: 0.060 Check model and map are aligned: 0.000 Set scattering table: 0.020 Process input model: 5.470 Find NCS groups from input model: 0.010 Set up NCS constraints: 0.010 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:5.540 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 11.610 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8613 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 : 0.006 0.121 4423 Z= 0.259 Angle : 0.782 12.420 6031 Z= 0.417 Chirality : 0.073 1.413 670 Planarity : 0.005 0.033 728 Dihedral : 16.303 81.423 1493 Min Nonbonded Distance : 2.078 Molprobity Statistics. All-atom Clashscore : 5.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.21 % Favored : 96.79 % Rotamer: Outliers : 1.11 % Allowed : 22.35 % Favored : 76.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.09 (0.34), residues: 530 helix: 0.62 (0.25), residues: 382 sheet: None (None), residues: 0 loop : -1.26 (0.47), residues: 148 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.002 ARG A 50 TYR 0.024 0.002 TYR A 72 PHE 0.022 0.003 PHE A 339 TRP 0.013 0.002 TRP A 116 HIS 0.002 0.001 HIS A 347 Details of bonding type rmsd/Z covalent geometry : bond 0.00497 / 0.23 ( 4419) covalent geometry : angle 0.72606 / 0.40 ( 6020) SS BOND : bond 0.00695 / 0.37 ( 1) SS BOND : angle 5.97461 / 3.47 ( 2) hydrogen bonds : bond 0.13768 / 9.02 ( 290) hydrogen bonds : angle 6.58099 / 4.76 ( 852) link_NAG-ASN : bond 0.09672 / 4.67 ( 3) link_NAG-ASN : angle 7.05430 / 3.72 ( 9) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1060 Ramachandran restraints generated. 530 Oldfield, 0 Emsley, 530 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1060 Ramachandran restraints generated. 530 Oldfield, 0 Emsley, 530 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 70 residues out of total 452 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 65 time to evaluate : 0.100 Fit side-chains REVERT: A 568 GLN cc_start: 0.7303 (mp10) cc_final: 0.6874 (tp40) outliers start: 5 outliers final: 1 residues processed: 69 average time/residue: 0.4731 time to fit residues: 33.9311 Evaluate side-chains 65 residues out of total 452 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 64 time to evaluate : 0.111 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 230 TRP Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 53 random chunks: chunk 24 optimal weight: 3.9990 chunk 48 optimal weight: 1.9990 chunk 26 optimal weight: 4.9990 chunk 2 optimal weight: 1.9990 chunk 16 optimal weight: 0.5980 chunk 32 optimal weight: 0.9980 chunk 31 optimal weight: 1.9990 chunk 25 optimal weight: 0.9990 chunk 50 optimal weight: 3.9990 chunk 19 optimal weight: 5.9990 chunk 30 optimal weight: 3.9990 overall best weight: 1.3186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 163 GLN A 418 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3604 r_free = 0.3604 target = 0.128798 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3156 r_free = 0.3156 target = 0.095886 restraints weight = 4179.877| |-----------------------------------------------------------------------------| r_work (start): 0.3155 rms_B_bonded: 1.48 r_work: 0.3042 rms_B_bonded: 1.91 restraints_weight: 0.5000 r_work: 0.2945 rms_B_bonded: 2.97 restraints_weight: 0.2500 r_work (final): 0.2945 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8681 moved from start: 0.1000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 4423 Z= 0.174 Angle : 0.666 10.943 6031 Z= 0.341 Chirality : 0.050 0.444 670 Planarity : 0.004 0.033 728 Dihedral : 5.324 37.516 578 Min Nonbonded Distance : 2.454 Molprobity Statistics. All-atom Clashscore : 4.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.64 % Favored : 97.36 % Rotamer: Outliers : 5.09 % Allowed : 17.26 % Favored : 77.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.01 (0.36), residues: 530 helix: 1.35 (0.26), residues: 383 sheet: None (None), residues: 0 loop : -1.10 (0.48), residues: 147 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 420 TYR 0.020 0.002 TYR A 72 PHE 0.020 0.002 PHE A 339 TRP 0.015 0.002 TRP A 116 HIS 0.002 0.001 HIS A 313 Details of bonding type rmsd/Z covalent geometry : bond 0.00382 / 0.17 ( 4419) covalent geometry : angle 0.62612 / 0.33 ( 6020) SS BOND : bond 0.00714 / 0.38 ( 1) SS BOND : angle 3.56750 / 2.09 ( 2) hydrogen bonds : bond 0.06379 / 4.41 ( 290) hydrogen bonds : angle 5.12554 / 3.64 ( 852) link_NAG-ASN : bond 0.01580 / 0.62 ( 3) link_NAG-ASN : angle 5.67921 / 2.88 ( 9) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1060 Ramachandran restraints generated. 530 Oldfield, 0 Emsley, 530 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1060 Ramachandran restraints generated. 530 Oldfield, 0 Emsley, 530 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 87 residues out of total 452 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 64 time to evaluate : 0.158 Fit side-chains revert: symmetry clash REVERT: A 184 ASN cc_start: 0.5740 (OUTLIER) cc_final: 0.5530 (m110) REVERT: A 380 LEU cc_start: 0.8779 (OUTLIER) cc_final: 0.8280 (tp) outliers start: 23 outliers final: 12 residues processed: 81 average time/residue: 0.5255 time to fit residues: 44.1528 Evaluate side-chains 70 residues out of total 452 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 56 time to evaluate : 0.157 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 72 TYR Chi-restraints excluded: chain A residue 145 SER Chi-restraints excluded: chain A residue 183 THR Chi-restraints excluded: chain A residue 184 ASN Chi-restraints excluded: chain A residue 230 TRP Chi-restraints excluded: chain A residue 348 VAL Chi-restraints excluded: chain A residue 372 VAL Chi-restraints excluded: chain A residue 378 SER Chi-restraints excluded: chain A residue 380 LEU Chi-restraints excluded: chain A residue 422 LEU Chi-restraints excluded: chain A residue 464 VAL Chi-restraints excluded: chain A residue 469 VAL Chi-restraints excluded: chain A residue 488 VAL Chi-restraints excluded: chain A residue 564 LYS Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 53 random chunks: chunk 12 optimal weight: 0.7980 chunk 36 optimal weight: 1.9990 chunk 39 optimal weight: 0.9990 chunk 37 optimal weight: 0.6980 chunk 4 optimal weight: 0.9990 chunk 26 optimal weight: 5.9990 chunk 18 optimal weight: 5.9990 chunk 52 optimal weight: 0.9980 chunk 44 optimal weight: 0.3980 chunk 43 optimal weight: 2.9990 chunk 2 optimal weight: 3.9990 overall best weight: 0.7782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 163 GLN A 534 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3626 r_free = 0.3626 target = 0.130446 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3188 r_free = 0.3188 target = 0.097871 restraints weight = 4165.128| |-----------------------------------------------------------------------------| r_work (start): 0.3186 rms_B_bonded: 1.47 r_work: 0.3074 rms_B_bonded: 1.92 restraints_weight: 0.5000 r_work: 0.2977 rms_B_bonded: 2.99 restraints_weight: 0.2500 r_work (final): 0.2977 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8652 moved from start: 0.1287 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 4423 Z= 0.138 Angle : 0.600 9.539 6031 Z= 0.305 Chirality : 0.045 0.350 670 Planarity : 0.004 0.033 728 Dihedral : 5.089 41.308 578 Min Nonbonded Distance : 2.445 Molprobity Statistics. All-atom Clashscore : 5.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.45 % Favored : 97.55 % Rotamer: Outliers : 3.76 % Allowed : 16.81 % Favored : 79.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.37 (0.36), residues: 530 helix: 1.64 (0.26), residues: 387 sheet: None (None), residues: 0 loop : -1.12 (0.48), residues: 143 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 414 TYR 0.018 0.002 TYR A 72 PHE 0.018 0.002 PHE A 339 TRP 0.011 0.001 TRP A 116 HIS 0.001 0.001 HIS A 313 Details of bonding type rmsd/Z covalent geometry : bond 0.00289 / 0.14 ( 4419) covalent geometry : angle 0.56676 / 0.30 ( 6020) SS BOND : bond 0.00731 / 0.38 ( 1) SS BOND : angle 3.20032 / 1.84 ( 2) hydrogen bonds : bond 0.05414 / 3.75 ( 290) hydrogen bonds : angle 4.82356 / 3.40 ( 852) link_NAG-ASN : bond 0.01366 / 0.54 ( 3) link_NAG-ASN : angle 4.88473 / 2.47 ( 9) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1060 Ramachandran restraints generated. 530 Oldfield, 0 Emsley, 530 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1060 Ramachandran restraints generated. 530 Oldfield, 0 Emsley, 530 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 74 residues out of total 452 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 57 time to evaluate : 0.190 Fit side-chains REVERT: A 172 ARG cc_start: 0.7648 (mtp85) cc_final: 0.7395 (mtp85) REVERT: A 184 ASN cc_start: 0.5871 (OUTLIER) cc_final: 0.4647 (m110) REVERT: A 230 TRP cc_start: 0.5299 (OUTLIER) cc_final: 0.4481 (p-90) REVERT: A 231 LYS cc_start: 0.4879 (OUTLIER) cc_final: 0.4192 (pptt) REVERT: A 278 LYS cc_start: 0.8810 (OUTLIER) cc_final: 0.8540 (tmtm) REVERT: A 380 LEU cc_start: 0.8704 (OUTLIER) cc_final: 0.8258 (tp) REVERT: A 564 LYS cc_start: 0.7770 (tttp) cc_final: 0.7552 (tptp) outliers start: 17 outliers final: 8 residues processed: 72 average time/residue: 0.5389 time to fit residues: 40.2729 Evaluate side-chains 71 residues out of total 452 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 58 time to evaluate : 0.152 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 72 TYR Chi-restraints excluded: chain A residue 117 LYS Chi-restraints excluded: chain A residue 145 SER Chi-restraints excluded: chain A residue 184 ASN Chi-restraints excluded: chain A residue 230 TRP Chi-restraints excluded: chain A residue 231 LYS Chi-restraints excluded: chain A residue 278 LYS Chi-restraints excluded: chain A residue 292 ILE Chi-restraints excluded: chain A residue 372 VAL Chi-restraints excluded: chain A residue 378 SER Chi-restraints excluded: chain A residue 380 LEU Chi-restraints excluded: chain A residue 422 LEU Chi-restraints excluded: chain A residue 464 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 53 random chunks: chunk 38 optimal weight: 0.9990 chunk 32 optimal weight: 1.9990 chunk 35 optimal weight: 3.9990 chunk 0 optimal weight: 10.0000 chunk 51 optimal weight: 7.9990 chunk 14 optimal weight: 3.9990 chunk 10 optimal weight: 2.9990 chunk 36 optimal weight: 1.9990 chunk 28 optimal weight: 0.3980 chunk 16 optimal weight: 0.7980 chunk 18 optimal weight: 6.9990 overall best weight: 1.2386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 163 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3604 r_free = 0.3604 target = 0.128661 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3158 r_free = 0.3158 target = 0.095923 restraints weight = 4128.694| |-----------------------------------------------------------------------------| r_work (start): 0.3157 rms_B_bonded: 1.46 r_work: 0.3043 rms_B_bonded: 1.91 restraints_weight: 0.5000 r_work: 0.2945 rms_B_bonded: 2.97 restraints_weight: 0.2500 r_work (final): 0.2945 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8677 moved from start: 0.1321 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.033 4423 Z= 0.162 Angle : 0.612 7.521 6031 Z= 0.316 Chirality : 0.046 0.257 670 Planarity : 0.004 0.037 728 Dihedral : 5.134 43.741 578 Min Nonbonded Distance : 2.426 Molprobity Statistics. All-atom Clashscore : 4.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.64 % Favored : 97.36 % Rotamer: Outliers : 5.09 % Allowed : 15.49 % Favored : 79.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.27 (0.36), residues: 530 helix: 1.55 (0.26), residues: 388 sheet: None (None), residues: 0 loop : -1.14 (0.48), residues: 142 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 351 TYR 0.022 0.002 TYR A 72 PHE 0.019 0.002 PHE A 339 TRP 0.014 0.002 TRP A 116 HIS 0.001 0.001 HIS A 313 Details of bonding type rmsd/Z covalent geometry : bond 0.00356 / 0.16 ( 4419) covalent geometry : angle 0.59238 / 0.31 ( 6020) SS BOND : bond 0.00612 / 0.32 ( 1) SS BOND : angle 2.50121 / 1.45 ( 2) hydrogen bonds : bond 0.06038 / 4.19 ( 290) hydrogen bonds : angle 4.91304 / 3.48 ( 852) link_NAG-ASN : bond 0.00999 / 0.40 ( 3) link_NAG-ASN : angle 3.83415 / 1.99 ( 9) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1060 Ramachandran restraints generated. 530 Oldfield, 0 Emsley, 530 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1060 Ramachandran restraints generated. 530 Oldfield, 0 Emsley, 530 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 82 residues out of total 452 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 59 time to evaluate : 0.157 Fit side-chains REVERT: A 184 ASN cc_start: 0.5827 (OUTLIER) cc_final: 0.5385 (m110) REVERT: A 230 TRP cc_start: 0.5392 (OUTLIER) cc_final: 0.4448 (p-90) REVERT: A 231 LYS cc_start: 0.4740 (OUTLIER) cc_final: 0.4425 (pptt) REVERT: A 278 LYS cc_start: 0.8796 (OUTLIER) cc_final: 0.8520 (tmtm) REVERT: A 380 LEU cc_start: 0.8757 (OUTLIER) cc_final: 0.8270 (tp) REVERT: A 564 LYS cc_start: 0.7766 (tttp) cc_final: 0.7547 (tptp) outliers start: 23 outliers final: 12 residues processed: 79 average time/residue: 0.4848 time to fit residues: 39.6789 Evaluate side-chains 75 residues out of total 452 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 58 time to evaluate : 0.094 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 72 TYR Chi-restraints excluded: chain A residue 76 LYS Chi-restraints excluded: chain A residue 145 SER Chi-restraints excluded: chain A residue 183 THR Chi-restraints excluded: chain A residue 184 ASN Chi-restraints excluded: chain A residue 230 TRP Chi-restraints excluded: chain A residue 231 LYS Chi-restraints excluded: chain A residue 233 VAL Chi-restraints excluded: chain A residue 278 LYS Chi-restraints excluded: chain A residue 292 ILE Chi-restraints excluded: chain A residue 348 VAL Chi-restraints excluded: chain A residue 372 VAL Chi-restraints excluded: chain A residue 378 SER Chi-restraints excluded: chain A residue 380 LEU Chi-restraints excluded: chain A residue 422 LEU Chi-restraints excluded: chain A residue 464 VAL Chi-restraints excluded: chain A residue 469 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 53 random chunks: chunk 41 optimal weight: 0.5980 chunk 17 optimal weight: 4.9990 chunk 14 optimal weight: 0.8980 chunk 47 optimal weight: 1.9990 chunk 2 optimal weight: 2.9990 chunk 48 optimal weight: 0.9990 chunk 34 optimal weight: 0.9990 chunk 52 optimal weight: 0.0270 chunk 39 optimal weight: 0.8980 chunk 21 optimal weight: 3.9990 chunk 5 optimal weight: 0.8980 overall best weight: 0.6638 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3634 r_free = 0.3634 target = 0.131076 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3197 r_free = 0.3197 target = 0.098468 restraints weight = 4218.149| |-----------------------------------------------------------------------------| r_work (start): 0.3196 rms_B_bonded: 1.48 r_work: 0.3084 rms_B_bonded: 1.95 restraints_weight: 0.5000 r_work: 0.2987 rms_B_bonded: 3.03 restraints_weight: 0.2500 r_work (final): 0.2987 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8644 moved from start: 0.1521 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.024 4423 Z= 0.129 Angle : 0.566 7.415 6031 Z= 0.290 Chirality : 0.043 0.217 670 Planarity : 0.004 0.040 728 Dihedral : 4.998 46.267 578 Min Nonbonded Distance : 2.423 Molprobity Statistics. All-atom Clashscore : 4.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.45 % Favored : 97.55 % Rotamer: Outliers : 3.32 % Allowed : 17.04 % Favored : 79.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.56 (0.36), residues: 530 helix: 1.76 (0.26), residues: 391 sheet: None (None), residues: 0 loop : -1.06 (0.50), residues: 139 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG A 172 TYR 0.017 0.001 TYR A 72 PHE 0.017 0.002 PHE A 339 TRP 0.011 0.001 TRP A 116 HIS 0.002 0.001 HIS A 313 Details of bonding type rmsd/Z covalent geometry : bond 0.00264 / 0.13 ( 4419) covalent geometry : angle 0.55033 / 0.29 ( 6020) SS BOND : bond 0.00559 / 0.29 ( 1) SS BOND : angle 2.05659 / 1.12 ( 2) hydrogen bonds : bond 0.05104 / 3.54 ( 290) hydrogen bonds : angle 4.68216 / 3.30 ( 852) link_NAG-ASN : bond 0.00995 / 0.39 ( 3) link_NAG-ASN : angle 3.33763 / 1.74 ( 9) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1060 Ramachandran restraints generated. 530 Oldfield, 0 Emsley, 530 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1060 Ramachandran restraints generated. 530 Oldfield, 0 Emsley, 530 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 73 residues out of total 452 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 58 time to evaluate : 0.176 Fit side-chains REVERT: A 230 TRP cc_start: 0.5419 (OUTLIER) cc_final: 0.5080 (t60) REVERT: A 231 LYS cc_start: 0.5026 (OUTLIER) cc_final: 0.4355 (pptt) REVERT: A 278 LYS cc_start: 0.8810 (OUTLIER) cc_final: 0.8535 (tmtm) REVERT: A 380 LEU cc_start: 0.8690 (OUTLIER) cc_final: 0.8240 (tp) REVERT: A 568 GLN cc_start: 0.7596 (mm-40) cc_final: 0.7321 (mm-40) outliers start: 15 outliers final: 9 residues processed: 71 average time/residue: 0.4702 time to fit residues: 34.6143 Evaluate side-chains 71 residues out of total 452 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 58 time to evaluate : 0.167 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 72 TYR Chi-restraints excluded: chain A residue 123 LYS Chi-restraints excluded: chain A residue 230 TRP Chi-restraints excluded: chain A residue 231 LYS Chi-restraints excluded: chain A residue 233 VAL Chi-restraints excluded: chain A residue 278 LYS Chi-restraints excluded: chain A residue 292 ILE Chi-restraints excluded: chain A residue 348 VAL Chi-restraints excluded: chain A residue 372 VAL Chi-restraints excluded: chain A residue 378 SER Chi-restraints excluded: chain A residue 380 LEU Chi-restraints excluded: chain A residue 422 LEU Chi-restraints excluded: chain A residue 464 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 53 random chunks: chunk 13 optimal weight: 0.9980 chunk 2 optimal weight: 0.4980 chunk 11 optimal weight: 4.9990 chunk 4 optimal weight: 2.9990 chunk 35 optimal weight: 2.9990 chunk 30 optimal weight: 0.5980 chunk 37 optimal weight: 1.9990 chunk 43 optimal weight: 3.9990 chunk 45 optimal weight: 0.9980 chunk 25 optimal weight: 2.9990 chunk 29 optimal weight: 0.9990 overall best weight: 0.8182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 418 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3625 r_free = 0.3625 target = 0.130347 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3184 r_free = 0.3184 target = 0.097645 restraints weight = 4240.652| |-----------------------------------------------------------------------------| r_work (start): 0.3184 rms_B_bonded: 1.48 r_work: 0.3073 rms_B_bonded: 1.93 restraints_weight: 0.5000 r_work: 0.2975 rms_B_bonded: 3.01 restraints_weight: 0.2500 r_work (final): 0.2975 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8653 moved from start: 0.1649 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 4423 Z= 0.135 Angle : 0.574 9.924 6031 Z= 0.295 Chirality : 0.045 0.348 670 Planarity : 0.004 0.044 728 Dihedral : 4.987 47.916 578 Min Nonbonded Distance : 2.452 Molprobity Statistics. All-atom Clashscore : 4.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.45 % Favored : 97.55 % Rotamer: Outliers : 4.20 % Allowed : 16.37 % Favored : 79.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.60 (0.36), residues: 530 helix: 1.76 (0.26), residues: 392 sheet: None (None), residues: 0 loop : -0.97 (0.51), residues: 138 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG A 414 TYR 0.019 0.002 TYR A 72 PHE 0.018 0.002 PHE A 339 TRP 0.012 0.001 TRP A 116 HIS 0.002 0.001 HIS A 313 Details of bonding type rmsd/Z covalent geometry : bond 0.00283 / 0.13 ( 4419) covalent geometry : angle 0.56499 / 0.29 ( 6020) SS BOND : bond 0.00420 / 0.22 ( 1) SS BOND : angle 1.69772 / 0.97 ( 2) hydrogen bonds : bond 0.05318 / 3.69 ( 290) hydrogen bonds : angle 4.70092 / 3.31 ( 852) link_NAG-ASN : bond 0.00389 / 0.18 ( 3) link_NAG-ASN : angle 2.53433 / 1.27 ( 9) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1060 Ramachandran restraints generated. 530 Oldfield, 0 Emsley, 530 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1060 Ramachandran restraints generated. 530 Oldfield, 0 Emsley, 530 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 77 residues out of total 452 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 58 time to evaluate : 0.160 Fit side-chains REVERT: A 230 TRP cc_start: 0.5441 (OUTLIER) cc_final: 0.5128 (t60) REVERT: A 231 LYS cc_start: 0.5145 (OUTLIER) cc_final: 0.4499 (pptt) REVERT: A 278 LYS cc_start: 0.8808 (OUTLIER) cc_final: 0.8531 (tmtm) REVERT: A 380 LEU cc_start: 0.8673 (OUTLIER) cc_final: 0.8242 (tp) REVERT: A 568 GLN cc_start: 0.7422 (mm-40) cc_final: 0.7208 (mm-40) outliers start: 19 outliers final: 12 residues processed: 75 average time/residue: 0.5394 time to fit residues: 42.0064 Evaluate side-chains 71 residues out of total 452 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 55 time to evaluate : 0.156 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 72 TYR Chi-restraints excluded: chain A residue 76 LYS Chi-restraints excluded: chain A residue 123 LYS Chi-restraints excluded: chain A residue 145 SER Chi-restraints excluded: chain A residue 230 TRP Chi-restraints excluded: chain A residue 231 LYS Chi-restraints excluded: chain A residue 233 VAL Chi-restraints excluded: chain A residue 278 LYS Chi-restraints excluded: chain A residue 292 ILE Chi-restraints excluded: chain A residue 348 VAL Chi-restraints excluded: chain A residue 372 VAL Chi-restraints excluded: chain A residue 378 SER Chi-restraints excluded: chain A residue 380 LEU Chi-restraints excluded: chain A residue 422 LEU Chi-restraints excluded: chain A residue 464 VAL Chi-restraints excluded: chain A residue 469 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 53 random chunks: chunk 31 optimal weight: 3.9990 chunk 45 optimal weight: 3.9990 chunk 39 optimal weight: 1.9990 chunk 18 optimal weight: 7.9990 chunk 34 optimal weight: 6.9990 chunk 11 optimal weight: 0.0170 chunk 47 optimal weight: 0.9980 chunk 17 optimal weight: 0.5980 chunk 20 optimal weight: 1.9990 chunk 51 optimal weight: 0.0980 chunk 43 optimal weight: 3.9990 overall best weight: 0.7420 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 418 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3632 r_free = 0.3632 target = 0.130906 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3194 r_free = 0.3194 target = 0.098229 restraints weight = 4228.114| |-----------------------------------------------------------------------------| r_work (start): 0.3193 rms_B_bonded: 1.48 r_work: 0.3080 rms_B_bonded: 1.94 restraints_weight: 0.5000 r_work: 0.2983 rms_B_bonded: 3.03 restraints_weight: 0.2500 r_work (final): 0.2983 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8646 moved from start: 0.1661 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.025 4423 Z= 0.130 Angle : 0.557 8.545 6031 Z= 0.288 Chirality : 0.044 0.226 670 Planarity : 0.004 0.037 728 Dihedral : 4.966 49.956 578 Min Nonbonded Distance : 2.447 Molprobity Statistics. All-atom Clashscore : 4.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.26 % Favored : 97.74 % Rotamer: Outliers : 3.54 % Allowed : 17.04 % Favored : 79.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.68 (0.37), residues: 530 helix: 1.83 (0.26), residues: 391 sheet: None (None), residues: 0 loop : -0.96 (0.50), residues: 139 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG A 414 TYR 0.018 0.001 TYR A 72 PHE 0.017 0.002 PHE A 339 TRP 0.011 0.001 TRP A 116 HIS 0.002 0.001 HIS A 198 Details of bonding type rmsd/Z covalent geometry : bond 0.00270 / 0.13 ( 4419) covalent geometry : angle 0.55271 / 0.29 ( 6020) SS BOND : bond 0.00397 / 0.21 ( 1) SS BOND : angle 1.60174 / 0.91 ( 2) hydrogen bonds : bond 0.05125 / 3.56 ( 290) hydrogen bonds : angle 4.68870 / 3.29 ( 852) link_NAG-ASN : bond 0.00439 / 0.20 ( 3) link_NAG-ASN : angle 1.74958 / 0.91 ( 9) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1060 Ramachandran restraints generated. 530 Oldfield, 0 Emsley, 530 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1060 Ramachandran restraints generated. 530 Oldfield, 0 Emsley, 530 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 74 residues out of total 452 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 58 time to evaluate : 0.159 Fit side-chains REVERT: A 230 TRP cc_start: 0.5568 (OUTLIER) cc_final: 0.5351 (t60) REVERT: A 231 LYS cc_start: 0.5147 (OUTLIER) cc_final: 0.4809 (pptt) REVERT: A 278 LYS cc_start: 0.8806 (OUTLIER) cc_final: 0.8526 (tmtm) REVERT: A 380 LEU cc_start: 0.8660 (OUTLIER) cc_final: 0.8225 (tp) REVERT: A 574 SER cc_start: 0.7308 (t) cc_final: 0.7067 (p) outliers start: 16 outliers final: 12 residues processed: 73 average time/residue: 0.5295 time to fit residues: 40.1470 Evaluate side-chains 73 residues out of total 452 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 57 time to evaluate : 0.157 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 72 TYR Chi-restraints excluded: chain A residue 76 LYS Chi-restraints excluded: chain A residue 123 LYS Chi-restraints excluded: chain A residue 145 SER Chi-restraints excluded: chain A residue 230 TRP Chi-restraints excluded: chain A residue 231 LYS Chi-restraints excluded: chain A residue 233 VAL Chi-restraints excluded: chain A residue 278 LYS Chi-restraints excluded: chain A residue 292 ILE Chi-restraints excluded: chain A residue 348 VAL Chi-restraints excluded: chain A residue 372 VAL Chi-restraints excluded: chain A residue 378 SER Chi-restraints excluded: chain A residue 380 LEU Chi-restraints excluded: chain A residue 422 LEU Chi-restraints excluded: chain A residue 464 VAL Chi-restraints excluded: chain A residue 469 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 53 random chunks: chunk 9 optimal weight: 0.7980 chunk 26 optimal weight: 0.0170 chunk 47 optimal weight: 0.7980 chunk 28 optimal weight: 0.9990 chunk 23 optimal weight: 2.9990 chunk 48 optimal weight: 0.6980 chunk 42 optimal weight: 5.9990 chunk 25 optimal weight: 1.9990 chunk 50 optimal weight: 2.9990 chunk 39 optimal weight: 0.9980 chunk 44 optimal weight: 0.6980 overall best weight: 0.6018 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 418 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3643 r_free = 0.3643 target = 0.131893 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3211 r_free = 0.3211 target = 0.099364 restraints weight = 4228.759| |-----------------------------------------------------------------------------| r_work (start): 0.3210 rms_B_bonded: 1.48 r_work: 0.3096 rms_B_bonded: 1.96 restraints_weight: 0.5000 r_work: 0.3000 rms_B_bonded: 3.06 restraints_weight: 0.2500 r_work (final): 0.3000 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8631 moved from start: 0.1798 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.025 4423 Z= 0.123 Angle : 0.543 8.045 6031 Z= 0.281 Chirality : 0.043 0.217 670 Planarity : 0.004 0.036 728 Dihedral : 4.919 51.933 578 Min Nonbonded Distance : 2.466 Molprobity Statistics. All-atom Clashscore : 5.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.26 % Favored : 97.74 % Rotamer: Outliers : 3.32 % Allowed : 17.48 % Favored : 79.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.78 (0.37), residues: 530 helix: 1.88 (0.26), residues: 392 sheet: None (None), residues: 0 loop : -0.87 (0.51), residues: 138 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG A 414 TYR 0.018 0.001 TYR A 246 PHE 0.016 0.002 PHE A 462 TRP 0.010 0.001 TRP A 116 HIS 0.001 0.001 HIS A 313 Details of bonding type rmsd/Z covalent geometry : bond 0.00252 / 0.12 ( 4419) covalent geometry : angle 0.54057 / 0.28 ( 6020) SS BOND : bond 0.00332 / 0.17 ( 1) SS BOND : angle 1.48371 / 0.84 ( 2) hydrogen bonds : bond 0.04859 / 3.37 ( 290) hydrogen bonds : angle 4.61352 / 3.24 ( 852) link_NAG-ASN : bond 0.00418 / 0.19 ( 3) link_NAG-ASN : angle 1.32546 / 0.73 ( 9) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1060 Ramachandran restraints generated. 530 Oldfield, 0 Emsley, 530 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1060 Ramachandran restraints generated. 530 Oldfield, 0 Emsley, 530 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 73 residues out of total 452 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 58 time to evaluate : 0.099 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 278 LYS cc_start: 0.8807 (OUTLIER) cc_final: 0.8525 (tmtm) REVERT: A 380 LEU cc_start: 0.8631 (OUTLIER) cc_final: 0.8212 (tp) outliers start: 15 outliers final: 10 residues processed: 71 average time/residue: 0.5229 time to fit residues: 38.5908 Evaluate side-chains 69 residues out of total 452 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 57 time to evaluate : 0.158 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 72 TYR Chi-restraints excluded: chain A residue 145 SER Chi-restraints excluded: chain A residue 233 VAL Chi-restraints excluded: chain A residue 278 LYS Chi-restraints excluded: chain A residue 292 ILE Chi-restraints excluded: chain A residue 348 VAL Chi-restraints excluded: chain A residue 372 VAL Chi-restraints excluded: chain A residue 378 SER Chi-restraints excluded: chain A residue 380 LEU Chi-restraints excluded: chain A residue 422 LEU Chi-restraints excluded: chain A residue 464 VAL Chi-restraints excluded: chain A residue 469 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 53 random chunks: chunk 48 optimal weight: 0.7980 chunk 23 optimal weight: 0.0060 chunk 20 optimal weight: 0.7980 chunk 6 optimal weight: 4.9990 chunk 35 optimal weight: 2.9990 chunk 28 optimal weight: 4.9990 chunk 31 optimal weight: 3.9990 chunk 50 optimal weight: 0.9990 chunk 4 optimal weight: 2.9990 chunk 10 optimal weight: 3.9990 chunk 42 optimal weight: 4.9990 overall best weight: 1.1200 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 418 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3612 r_free = 0.3612 target = 0.129476 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3169 r_free = 0.3169 target = 0.096668 restraints weight = 4194.603| |-----------------------------------------------------------------------------| r_work (start): 0.3169 rms_B_bonded: 1.46 r_work: 0.3054 rms_B_bonded: 1.95 restraints_weight: 0.5000 r_work: 0.2957 rms_B_bonded: 3.02 restraints_weight: 0.2500 r_work (final): 0.2957 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8667 moved from start: 0.1664 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 4423 Z= 0.152 Angle : 0.583 8.109 6031 Z= 0.305 Chirality : 0.045 0.211 670 Planarity : 0.004 0.053 728 Dihedral : 4.485 17.717 576 Min Nonbonded Distance : 2.459 Molprobity Statistics. All-atom Clashscore : 5.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.26 % Favored : 97.74 % Rotamer: Outliers : 3.10 % Allowed : 17.04 % Favored : 79.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.64 (0.37), residues: 530 helix: 1.74 (0.26), residues: 393 sheet: None (None), residues: 0 loop : -0.81 (0.51), residues: 137 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG A 414 TYR 0.021 0.002 TYR A 72 PHE 0.016 0.002 PHE A 339 TRP 0.013 0.001 TRP A 116 HIS 0.002 0.001 HIS A 347 Details of bonding type rmsd/Z covalent geometry : bond 0.00332 / 0.15 ( 4419) covalent geometry : angle 0.58121 / 0.30 ( 6020) SS BOND : bond 0.00425 / 0.22 ( 1) SS BOND : angle 1.52648 / 0.88 ( 2) hydrogen bonds : bond 0.05723 / 3.97 ( 290) hydrogen bonds : angle 4.79159 / 3.38 ( 852) link_NAG-ASN : bond 0.00428 / 0.19 ( 3) link_NAG-ASN : angle 1.15620 / 0.65 ( 9) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1060 Ramachandran restraints generated. 530 Oldfield, 0 Emsley, 530 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1060 Ramachandran restraints generated. 530 Oldfield, 0 Emsley, 530 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 74 residues out of total 452 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 60 time to evaluate : 0.160 Fit side-chains revert: symmetry clash REVERT: A 278 LYS cc_start: 0.8802 (OUTLIER) cc_final: 0.8520 (tmtm) REVERT: A 380 LEU cc_start: 0.8724 (OUTLIER) cc_final: 0.8256 (tp) outliers start: 14 outliers final: 11 residues processed: 72 average time/residue: 0.5699 time to fit residues: 42.4886 Evaluate side-chains 67 residues out of total 452 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 54 time to evaluate : 0.161 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 72 TYR Chi-restraints excluded: chain A residue 76 LYS Chi-restraints excluded: chain A residue 145 SER Chi-restraints excluded: chain A residue 233 VAL Chi-restraints excluded: chain A residue 278 LYS Chi-restraints excluded: chain A residue 292 ILE Chi-restraints excluded: chain A residue 348 VAL Chi-restraints excluded: chain A residue 372 VAL Chi-restraints excluded: chain A residue 378 SER Chi-restraints excluded: chain A residue 380 LEU Chi-restraints excluded: chain A residue 422 LEU Chi-restraints excluded: chain A residue 464 VAL Chi-restraints excluded: chain A residue 469 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 53 random chunks: chunk 9 optimal weight: 0.7980 chunk 31 optimal weight: 3.9990 chunk 7 optimal weight: 0.8980 chunk 47 optimal weight: 0.7980 chunk 45 optimal weight: 1.9990 chunk 36 optimal weight: 0.7980 chunk 39 optimal weight: 0.9990 chunk 5 optimal weight: 0.6980 chunk 37 optimal weight: 1.9990 chunk 22 optimal weight: 1.9990 chunk 38 optimal weight: 0.8980 overall best weight: 0.7980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 418 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3627 r_free = 0.3627 target = 0.130618 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3190 r_free = 0.3190 target = 0.097944 restraints weight = 4202.907| |-----------------------------------------------------------------------------| r_work (start): 0.3189 rms_B_bonded: 1.48 r_work: 0.3075 rms_B_bonded: 1.95 restraints_weight: 0.5000 r_work: 0.2978 rms_B_bonded: 3.02 restraints_weight: 0.2500 r_work (final): 0.2978 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8652 moved from start: 0.1742 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 4423 Z= 0.133 Angle : 0.562 7.842 6031 Z= 0.293 Chirality : 0.044 0.210 670 Planarity : 0.004 0.045 728 Dihedral : 4.424 17.455 576 Min Nonbonded Distance : 2.459 Molprobity Statistics. All-atom Clashscore : 4.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.26 % Favored : 97.74 % Rotamer: Outliers : 2.88 % Allowed : 17.04 % Favored : 80.09 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.72 (0.37), residues: 530 helix: 1.83 (0.26), residues: 392 sheet: None (None), residues: 0 loop : -0.87 (0.51), residues: 138 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG A 414 TYR 0.020 0.002 TYR A 246 PHE 0.018 0.002 PHE A 339 TRP 0.013 0.001 TRP A 116 HIS 0.002 0.001 HIS A 313 Details of bonding type rmsd/Z covalent geometry : bond 0.00281 / 0.13 ( 4419) covalent geometry : angle 0.56050 / 0.29 ( 6020) SS BOND : bond 0.00352 / 0.19 ( 1) SS BOND : angle 1.48486 / 0.85 ( 2) hydrogen bonds : bond 0.05238 / 3.64 ( 290) hydrogen bonds : angle 4.71529 / 3.31 ( 852) link_NAG-ASN : bond 0.00393 / 0.18 ( 3) link_NAG-ASN : angle 1.07327 / 0.61 ( 9) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1060 Ramachandran restraints generated. 530 Oldfield, 0 Emsley, 530 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1060 Ramachandran restraints generated. 530 Oldfield, 0 Emsley, 530 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 67 residues out of total 452 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 54 time to evaluate : 0.132 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 50 ARG cc_start: 0.7245 (mmm160) cc_final: 0.6728 (tpt170) REVERT: A 278 LYS cc_start: 0.8801 (OUTLIER) cc_final: 0.8521 (tmtm) REVERT: A 380 LEU cc_start: 0.8694 (OUTLIER) cc_final: 0.8247 (tp) outliers start: 13 outliers final: 10 residues processed: 66 average time/residue: 0.5144 time to fit residues: 35.1627 Evaluate side-chains 66 residues out of total 452 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 54 time to evaluate : 0.118 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 72 TYR Chi-restraints excluded: chain A residue 145 SER Chi-restraints excluded: chain A residue 233 VAL Chi-restraints excluded: chain A residue 278 LYS Chi-restraints excluded: chain A residue 292 ILE Chi-restraints excluded: chain A residue 348 VAL Chi-restraints excluded: chain A residue 372 VAL Chi-restraints excluded: chain A residue 378 SER Chi-restraints excluded: chain A residue 380 LEU Chi-restraints excluded: chain A residue 422 LEU Chi-restraints excluded: chain A residue 464 VAL Chi-restraints excluded: chain A residue 469 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 53 random chunks: chunk 37 optimal weight: 0.9980 chunk 40 optimal weight: 0.5980 chunk 2 optimal weight: 2.9990 chunk 14 optimal weight: 5.9990 chunk 10 optimal weight: 2.9990 chunk 25 optimal weight: 0.9990 chunk 52 optimal weight: 0.9990 chunk 29 optimal weight: 0.8980 chunk 8 optimal weight: 2.9990 chunk 47 optimal weight: 0.5980 chunk 4 optimal weight: 0.8980 overall best weight: 0.7980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 418 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3626 r_free = 0.3626 target = 0.130684 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3191 r_free = 0.3191 target = 0.098104 restraints weight = 4202.795| |-----------------------------------------------------------------------------| r_work (start): 0.3190 rms_B_bonded: 1.47 r_work: 0.3076 rms_B_bonded: 1.95 restraints_weight: 0.5000 r_work: 0.2980 rms_B_bonded: 3.03 restraints_weight: 0.2500 r_work (final): 0.2980 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8655 moved from start: 0.1796 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 4423 Z= 0.135 Angle : 0.563 7.729 6031 Z= 0.293 Chirality : 0.043 0.207 670 Planarity : 0.004 0.047 728 Dihedral : 4.428 17.385 576 Min Nonbonded Distance : 2.459 Molprobity Statistics. All-atom Clashscore : 4.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.08 % Favored : 97.92 % Rotamer: Outliers : 3.10 % Allowed : 17.04 % Favored : 79.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.73 (0.36), residues: 530 helix: 1.84 (0.26), residues: 392 sheet: None (None), residues: 0 loop : -0.86 (0.51), residues: 138 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG A 414 TYR 0.020 0.002 TYR A 246 PHE 0.017 0.002 PHE A 339 TRP 0.012 0.001 TRP A 116 HIS 0.001 0.001 HIS A 313 Details of bonding type rmsd/Z covalent geometry : bond 0.00283 / 0.13 ( 4419) covalent geometry : angle 0.56194 / 0.29 ( 6020) SS BOND : bond 0.00360 / 0.19 ( 1) SS BOND : angle 1.46447 / 0.84 ( 2) hydrogen bonds : bond 0.05245 / 3.64 ( 290) hydrogen bonds : angle 4.69854 / 3.30 ( 852) link_NAG-ASN : bond 0.00385 / 0.18 ( 3) link_NAG-ASN : angle 1.01096 / 0.57 ( 9) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1840.87 seconds wall clock time: 32 minutes 3.51 seconds (1923.51 seconds total)