Starting phenix.real_space_refine on Wed Sep 17 04:58:26 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9jdg_61392/09_2025/9jdg_61392_neut.cif Found real_map, /net/cci-nas-00/data/ceres_data/9jdg_61392/09_2025/9jdg_61392.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.23 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/9jdg_61392/09_2025/9jdg_61392_neut.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9jdg_61392/09_2025/9jdg_61392_neut.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9jdg_61392/09_2025/9jdg_61392.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9jdg_61392/09_2025/9jdg_61392.map" } resolution = 3.23 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.049 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 32 5.16 5 Cl 1 4.86 5 C 3021 2.51 5 N 655 2.21 5 O 750 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 12 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: 4459 Number of models: 1 Model: "" Number of chains: 2 Chain: "A" Number of atoms: 4311 Number of conformers: 1 Conformer: "" Number of residues, atoms: 545, 4311 Classifications: {'peptide': 545} Incomplete info: {'truncation_to_alanine': 5} Link IDs: {'PTRANS': 28, 'TRANS': 516} Chain breaks: 1 Unresolved non-hydrogen bonds: 24 Unresolved non-hydrogen angles: 26 Unresolved non-hydrogen dihedrals: 22 Planarities with less than four sites: {'ARG:plan': 2} Unresolved non-hydrogen planarities: 10 Chain: "A" Number of atoms: 148 Number of conformers: 1 Conformer: "" Number of residues, atoms: 22, 148 Unusual residues: {' CL': 1, 'D10': 5, 'D12': 3, 'NAG': 1, 'OCT': 5} Classifications: {'undetermined': 15, 'water': 7} Link IDs: {None: 21} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Time building chain proxies: 1.23, per 1000 atoms: 0.28 Number of scatterers: 4459 At special positions: 0 Unit cell: (87.565, 67.52, 88.62, 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 32 16.00 O 750 8.00 N 655 7.00 C 3021 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=1, symmetry=0 Simple disulfide: pdb=" SG CYS A 162 " - pdb=" SG CYS A 171 " distance=2.03 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 715 " - " ASN A 190 " Time building additional restraints: 0.40 Conformation dependent library (CDL) restraints added in 179.8 milliseconds Enol-peptide restraints added in 715.3 nanoseconds 1082 Ramachandran restraints generated. 541 Oldfield, 0 Emsley, 541 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 992 Finding SS restraints... Secondary structure from input PDB file: 32 helices and 1 sheets defined 77.6% alpha, 0.4% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.15 Creating SS restraints... Processing helix chain 'A' and resid 47 through 54 Processing helix chain 'A' and resid 60 through 65 removed outlier: 3.616A pdb=" N VAL A 64 " --> pdb=" O GLY A 60 " (cutoff:3.500A) Processing helix chain 'A' and resid 65 through 74 removed outlier: 4.080A pdb=" N TYR A 69 " --> pdb=" O TRP A 65 " (cutoff:3.500A) Processing helix chain 'A' and resid 76 through 78 No H-bonds generated for 'chain 'A' and resid 76 through 78' Processing helix chain 'A' and resid 79 through 90 Processing helix chain 'A' and resid 90 through 106 Processing helix chain 'A' and resid 108 through 117 removed outlier: 4.238A pdb=" N TRP A 113 " --> pdb=" O GLY A 109 " (cutoff:3.500A) Processing helix chain 'A' and resid 121 through 152 removed outlier: 4.347A pdb=" N TYR A 125 " --> pdb=" O SER A 121 " (cutoff:3.500A) removed outlier: 3.914A pdb=" N ILE A 139 " --> pdb=" O ASN A 135 " (cutoff:3.500A) removed outlier: 4.803A pdb=" N VAL A 140 " --> pdb=" O VAL A 136 " (cutoff:3.500A) removed outlier: 4.469A pdb=" N ILE A 141 " --> pdb=" O TYR A 137 " (cutoff:3.500A) removed outlier: 3.908A pdb=" N LEU A 142 " --> pdb=" O TYR A 138 " (cutoff:3.500A) Processing helix chain 'A' and resid 173 through 180 removed outlier: 4.595A pdb=" N LYS A 178 " --> pdb=" O ASP A 174 " (cutoff:3.500A) removed outlier: 3.526A pdb=" N LYS A 180 " --> pdb=" O MET A 176 " (cutoff:3.500A) Processing helix chain 'A' and resid 193 through 202 Processing helix chain 'A' and resid 217 through 237 removed outlier: 3.563A pdb=" N VAL A 227 " --> pdb=" O CYS A 223 " (cutoff:3.500A) Processing helix chain 'A' and resid 245 through 266 removed outlier: 4.046A pdb=" N THR A 249 " --> pdb=" O VAL A 245 " (cutoff:3.500A) Proline residue: A 253 - end of helix Processing helix chain 'A' and resid 269 through 279 Processing helix chain 'A' and resid 281 through 286 removed outlier: 3.708A pdb=" N LEU A 285 " --> pdb=" O ASP A 281 " (cutoff:3.500A) removed outlier: 3.664A pdb=" N GLU A 286 " --> pdb=" O ILE A 282 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 281 through 286' Processing helix chain 'A' and resid 288 through 303 removed outlier: 3.522A pdb=" N ILE A 292 " --> pdb=" O PRO A 288 " (cutoff:3.500A) removed outlier: 3.522A pdb=" N PHE A 299 " --> pdb=" O GLY A 295 " (cutoff:3.500A) Processing helix chain 'A' and resid 307 through 315 removed outlier: 3.551A pdb=" N SER A 311 " --> pdb=" O GLY A 307 " (cutoff:3.500A) removed outlier: 3.731A pdb=" N TYR A 315 " --> pdb=" O SER A 311 " (cutoff:3.500A) Processing helix chain 'A' and resid 321 through 356 removed outlier: 3.798A pdb=" N ASP A 325 " --> pdb=" O ASN A 321 " (cutoff:3.500A) removed outlier: 3.531A pdb=" N ALA A 343 " --> pdb=" O VAL A 339 " (cutoff:3.500A) Processing helix chain 'A' and resid 358 through 362 removed outlier: 3.641A pdb=" N VAL A 362 " --> pdb=" O ILE A 359 " (cutoff:3.500A) Processing helix chain 'A' and resid 373 through 378 Processing helix chain 'A' and resid 379 through 381 No H-bonds generated for 'chain 'A' and resid 379 through 381' Processing helix chain 'A' and resid 383 through 418 removed outlier: 3.568A pdb=" N GLY A 399 " --> pdb=" O LEU A 395 " (cutoff:3.500A) Processing helix chain 'A' and resid 425 through 444 Processing helix chain 'A' and resid 445 through 447 No H-bonds generated for 'chain 'A' and resid 445 through 447' Processing helix chain 'A' and resid 448 through 449 No H-bonds generated for 'chain 'A' and resid 448 through 449' Processing helix chain 'A' and resid 450 through 462 removed outlier: 4.043A pdb=" N VAL A 454 " --> pdb=" O GLY A 450 " (cutoff:3.500A) Processing helix chain 'A' and resid 465 through 482 Processing helix chain 'A' and resid 484 through 496 Processing helix chain 'A' and resid 501 through 510 removed outlier: 4.563A pdb=" N LYS A 505 " --> pdb=" O GLY A 501 " (cutoff:3.500A) removed outlier: 3.587A pdb=" N VAL A 510 " --> pdb=" O TYR A 506 " (cutoff:3.500A) Processing helix chain 'A' and resid 510 through 526 Processing helix chain 'A' and resid 539 through 555 removed outlier: 3.960A pdb=" N SER A 553 " --> pdb=" O LEU A 549 " (cutoff:3.500A) Processing helix chain 'A' and resid 555 through 568 Processing helix chain 'A' and resid 571 through 579 Processing sheet with id=AA1, first strand: chain 'A' and resid 531 through 532 274 hydrogen bonds defined for protein. 816 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: 0.61 Time building geometry restraints manager: 0.54 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 1257 1.34 - 1.46: 957 1.46 - 1.57: 2319 1.57 - 1.69: 0 1.69 - 1.81: 46 Bond restraints: 4579 Sorted by residual: bond pdb=" N ILE A 196 " pdb=" CA ILE A 196 " ideal model delta sigma weight residual 1.461 1.495 -0.035 1.19e-02 7.06e+03 8.46e+00 bond pdb=" N VAL A 203 " pdb=" CA VAL A 203 " ideal model delta sigma weight residual 1.460 1.494 -0.034 1.19e-02 7.06e+03 8.21e+00 bond pdb=" N PHE A 191 " pdb=" CA PHE A 191 " ideal model delta sigma weight residual 1.454 1.489 -0.035 1.23e-02 6.61e+03 8.17e+00 bond pdb=" N ASN A 190 " pdb=" CA ASN A 190 " ideal model delta sigma weight residual 1.454 1.491 -0.036 1.27e-02 6.20e+03 8.13e+00 bond pdb=" N VAL A 195 " pdb=" CA VAL A 195 " ideal model delta sigma weight residual 1.461 1.494 -0.033 1.17e-02 7.31e+03 7.77e+00 ... (remaining 4574 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.52: 5956 1.52 - 3.04: 207 3.04 - 4.56: 25 4.56 - 6.08: 6 6.08 - 7.59: 3 Bond angle restraints: 6197 Sorted by residual: angle pdb=" CA GLY A 594 " pdb=" C GLY A 594 " pdb=" O GLY A 594 " ideal model delta sigma weight residual 121.58 118.17 3.41 9.00e-01 1.23e+00 1.44e+01 angle pdb=" CA ARG A 587 " pdb=" C ARG A 587 " pdb=" O ARG A 587 " ideal model delta sigma weight residual 122.63 118.06 4.57 1.29e+00 6.01e-01 1.26e+01 angle pdb=" CA VAL A 203 " pdb=" C VAL A 203 " pdb=" O VAL A 203 " ideal model delta sigma weight residual 121.05 117.51 3.54 1.11e+00 8.12e-01 1.02e+01 angle pdb=" CA SER A 205 " pdb=" C SER A 205 " pdb=" O SER A 205 " ideal model delta sigma weight residual 122.14 118.31 3.83 1.24e+00 6.50e-01 9.53e+00 angle pdb=" N SER A 205 " pdb=" CA SER A 205 " pdb=" C SER A 205 " ideal model delta sigma weight residual 111.24 106.99 4.25 1.38e+00 5.25e-01 9.48e+00 ... (remaining 6192 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.12: 2328 16.12 - 32.24: 222 32.24 - 48.36: 55 48.36 - 64.48: 10 64.48 - 80.60: 4 Dihedral angle restraints: 2619 sinusoidal: 1051 harmonic: 1568 Sorted by residual: dihedral pdb=" CA VAL A 510 " pdb=" C VAL A 510 " pdb=" N ILE A 511 " pdb=" CA ILE A 511 " ideal model delta harmonic sigma weight residual -180.00 -163.18 -16.82 0 5.00e+00 4.00e-02 1.13e+01 dihedral pdb=" CA TRP A 166 " pdb=" C TRP A 166 " pdb=" N ASN A 167 " pdb=" CA ASN A 167 " ideal model delta harmonic sigma weight residual -180.00 -164.56 -15.44 0 5.00e+00 4.00e-02 9.54e+00 dihedral pdb=" CB MET A 452 " pdb=" CG MET A 452 " pdb=" SD MET A 452 " pdb=" CE MET A 452 " ideal model delta sinusoidal sigma weight residual -180.00 -125.19 -54.81 3 1.50e+01 4.44e-03 9.31e+00 ... (remaining 2616 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.112: 662 0.112 - 0.224: 14 0.224 - 0.336: 0 0.336 - 0.448: 0 0.448 - 0.560: 1 Chirality restraints: 677 Sorted by residual: chirality pdb=" C1 NAG A 715 " pdb=" ND2 ASN A 190 " pdb=" C2 NAG A 715 " pdb=" O5 NAG A 715 " both_signs ideal model delta sigma weight residual False -2.40 -1.84 -0.56 2.00e-01 2.50e+01 7.85e+00 chirality pdb=" CA ILE A 196 " pdb=" N ILE A 196 " pdb=" C ILE A 196 " pdb=" CB ILE A 196 " both_signs ideal model delta sigma weight residual False 2.43 2.62 -0.19 2.00e-01 2.50e+01 8.66e-01 chirality pdb=" CA VAL A 590 " pdb=" N VAL A 590 " pdb=" C VAL A 590 " pdb=" CB VAL A 590 " both_signs ideal model delta sigma weight residual False 2.44 2.59 -0.15 2.00e-01 2.50e+01 5.64e-01 ... (remaining 674 not shown) Planarity restraints: 746 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB ASN A 190 " -0.161 2.00e-02 2.50e+03 2.08e-01 5.42e+02 pdb=" CG ASN A 190 " 0.070 2.00e-02 2.50e+03 pdb=" OD1 ASN A 190 " 0.026 2.00e-02 2.50e+03 pdb=" ND2 ASN A 190 " 0.335 2.00e-02 2.50e+03 pdb=" C1 NAG A 715 " -0.270 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C2 NAG A 715 " -0.044 2.00e-02 2.50e+03 3.64e-02 1.66e+01 pdb=" C7 NAG A 715 " 0.012 2.00e-02 2.50e+03 pdb=" C8 NAG A 715 " -0.033 2.00e-02 2.50e+03 pdb=" N2 NAG A 715 " 0.058 2.00e-02 2.50e+03 pdb=" O7 NAG A 715 " 0.008 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CD ARG A 587 " -0.158 9.50e-02 1.11e+02 7.10e-02 3.10e+00 pdb=" NE ARG A 587 " 0.010 2.00e-02 2.50e+03 pdb=" CZ ARG A 587 " 0.001 2.00e-02 2.50e+03 pdb=" NH1 ARG A 587 " 0.002 2.00e-02 2.50e+03 pdb=" NH2 ARG A 587 " -0.005 2.00e-02 2.50e+03 ... (remaining 743 not shown) Histogram of nonbonded interaction distances: 2.11 - 2.67: 60 2.67 - 3.23: 4352 3.23 - 3.78: 6909 3.78 - 4.34: 9759 4.34 - 4.90: 16317 Nonbonded interactions: 37397 Sorted by model distance: nonbonded pdb=" OH TYR A 69 " pdb=" OD2 ASP A 459 " model vdw 2.109 3.040 nonbonded pdb=" ND2 ASN A 190 " pdb=" N2 NAG A 715 " model vdw 2.113 2.560 nonbonded pdb=" ND2 ASN A 63 " pdb=" OG SER A 337 " model vdw 2.275 3.120 nonbonded pdb=" NE2 GLN A 289 " pdb=" OD1 ASP A 293 " model vdw 2.280 3.120 nonbonded pdb=" O ALA A 433 " pdb=" OG SER A 437 " model vdw 2.356 3.040 ... (remaining 37392 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: 0.880 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.070 Check model and map are aligned: 0.010 Set scattering table: 0.020 Process input model: 6.120 Find NCS groups from input model: 0.020 Set up NCS constraints: 0.010 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.360 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 8.500 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7929 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 0.177 4581 Z= 0.316 Angle : 0.839 33.872 6202 Z= 0.431 Chirality : 0.047 0.560 677 Planarity : 0.006 0.071 745 Dihedral : 13.695 80.598 1624 Min Nonbonded Distance : 2.109 Molprobity Statistics. All-atom Clashscore : 6.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.03 % Favored : 97.97 % Rotamer: Outliers : 0.22 % Allowed : 0.43 % Favored : 99.35 % 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: -0.46 (0.35), residues: 541 helix: 0.21 (0.26), residues: 385 sheet: None (None), residues: 0 loop : -1.39 (0.46), residues: 156 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 564 TYR 0.019 0.001 TYR A 578 PHE 0.017 0.001 PHE A 95 TRP 0.013 0.001 TRP A 470 HIS 0.005 0.001 HIS A 161 Details of bonding type rmsd covalent geometry : bond 0.00534 ( 4579) covalent geometry : angle 0.65574 ( 6197) SS BOND : bond 0.00160 ( 1) SS BOND : angle 1.97443 ( 2) hydrogen bonds : bond 0.23369 ( 274) hydrogen bonds : angle 7.71198 ( 816) link_NAG-ASN : bond 0.17731 ( 1) link_NAG-ASN : angle 23.72417 ( 3) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1082 Ramachandran restraints generated. 541 Oldfield, 0 Emsley, 541 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1082 Ramachandran restraints generated. 541 Oldfield, 0 Emsley, 541 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 58 residues out of total 465 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 57 time to evaluate : 0.096 Fit side-chains revert: symmetry clash REVERT: A 309 MET cc_start: 0.7703 (mmp) cc_final: 0.7380 (mmp) REVERT: A 427 ARG cc_start: 0.7043 (mtm180) cc_final: 0.6096 (mtm180) REVERT: A 460 TYR cc_start: 0.8990 (t80) cc_final: 0.8752 (t80) REVERT: A 566 CYS cc_start: 0.8157 (m) cc_final: 0.7941 (m) outliers start: 1 outliers final: 0 residues processed: 57 average time/residue: 0.0650 time to fit residues: 4.9149 Evaluate side-chains 49 residues out of total 465 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 49 time to evaluate : 0.167 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 54 random chunks: chunk 24 optimal weight: 0.9980 chunk 48 optimal weight: 0.9990 chunk 26 optimal weight: 2.9990 chunk 2 optimal weight: 0.4980 chunk 16 optimal weight: 2.9990 chunk 32 optimal weight: 0.6980 chunk 31 optimal weight: 0.9990 chunk 25 optimal weight: 0.9980 chunk 50 optimal weight: 0.8980 chunk 53 optimal weight: 0.0570 chunk 19 optimal weight: 4.9990 overall best weight: 0.6298 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 297 GLN A 355 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3271 r_free = 0.3271 target = 0.120553 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.2913 r_free = 0.2913 target = 0.093185 restraints weight = 5510.551| |-----------------------------------------------------------------------------| r_work (start): 0.2926 rms_B_bonded: 1.76 r_work: 0.2821 rms_B_bonded: 2.46 restraints_weight: 0.5000 r_work: 0.2682 rms_B_bonded: 4.00 restraints_weight: 0.2500 r_work (final): 0.2682 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7878 moved from start: 0.1211 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 4581 Z= 0.154 Angle : 0.551 7.499 6202 Z= 0.285 Chirality : 0.040 0.139 677 Planarity : 0.004 0.039 745 Dihedral : 6.020 42.403 698 Min Nonbonded Distance : 2.587 Molprobity Statistics. All-atom Clashscore : 6.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.22 % Favored : 97.78 % Rotamer: Outliers : 0.87 % Allowed : 7.17 % Favored : 91.96 % 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: 0.48 (0.35), residues: 541 helix: 0.99 (0.27), residues: 383 sheet: None (None), residues: 0 loop : -1.26 (0.45), residues: 158 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 66 TYR 0.016 0.001 TYR A 69 PHE 0.012 0.001 PHE A 345 TRP 0.017 0.001 TRP A 470 HIS 0.002 0.001 HIS A 161 Details of bonding type rmsd covalent geometry : bond 0.00355 ( 4579) covalent geometry : angle 0.54941 ( 6197) SS BOND : bond 0.00129 ( 1) SS BOND : angle 1.57362 ( 2) hydrogen bonds : bond 0.05153 ( 274) hydrogen bonds : angle 4.90930 ( 816) link_NAG-ASN : bond 0.00020 ( 1) link_NAG-ASN : angle 1.40207 ( 3) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1082 Ramachandran restraints generated. 541 Oldfield, 0 Emsley, 541 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1082 Ramachandran restraints generated. 541 Oldfield, 0 Emsley, 541 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 66 residues out of total 465 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 62 time to evaluate : 0.167 Fit side-chains REVERT: A 351 MET cc_start: 0.8602 (mtp) cc_final: 0.8335 (mtm) REVERT: A 427 ARG cc_start: 0.6918 (mtm180) cc_final: 0.6206 (mtm180) outliers start: 4 outliers final: 1 residues processed: 64 average time/residue: 0.0598 time to fit residues: 5.2033 Evaluate side-chains 52 residues out of total 465 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 51 time to evaluate : 0.158 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 358 ASP Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 54 random chunks: chunk 2 optimal weight: 0.0980 chunk 1 optimal weight: 0.7980 chunk 26 optimal weight: 3.9990 chunk 35 optimal weight: 0.8980 chunk 5 optimal weight: 0.9980 chunk 51 optimal weight: 0.9980 chunk 17 optimal weight: 0.8980 chunk 45 optimal weight: 0.6980 chunk 31 optimal weight: 0.5980 chunk 43 optimal weight: 0.5980 chunk 24 optimal weight: 0.9990 overall best weight: 0.5580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3274 r_free = 0.3274 target = 0.120873 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.2935 r_free = 0.2935 target = 0.094795 restraints weight = 5533.271| |-----------------------------------------------------------------------------| r_work (start): 0.2947 rms_B_bonded: 1.67 r_work: 0.2840 rms_B_bonded: 2.39 restraints_weight: 0.5000 r_work: 0.2703 rms_B_bonded: 3.91 restraints_weight: 0.2500 r_work (final): 0.2703 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7930 moved from start: 0.1615 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 4581 Z= 0.131 Angle : 0.511 7.220 6202 Z= 0.259 Chirality : 0.039 0.122 677 Planarity : 0.004 0.034 745 Dihedral : 5.591 32.275 698 Min Nonbonded Distance : 2.605 Molprobity Statistics. All-atom Clashscore : 6.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.22 % Favored : 97.78 % Rotamer: Outliers : 1.52 % Allowed : 8.91 % Favored : 89.57 % 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: 0.82 (0.35), residues: 541 helix: 1.29 (0.26), residues: 384 sheet: None (None), residues: 0 loop : -1.30 (0.44), residues: 157 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 66 TYR 0.031 0.001 TYR A 460 PHE 0.012 0.001 PHE A 338 TRP 0.017 0.001 TRP A 470 HIS 0.002 0.001 HIS A 161 Details of bonding type rmsd covalent geometry : bond 0.00302 ( 4579) covalent geometry : angle 0.51017 ( 6197) SS BOND : bond 0.00059 ( 1) SS BOND : angle 1.35648 ( 2) hydrogen bonds : bond 0.04293 ( 274) hydrogen bonds : angle 4.54797 ( 816) link_NAG-ASN : bond 0.00117 ( 1) link_NAG-ASN : angle 1.04600 ( 3) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1082 Ramachandran restraints generated. 541 Oldfield, 0 Emsley, 541 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1082 Ramachandran restraints generated. 541 Oldfield, 0 Emsley, 541 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 62 residues out of total 465 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 55 time to evaluate : 0.178 Fit side-chains REVERT: A 351 MET cc_start: 0.8707 (mtp) cc_final: 0.8496 (mtm) REVERT: A 427 ARG cc_start: 0.6924 (mtm180) cc_final: 0.6241 (mtm180) REVERT: A 577 LYS cc_start: 0.8156 (ttmm) cc_final: 0.7826 (tppt) outliers start: 7 outliers final: 6 residues processed: 60 average time/residue: 0.0636 time to fit residues: 5.1322 Evaluate side-chains 56 residues out of total 465 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 50 time to evaluate : 0.133 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 69 TYR Chi-restraints excluded: chain A residue 111 THR Chi-restraints excluded: chain A residue 358 ASP Chi-restraints excluded: chain A residue 514 VAL Chi-restraints excluded: chain A residue 524 LEU Chi-restraints excluded: chain A residue 596 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 54 random chunks: chunk 11 optimal weight: 0.9980 chunk 5 optimal weight: 2.9990 chunk 49 optimal weight: 0.7980 chunk 7 optimal weight: 0.0040 chunk 8 optimal weight: 0.5980 chunk 25 optimal weight: 0.5980 chunk 17 optimal weight: 0.5980 chunk 34 optimal weight: 1.9990 chunk 37 optimal weight: 0.0470 chunk 45 optimal weight: 0.6980 chunk 18 optimal weight: 1.9990 overall best weight: 0.3690 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 167 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3301 r_free = 0.3301 target = 0.122857 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.2957 r_free = 0.2957 target = 0.096431 restraints weight = 5543.736| |-----------------------------------------------------------------------------| r_work (start): 0.2958 rms_B_bonded: 1.72 r_work: 0.2852 rms_B_bonded: 2.44 restraints_weight: 0.5000 r_work: 0.2715 rms_B_bonded: 4.00 restraints_weight: 0.2500 r_work (final): 0.2715 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7778 moved from start: 0.1908 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.035 4581 Z= 0.108 Angle : 0.479 6.999 6202 Z= 0.241 Chirality : 0.037 0.117 677 Planarity : 0.004 0.032 745 Dihedral : 5.183 34.256 698 Min Nonbonded Distance : 2.619 Molprobity Statistics. All-atom Clashscore : 4.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.22 % Favored : 97.78 % Rotamer: Outliers : 1.52 % Allowed : 10.43 % Favored : 88.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.19 (0.35), residues: 541 helix: 1.59 (0.26), residues: 389 sheet: None (None), residues: 0 loop : -1.31 (0.45), residues: 152 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 66 TYR 0.019 0.001 TYR A 460 PHE 0.010 0.001 PHE A 474 TRP 0.015 0.001 TRP A 470 HIS 0.005 0.001 HIS A 161 Details of bonding type rmsd covalent geometry : bond 0.00240 ( 4579) covalent geometry : angle 0.47814 ( 6197) SS BOND : bond 0.00003 ( 1) SS BOND : angle 0.90136 ( 2) hydrogen bonds : bond 0.03759 ( 274) hydrogen bonds : angle 4.31955 ( 816) link_NAG-ASN : bond 0.00025 ( 1) link_NAG-ASN : angle 0.92842 ( 3) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1082 Ramachandran restraints generated. 541 Oldfield, 0 Emsley, 541 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1082 Ramachandran restraints generated. 541 Oldfield, 0 Emsley, 541 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 64 residues out of total 465 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 57 time to evaluate : 0.158 Fit side-chains REVERT: A 321 ASN cc_start: 0.8171 (t0) cc_final: 0.7705 (t0) REVERT: A 427 ARG cc_start: 0.6864 (mtm180) cc_final: 0.6171 (mtm180) REVERT: A 577 LYS cc_start: 0.8020 (ttmm) cc_final: 0.7646 (tppt) outliers start: 7 outliers final: 4 residues processed: 61 average time/residue: 0.0595 time to fit residues: 4.8806 Evaluate side-chains 58 residues out of total 465 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 54 time to evaluate : 0.156 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 69 TYR Chi-restraints excluded: chain A residue 111 THR Chi-restraints excluded: chain A residue 555 LEU Chi-restraints excluded: chain A residue 596 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 54 random chunks: chunk 30 optimal weight: 2.9990 chunk 19 optimal weight: 0.7980 chunk 18 optimal weight: 0.8980 chunk 35 optimal weight: 0.9990 chunk 7 optimal weight: 0.4980 chunk 40 optimal weight: 0.9990 chunk 37 optimal weight: 3.9990 chunk 1 optimal weight: 0.1980 chunk 12 optimal weight: 1.9990 chunk 38 optimal weight: 1.9990 chunk 22 optimal weight: 2.9990 overall best weight: 0.6782 ------------------------------------------------------------------------------- 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 = 0.3290 r_free = 0.3290 target = 0.121865 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.2934 r_free = 0.2934 target = 0.094444 restraints weight = 5542.774| |-----------------------------------------------------------------------------| r_work (start): 0.2933 rms_B_bonded: 1.78 r_work: 0.2824 rms_B_bonded: 2.51 restraints_weight: 0.5000 r_work: 0.2686 rms_B_bonded: 4.08 restraints_weight: 0.2500 r_work (final): 0.2686 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7719 moved from start: 0.1922 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 4581 Z= 0.141 Angle : 0.501 7.019 6202 Z= 0.252 Chirality : 0.039 0.124 677 Planarity : 0.004 0.033 745 Dihedral : 5.354 36.720 698 Min Nonbonded Distance : 2.610 Molprobity Statistics. All-atom Clashscore : 5.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.22 % Favored : 97.78 % Rotamer: Outliers : 1.74 % Allowed : 11.30 % Favored : 86.96 % 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: 1.27 (0.35), residues: 541 helix: 1.70 (0.26), residues: 384 sheet: None (None), residues: 0 loop : -1.34 (0.44), residues: 157 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 66 TYR 0.019 0.001 TYR A 69 PHE 0.013 0.001 PHE A 474 TRP 0.013 0.001 TRP A 470 HIS 0.003 0.001 HIS A 161 Details of bonding type rmsd covalent geometry : bond 0.00336 ( 4579) covalent geometry : angle 0.49990 ( 6197) SS BOND : bond 0.00111 ( 1) SS BOND : angle 1.58618 ( 2) hydrogen bonds : bond 0.03912 ( 274) hydrogen bonds : angle 4.34500 ( 816) link_NAG-ASN : bond 0.00008 ( 1) link_NAG-ASN : angle 0.86145 ( 3) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1082 Ramachandran restraints generated. 541 Oldfield, 0 Emsley, 541 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1082 Ramachandran restraints generated. 541 Oldfield, 0 Emsley, 541 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 64 residues out of total 465 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 56 time to evaluate : 0.200 Fit side-chains REVERT: A 292 ILE cc_start: 0.8057 (mm) cc_final: 0.7831 (mt) REVERT: A 321 ASN cc_start: 0.8158 (t0) cc_final: 0.7662 (t0) REVERT: A 427 ARG cc_start: 0.6864 (mtm180) cc_final: 0.6198 (mtm180) REVERT: A 577 LYS cc_start: 0.7987 (ttmm) cc_final: 0.7612 (tppt) outliers start: 8 outliers final: 7 residues processed: 63 average time/residue: 0.0718 time to fit residues: 5.9191 Evaluate side-chains 61 residues out of total 465 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 54 time to evaluate : 0.173 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 69 TYR Chi-restraints excluded: chain A residue 111 THR Chi-restraints excluded: chain A residue 358 ASP Chi-restraints excluded: chain A residue 514 VAL Chi-restraints excluded: chain A residue 528 VAL Chi-restraints excluded: chain A residue 555 LEU Chi-restraints excluded: chain A residue 596 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 54 random chunks: chunk 45 optimal weight: 0.3980 chunk 40 optimal weight: 0.8980 chunk 29 optimal weight: 0.5980 chunk 28 optimal weight: 0.7980 chunk 31 optimal weight: 0.5980 chunk 1 optimal weight: 0.3980 chunk 32 optimal weight: 0.6980 chunk 7 optimal weight: 0.0970 chunk 52 optimal weight: 0.0970 chunk 26 optimal weight: 0.0020 chunk 50 optimal weight: 0.8980 overall best weight: 0.1984 ------------------------------------------------------------------------------- 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 = 0.3343 r_free = 0.3343 target = 0.126232 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.2986 r_free = 0.2986 target = 0.098496 restraints weight = 5616.569| |-----------------------------------------------------------------------------| r_work (start): 0.2981 rms_B_bonded: 1.88 r_work: 0.2873 rms_B_bonded: 2.62 restraints_weight: 0.5000 r_work: 0.2734 rms_B_bonded: 4.26 restraints_weight: 0.2500 r_work (final): 0.2734 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7620 moved from start: 0.2250 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.034 4581 Z= 0.095 Angle : 0.467 7.012 6202 Z= 0.234 Chirality : 0.037 0.123 677 Planarity : 0.003 0.031 745 Dihedral : 4.913 37.499 698 Min Nonbonded Distance : 2.623 Molprobity Statistics. All-atom Clashscore : 5.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.59 % Favored : 97.41 % Rotamer: Outliers : 1.52 % Allowed : 11.96 % Favored : 86.52 % 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: 1.60 (0.36), residues: 541 helix: 1.99 (0.26), residues: 384 sheet: None (None), residues: 0 loop : -1.38 (0.44), residues: 157 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 66 TYR 0.024 0.001 TYR A 460 PHE 0.008 0.001 PHE A 474 TRP 0.014 0.001 TRP A 470 HIS 0.002 0.001 HIS A 161 Details of bonding type rmsd covalent geometry : bond 0.00202 ( 4579) covalent geometry : angle 0.46647 ( 6197) SS BOND : bond 0.00093 ( 1) SS BOND : angle 1.01318 ( 2) hydrogen bonds : bond 0.03391 ( 274) hydrogen bonds : angle 4.18382 ( 816) link_NAG-ASN : bond 0.00080 ( 1) link_NAG-ASN : angle 0.90467 ( 3) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1082 Ramachandran restraints generated. 541 Oldfield, 0 Emsley, 541 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1082 Ramachandran restraints generated. 541 Oldfield, 0 Emsley, 541 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 63 residues out of total 465 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 56 time to evaluate : 0.160 Fit side-chains revert: symmetry clash REVERT: A 292 ILE cc_start: 0.7901 (mm) cc_final: 0.7645 (mt) REVERT: A 321 ASN cc_start: 0.8118 (t0) cc_final: 0.7632 (t0) REVERT: A 427 ARG cc_start: 0.6783 (mtm180) cc_final: 0.6095 (mtm180) REVERT: A 429 GLU cc_start: 0.7271 (mt-10) cc_final: 0.6837 (tt0) REVERT: A 494 ASP cc_start: 0.8648 (t70) cc_final: 0.8388 (t0) REVERT: A 577 LYS cc_start: 0.7822 (ttmm) cc_final: 0.7469 (tppt) outliers start: 7 outliers final: 5 residues processed: 60 average time/residue: 0.0652 time to fit residues: 5.2263 Evaluate side-chains 59 residues out of total 465 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 54 time to evaluate : 0.166 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 69 TYR Chi-restraints excluded: chain A residue 111 THR Chi-restraints excluded: chain A residue 310 THR Chi-restraints excluded: chain A residue 528 VAL Chi-restraints excluded: chain A residue 596 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 54 random chunks: chunk 32 optimal weight: 0.9980 chunk 11 optimal weight: 3.9990 chunk 13 optimal weight: 0.7980 chunk 21 optimal weight: 0.8980 chunk 3 optimal weight: 0.6980 chunk 52 optimal weight: 0.0870 chunk 40 optimal weight: 0.5980 chunk 48 optimal weight: 0.6980 chunk 51 optimal weight: 0.9990 chunk 6 optimal weight: 0.9980 chunk 35 optimal weight: 1.9990 overall best weight: 0.5758 ------------------------------------------------------------------------------- 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 = 0.3321 r_free = 0.3321 target = 0.123813 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.2966 r_free = 0.2966 target = 0.096252 restraints weight = 5611.041| |-----------------------------------------------------------------------------| r_work (start): 0.2952 rms_B_bonded: 1.87 r_work: 0.2840 rms_B_bonded: 2.62 restraints_weight: 0.5000 r_work: 0.2700 rms_B_bonded: 4.27 restraints_weight: 0.2500 r_work (final): 0.2700 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7660 moved from start: 0.2247 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 4581 Z= 0.129 Angle : 0.488 6.978 6202 Z= 0.244 Chirality : 0.038 0.133 677 Planarity : 0.004 0.033 745 Dihedral : 5.094 38.641 698 Min Nonbonded Distance : 2.614 Molprobity Statistics. All-atom Clashscore : 6.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.03 % Favored : 97.97 % Rotamer: Outliers : 1.52 % Allowed : 12.39 % Favored : 86.09 % 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 aren not related in a simple way. whole: 1.57 (0.36), residues: 541 helix: 1.97 (0.26), residues: 383 sheet: None (None), residues: 0 loop : -1.34 (0.44), residues: 158 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 66 TYR 0.021 0.001 TYR A 460 PHE 0.012 0.001 PHE A 474 TRP 0.013 0.001 TRP A 470 HIS 0.001 0.000 HIS A 161 Details of bonding type rmsd covalent geometry : bond 0.00305 ( 4579) covalent geometry : angle 0.48718 ( 6197) SS BOND : bond 0.00051 ( 1) SS BOND : angle 1.28963 ( 2) hydrogen bonds : bond 0.03654 ( 274) hydrogen bonds : angle 4.23801 ( 816) link_NAG-ASN : bond 0.00061 ( 1) link_NAG-ASN : angle 0.81990 ( 3) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1082 Ramachandran restraints generated. 541 Oldfield, 0 Emsley, 541 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1082 Ramachandran restraints generated. 541 Oldfield, 0 Emsley, 541 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 64 residues out of total 465 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 57 time to evaluate : 0.183 Fit side-chains revert: symmetry clash REVERT: A 292 ILE cc_start: 0.7936 (mm) cc_final: 0.7734 (mt) REVERT: A 321 ASN cc_start: 0.8131 (t0) cc_final: 0.7629 (t0) REVERT: A 427 ARG cc_start: 0.6811 (mtm180) cc_final: 0.6127 (mtm180) REVERT: A 494 ASP cc_start: 0.8642 (t70) cc_final: 0.8356 (t0) REVERT: A 577 LYS cc_start: 0.7846 (ttmm) cc_final: 0.7530 (tppt) outliers start: 7 outliers final: 6 residues processed: 63 average time/residue: 0.0607 time to fit residues: 5.2135 Evaluate side-chains 64 residues out of total 465 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 58 time to evaluate : 0.131 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 69 TYR Chi-restraints excluded: chain A residue 111 THR Chi-restraints excluded: chain A residue 358 ASP Chi-restraints excluded: chain A residue 426 TYR Chi-restraints excluded: chain A residue 528 VAL Chi-restraints excluded: chain A residue 596 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 54 random chunks: chunk 46 optimal weight: 1.9990 chunk 16 optimal weight: 2.9990 chunk 10 optimal weight: 0.8980 chunk 14 optimal weight: 0.8980 chunk 2 optimal weight: 0.1980 chunk 34 optimal weight: 0.9980 chunk 42 optimal weight: 0.7980 chunk 24 optimal weight: 0.9980 chunk 19 optimal weight: 3.9990 chunk 49 optimal weight: 1.9990 chunk 17 optimal weight: 0.5980 overall best weight: 0.6780 ------------------------------------------------------------------------------- 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 = 0.3297 r_free = 0.3297 target = 0.122274 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.2941 r_free = 0.2941 target = 0.094805 restraints weight = 5628.998| |-----------------------------------------------------------------------------| r_work (start): 0.2931 rms_B_bonded: 1.83 r_work: 0.2821 rms_B_bonded: 2.57 restraints_weight: 0.5000 r_work: 0.2684 rms_B_bonded: 4.18 restraints_weight: 0.2500 r_work (final): 0.2684 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7786 moved from start: 0.2223 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 4581 Z= 0.140 Angle : 0.500 6.991 6202 Z= 0.251 Chirality : 0.039 0.132 677 Planarity : 0.004 0.033 745 Dihedral : 5.271 38.703 698 Min Nonbonded Distance : 2.606 Molprobity Statistics. All-atom Clashscore : 6.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.40 % Favored : 97.60 % Rotamer: Outliers : 1.74 % Allowed : 13.04 % Favored : 85.22 % 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: 1.53 (0.36), residues: 541 helix: 1.91 (0.26), residues: 383 sheet: None (None), residues: 0 loop : -1.28 (0.45), residues: 158 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 66 TYR 0.022 0.001 TYR A 460 PHE 0.013 0.001 PHE A 474 TRP 0.013 0.001 TRP A 470 HIS 0.002 0.001 HIS A 161 Details of bonding type rmsd covalent geometry : bond 0.00333 ( 4579) covalent geometry : angle 0.49912 ( 6197) SS BOND : bond 0.00080 ( 1) SS BOND : angle 1.28332 ( 2) hydrogen bonds : bond 0.03747 ( 274) hydrogen bonds : angle 4.26959 ( 816) link_NAG-ASN : bond 0.00047 ( 1) link_NAG-ASN : angle 0.81812 ( 3) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1082 Ramachandran restraints generated. 541 Oldfield, 0 Emsley, 541 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1082 Ramachandran restraints generated. 541 Oldfield, 0 Emsley, 541 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 64 residues out of total 465 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 56 time to evaluate : 0.100 Fit side-chains revert: symmetry clash REVERT: A 292 ILE cc_start: 0.8093 (mm) cc_final: 0.7887 (mt) REVERT: A 321 ASN cc_start: 0.8178 (t0) cc_final: 0.7710 (t0) REVERT: A 427 ARG cc_start: 0.6900 (mtm180) cc_final: 0.6207 (mtm180) REVERT: A 494 ASP cc_start: 0.8648 (t70) cc_final: 0.8372 (t0) REVERT: A 577 LYS cc_start: 0.7947 (ttmm) cc_final: 0.7595 (tppt) outliers start: 8 outliers final: 7 residues processed: 63 average time/residue: 0.0531 time to fit residues: 4.5334 Evaluate side-chains 61 residues out of total 465 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 54 time to evaluate : 0.115 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 69 TYR Chi-restraints excluded: chain A residue 100 ILE Chi-restraints excluded: chain A residue 111 THR Chi-restraints excluded: chain A residue 358 ASP Chi-restraints excluded: chain A residue 447 VAL Chi-restraints excluded: chain A residue 514 VAL Chi-restraints excluded: chain A residue 528 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 54 random chunks: chunk 11 optimal weight: 0.9980 chunk 7 optimal weight: 0.3980 chunk 30 optimal weight: 4.9990 chunk 40 optimal weight: 0.5980 chunk 15 optimal weight: 0.3980 chunk 23 optimal weight: 0.3980 chunk 45 optimal weight: 0.6980 chunk 8 optimal weight: 0.9990 chunk 20 optimal weight: 0.5980 chunk 13 optimal weight: 0.9990 chunk 38 optimal weight: 0.6980 overall best weight: 0.4780 ------------------------------------------------------------------------------- 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 = 0.3317 r_free = 0.3317 target = 0.123606 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.2962 r_free = 0.2962 target = 0.096268 restraints weight = 5594.939| |-----------------------------------------------------------------------------| r_work (start): 0.2950 rms_B_bonded: 1.86 r_work: 0.2838 rms_B_bonded: 2.62 restraints_weight: 0.5000 r_work: 0.2699 rms_B_bonded: 4.27 restraints_weight: 0.2500 r_work (final): 0.2699 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7709 moved from start: 0.2351 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 4581 Z= 0.115 Angle : 0.484 6.428 6202 Z= 0.243 Chirality : 0.038 0.125 677 Planarity : 0.003 0.032 745 Dihedral : 5.143 38.579 698 Min Nonbonded Distance : 2.580 Molprobity Statistics. All-atom Clashscore : 5.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.22 % Favored : 97.78 % Rotamer: Outliers : 1.52 % Allowed : 13.26 % Favored : 85.22 % 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: 1.64 (0.36), residues: 541 helix: 2.01 (0.26), residues: 382 sheet: None (None), residues: 0 loop : -1.24 (0.45), residues: 159 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 66 TYR 0.020 0.001 TYR A 460 PHE 0.011 0.001 PHE A 404 TRP 0.013 0.001 TRP A 470 HIS 0.002 0.001 HIS A 161 Details of bonding type rmsd covalent geometry : bond 0.00267 ( 4579) covalent geometry : angle 0.48378 ( 6197) SS BOND : bond 0.00079 ( 1) SS BOND : angle 1.21540 ( 2) hydrogen bonds : bond 0.03603 ( 274) hydrogen bonds : angle 4.20999 ( 816) link_NAG-ASN : bond 0.00080 ( 1) link_NAG-ASN : angle 0.82918 ( 3) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1082 Ramachandran restraints generated. 541 Oldfield, 0 Emsley, 541 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1082 Ramachandran restraints generated. 541 Oldfield, 0 Emsley, 541 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 63 residues out of total 465 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 56 time to evaluate : 0.136 Fit side-chains revert: symmetry clash REVERT: A 321 ASN cc_start: 0.8150 (t0) cc_final: 0.7681 (t0) REVERT: A 427 ARG cc_start: 0.6867 (mtm180) cc_final: 0.6180 (mtm180) REVERT: A 429 GLU cc_start: 0.7289 (mt-10) cc_final: 0.6861 (tt0) REVERT: A 494 ASP cc_start: 0.8639 (t70) cc_final: 0.8340 (t0) REVERT: A 577 LYS cc_start: 0.7915 (ttmm) cc_final: 0.7602 (tppt) outliers start: 7 outliers final: 7 residues processed: 61 average time/residue: 0.0616 time to fit residues: 5.0632 Evaluate side-chains 61 residues out of total 465 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 54 time to evaluate : 0.159 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 69 TYR Chi-restraints excluded: chain A residue 100 ILE Chi-restraints excluded: chain A residue 111 THR Chi-restraints excluded: chain A residue 310 THR Chi-restraints excluded: chain A residue 447 VAL Chi-restraints excluded: chain A residue 514 VAL Chi-restraints excluded: chain A residue 528 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 54 random chunks: chunk 44 optimal weight: 1.9990 chunk 29 optimal weight: 0.6980 chunk 43 optimal weight: 0.5980 chunk 30 optimal weight: 0.9980 chunk 33 optimal weight: 0.7980 chunk 14 optimal weight: 0.3980 chunk 0 optimal weight: 10.0000 chunk 3 optimal weight: 0.6980 chunk 27 optimal weight: 0.7980 chunk 1 optimal weight: 0.1980 chunk 49 optimal weight: 0.7980 overall best weight: 0.5180 ------------------------------------------------------------------------------- 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 = 0.3309 r_free = 0.3309 target = 0.123160 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.2956 r_free = 0.2956 target = 0.095959 restraints weight = 5600.965| |-----------------------------------------------------------------------------| r_work (start): 0.2961 rms_B_bonded: 1.81 r_work: 0.2848 rms_B_bonded: 2.58 restraints_weight: 0.5000 r_work: 0.2710 rms_B_bonded: 4.20 restraints_weight: 0.2500 r_work (final): 0.2710 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7653 moved from start: 0.2388 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 4581 Z= 0.121 Angle : 0.486 6.264 6202 Z= 0.244 Chirality : 0.038 0.127 677 Planarity : 0.003 0.032 745 Dihedral : 5.156 38.497 698 Min Nonbonded Distance : 2.593 Molprobity Statistics. All-atom Clashscore : 5.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.03 % Favored : 97.97 % Rotamer: Outliers : 1.52 % Allowed : 13.48 % Favored : 85.00 % 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: 1.63 (0.36), residues: 541 helix: 1.97 (0.26), residues: 387 sheet: None (None), residues: 0 loop : -1.26 (0.46), residues: 154 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 66 TYR 0.020 0.001 TYR A 460 PHE 0.011 0.001 PHE A 474 TRP 0.013 0.001 TRP A 470 HIS 0.002 0.001 HIS A 161 Details of bonding type rmsd covalent geometry : bond 0.00286 ( 4579) covalent geometry : angle 0.48555 ( 6197) SS BOND : bond 0.00070 ( 1) SS BOND : angle 1.20349 ( 2) hydrogen bonds : bond 0.03601 ( 274) hydrogen bonds : angle 4.21830 ( 816) link_NAG-ASN : bond 0.00073 ( 1) link_NAG-ASN : angle 0.85233 ( 3) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1082 Ramachandran restraints generated. 541 Oldfield, 0 Emsley, 541 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1082 Ramachandran restraints generated. 541 Oldfield, 0 Emsley, 541 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 61 residues out of total 465 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 54 time to evaluate : 0.123 Fit side-chains revert: symmetry clash REVERT: A 321 ASN cc_start: 0.8132 (t0) cc_final: 0.7657 (t0) REVERT: A 427 ARG cc_start: 0.6826 (mtm180) cc_final: 0.6138 (mtm180) REVERT: A 429 GLU cc_start: 0.7255 (mt-10) cc_final: 0.6825 (tt0) REVERT: A 494 ASP cc_start: 0.8628 (t70) cc_final: 0.8337 (t0) REVERT: A 577 LYS cc_start: 0.7877 (ttmm) cc_final: 0.7556 (tppt) outliers start: 7 outliers final: 7 residues processed: 59 average time/residue: 0.0632 time to fit residues: 4.9344 Evaluate side-chains 60 residues out of total 465 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 53 time to evaluate : 0.159 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 69 TYR Chi-restraints excluded: chain A residue 100 ILE Chi-restraints excluded: chain A residue 111 THR Chi-restraints excluded: chain A residue 310 THR Chi-restraints excluded: chain A residue 447 VAL Chi-restraints excluded: chain A residue 514 VAL Chi-restraints excluded: chain A residue 528 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 54 random chunks: chunk 31 optimal weight: 0.9980 chunk 5 optimal weight: 1.9990 chunk 16 optimal weight: 0.2980 chunk 15 optimal weight: 0.5980 chunk 41 optimal weight: 0.8980 chunk 47 optimal weight: 0.9990 chunk 24 optimal weight: 0.5980 chunk 11 optimal weight: 1.9990 chunk 27 optimal weight: 0.8980 chunk 6 optimal weight: 1.9990 chunk 22 optimal weight: 0.6980 overall best weight: 0.6180 ------------------------------------------------------------------------------- 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 = 0.3286 r_free = 0.3286 target = 0.121524 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.2951 r_free = 0.2951 target = 0.095720 restraints weight = 5565.478| |-----------------------------------------------------------------------------| r_work (start): 0.2955 rms_B_bonded: 1.66 r_work: 0.2848 rms_B_bonded: 2.40 restraints_weight: 0.5000 r_work: 0.2712 rms_B_bonded: 3.94 restraints_weight: 0.2500 r_work (final): 0.2712 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7915 moved from start: 0.2356 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 4581 Z= 0.133 Angle : 0.495 6.200 6202 Z= 0.249 Chirality : 0.038 0.129 677 Planarity : 0.003 0.032 745 Dihedral : 5.289 38.253 698 Min Nonbonded Distance : 2.537 Molprobity Statistics. All-atom Clashscore : 5.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.22 % Favored : 97.78 % Rotamer: Outliers : 1.30 % Allowed : 13.91 % Favored : 84.78 % 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: 1.59 (0.36), residues: 541 helix: 1.94 (0.26), residues: 387 sheet: None (None), residues: 0 loop : -1.28 (0.46), residues: 154 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 66 TYR 0.021 0.001 TYR A 460 PHE 0.012 0.001 PHE A 474 TRP 0.014 0.001 TRP A 470 HIS 0.002 0.001 HIS A 161 Details of bonding type rmsd covalent geometry : bond 0.00316 ( 4579) covalent geometry : angle 0.49448 ( 6197) SS BOND : bond 0.00061 ( 1) SS BOND : angle 1.30392 ( 2) hydrogen bonds : bond 0.03699 ( 274) hydrogen bonds : angle 4.22690 ( 816) link_NAG-ASN : bond 0.00068 ( 1) link_NAG-ASN : angle 0.82985 ( 3) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1241.04 seconds wall clock time: 21 minutes 55.36 seconds (1315.36 seconds total)