Starting phenix.real_space_refine on Fri Jul 3 02:43:00 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9pym_72036/07_2026/9pym_72036_trim.cif Found real_map, /net/cci-nas-00/data/ceres_data/9pym_72036/07_2026/9pym_72036.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.98 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/9pym_72036/07_2026/9pym_72036_trim.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9pym_72036/07_2026/9pym_72036_trim.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9pym_72036/07_2026/9pym_72036.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9pym_72036/07_2026/9pym_72036.map" } resolution = 2.98 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= 0.008 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: 7 Type Number sf(0) Gaussians P 3 5.49 5 S 39 5.16 5 Na 1 4.78 5 C 3654 2.51 5 N 857 2.21 5 O 963 1.98 5 H 5627 0.53 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 3 residue(s): 0.01s 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: 11144 Number of models: 1 Model: "" Number of chains: 3 Chain: "A" Number of atoms: 9142 Number of conformers: 1 Conformer: "" Number of residues, atoms: 592, 9142 Classifications: {'peptide': 592} Link IDs: {'PCIS': 2, 'PTRANS': 31, 'TRANS': 558} Chain breaks: 2 Chain: "B" Number of atoms: 1909 Number of conformers: 1 Conformer: "" Number of residues, atoms: 125, 1909 Classifications: {'peptide': 125} Modifications used: {'NH3': 1} Link IDs: {'PTRANS': 2, 'TRANS': 122} Chain breaks: 1 Chain: "A" Number of atoms: 93 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 92 Ad-hoc single atom residues: {' NA': 1} Unusual residues: {'8X3': 1, 'PTY': 3} Classifications: {'undetermined': 4} Link IDs: {None: 3} Chain breaks: 1 Unresolved non-hydrogen bonds: 65 Unresolved non-hydrogen angles: 66 Unresolved non-hydrogen dihedrals: 64 Planarities with less than four sites: {'PTY:plan-2': 1} Unresolved non-hydrogen planarities: 1 Time building chain proxies: 2.18, per 1000 atoms: 0.20 Number of scatterers: 11144 At special positions: 0 Unit cell: (77.958, 97.128, 83.07, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 7 Type Number sf(0) S 39 16.00 P 3 15.00 Na 1 11.00 O 963 8.00 N 857 7.00 C 3654 6.00 H 5627 1.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=1, symmetry=0 Simple disulfide: pdb=" SG CYS B 411 " - pdb=" SG CYS B 484 " 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 Time building additional restraints: 1.32 Conformation dependent library (CDL) restraints added in 234.0 milliseconds 1414 Ramachandran restraints generated. 707 Oldfield, 0 Emsley, 707 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1306 Finding SS restraints... Secondary structure from input PDB file: 31 helices and 3 sheets defined 71.4% alpha, 5.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.25 Creating SS restraints... Processing helix chain 'A' and resid 29 through 36 removed outlier: 3.851A pdb=" N PHE A 36 " --> pdb=" O LEU A 32 " (cutoff:3.500A) Processing helix chain 'A' and resid 37 through 62 Processing helix chain 'A' and resid 74 through 97 removed outlier: 4.131A pdb=" N VAL A 91 " --> pdb=" O SER A 87 " (cutoff:3.500A) Proline residue: A 92 - end of helix Processing helix chain 'A' and resid 111 through 147 Processing helix chain 'A' and resid 160 through 162 No H-bonds generated for 'chain 'A' and resid 160 through 162' Processing helix chain 'A' and resid 163 through 188 Processing helix chain 'A' and resid 188 through 209 Proline residue: A 205 - end of helix Processing helix chain 'A' and resid 213 through 229 removed outlier: 3.569A pdb=" N VAL A 217 " --> pdb=" O ASP A 213 " (cutoff:3.500A) Processing helix chain 'A' and resid 231 through 247 Processing helix chain 'A' and resid 253 through 262 removed outlier: 3.888A pdb=" N GLN A 257 " --> pdb=" O ASP A 253 " (cutoff:3.500A) Processing helix chain 'A' and resid 266 through 268 No H-bonds generated for 'chain 'A' and resid 266 through 268' Processing helix chain 'A' and resid 269 through 283 removed outlier: 3.521A pdb=" N PHE A 273 " --> pdb=" O MET A 269 " (cutoff:3.500A) Processing helix chain 'A' and resid 286 through 299 Processing helix chain 'A' and resid 303 through 318 removed outlier: 3.603A pdb=" N ALA A 318 " --> pdb=" O MET A 314 " (cutoff:3.500A) Processing helix chain 'A' and resid 322 through 342 removed outlier: 3.552A pdb=" N THR A 326 " --> pdb=" O SER A 322 " (cutoff:3.500A) removed outlier: 4.923A pdb=" N LEU A 333 " --> pdb=" O ALA A 329 " (cutoff:3.500A) Proline residue: A 336 - end of helix Processing helix chain 'A' and resid 344 through 357 Processing helix chain 'A' and resid 357 through 362 removed outlier: 3.958A pdb=" N MET A 361 " --> pdb=" O ALA A 357 " (cutoff:3.500A) Processing helix chain 'A' and resid 365 through 375 Processing helix chain 'A' and resid 378 through 386 removed outlier: 4.008A pdb=" N MET A 384 " --> pdb=" O GLY A 380 " (cutoff:3.500A) Processing helix chain 'A' and resid 386 through 409 Processing helix chain 'A' and resid 418 through 429 Processing helix chain 'A' and resid 429 through 445 removed outlier: 3.946A pdb=" N VAL A 435 " --> pdb=" O TRP A 431 " (cutoff:3.500A) Proline residue: A 436 - end of helix Processing helix chain 'A' and resid 449 through 467 Processing helix chain 'A' and resid 475 through 508 removed outlier: 3.512A pdb=" N MET A 490 " --> pdb=" O GLY A 486 " (cutoff:3.500A) removed outlier: 3.793A pdb=" N VAL A 491 " --> pdb=" O THR A 487 " (cutoff:3.500A) removed outlier: 3.884A pdb=" N LEU A 494 " --> pdb=" O MET A 490 " (cutoff:3.500A) Processing helix chain 'A' and resid 509 through 522 removed outlier: 3.511A pdb=" N ALA A 517 " --> pdb=" O THR A 513 " (cutoff:3.500A) Processing helix chain 'A' and resid 524 through 541 removed outlier: 3.582A pdb=" N THR A 541 " --> pdb=" O LEU A 537 " (cutoff:3.500A) Processing helix chain 'A' and resid 544 through 563 Proline residue: A 554 - end of helix Proline residue: A 558 - end of helix Processing helix chain 'A' and resid 566 through 580 Processing helix chain 'A' and resid 581 through 584 removed outlier: 3.643A pdb=" N THR A 584 " --> pdb=" O GLY A 581 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 581 through 584' Processing helix chain 'A' and resid 590 through 599 Processing helix chain 'A' and resid 601 through 626 removed outlier: 4.123A pdb=" N LYS A 607 " --> pdb=" O GLU A 603 " (cutoff:3.500A) removed outlier: 3.606A pdb=" N VAL A 608 " --> pdb=" O GLN A 604 " (cutoff:3.500A) Proline residue: A 611 - end of helix removed outlier: 3.526A pdb=" N VAL A 619 " --> pdb=" O LEU A 615 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'B' and resid 3 through 7 removed outlier: 3.697A pdb=" N SER B 414 " --> pdb=" O SER B 3 " (cutoff:3.500A) removed outlier: 3.596A pdb=" N ALA B 412 " --> pdb=" O GLN B 5 " (cutoff:3.500A) removed outlier: 3.582A pdb=" N THR B 457 " --> pdb=" O GLN B 470 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'B' and resid 446 through 448 removed outlier: 3.976A pdb=" N VAL B 481 " --> pdb=" O GLN B 428 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 493 through 494 removed outlier: 3.500A pdb=" N THR B 493 " --> pdb=" O TYR B 500 " (cutoff:3.500A) 379 hydrogen bonds defined for protein. 1119 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: 2.39 Time building geometry restraints manager: 1.71 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.84 - 1.03: 5619 1.03 - 1.23: 20 1.23 - 1.42: 2261 1.42 - 1.61: 3294 1.61 - 1.81: 73 Bond restraints: 11267 Sorted by residual: bond pdb=" CB CYS B 484 " pdb=" SG CYS B 484 " ideal model delta sigma weight residual 1.808 1.766 0.042 3.30e-02 9.18e+02 1.58e+00 bond pdb=" CB CYS B 411 " pdb=" SG CYS B 411 " ideal model delta sigma weight residual 1.808 1.773 0.035 3.30e-02 9.18e+02 1.14e+00 bond pdb=" CB PRO A 630 " pdb=" CG PRO A 630 " ideal model delta sigma weight residual 1.492 1.440 0.052 5.00e-02 4.00e+02 1.08e+00 bond pdb=" CG1 ILE B 417 " pdb=" CD1 ILE B 417 " ideal model delta sigma weight residual 1.513 1.476 0.037 3.90e-02 6.57e+02 9.02e-01 bond pdb=" CD2 TYR A 162 " pdb=" CE2 TYR A 162 " ideal model delta sigma weight residual 1.382 1.355 0.027 3.00e-02 1.11e+03 7.84e-01 ... (remaining 11262 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.19: 19485 1.19 - 2.38: 859 2.38 - 3.57: 36 3.57 - 4.75: 18 4.75 - 5.94: 2 Bond angle restraints: 20400 Sorted by residual: angle pdb=" CA ILE A 629 " pdb=" C ILE A 629 " pdb=" N PRO A 630 " ideal model delta sigma weight residual 118.88 121.80 -2.92 1.54e+00 4.22e-01 3.58e+00 angle pdb=" C VAL A 510 " pdb=" CA VAL A 510 " pdb=" CB VAL A 510 " ideal model delta sigma weight residual 114.35 112.40 1.95 1.06e+00 8.90e-01 3.37e+00 angle pdb=" N VAL A 468 " pdb=" CA VAL A 468 " pdb=" C VAL A 468 " ideal model delta sigma weight residual 109.34 112.51 -3.17 2.08e+00 2.31e-01 2.33e+00 angle pdb=" CA VAL A 468 " pdb=" C VAL A 468 " pdb=" N HIS A 469 " ideal model delta sigma weight residual 116.60 118.80 -2.20 1.45e+00 4.76e-01 2.31e+00 angle pdb=" N ILE A 629 " pdb=" CA ILE A 629 " pdb=" C ILE A 629 " ideal model delta sigma weight residual 108.88 112.07 -3.19 2.16e+00 2.14e-01 2.18e+00 ... (remaining 20395 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 26.91: 5033 26.91 - 53.81: 243 53.81 - 80.72: 47 80.72 - 107.62: 3 107.62 - 134.53: 1 Dihedral angle restraints: 5327 sinusoidal: 2877 harmonic: 2450 Sorted by residual: dihedral pdb=" N1 PTY A 705 " pdb=" C2 PTY A 705 " pdb=" C3 PTY A 705 " pdb=" O11 PTY A 705 " ideal model delta sinusoidal sigma weight residual 65.33 -160.14 -134.53 1 3.00e+01 1.11e-03 1.81e+01 dihedral pdb=" CA TYR B 504 " pdb=" C TYR B 504 " pdb=" N TRP B 505 " pdb=" CA TRP B 505 " ideal model delta harmonic sigma weight residual 180.00 -162.78 -17.22 0 5.00e+00 4.00e-02 1.19e+01 dihedral pdb=" CB GLU A 428 " pdb=" CG GLU A 428 " pdb=" CD GLU A 428 " pdb=" OE1 GLU A 428 " ideal model delta sinusoidal sigma weight residual 0.00 86.10 -86.10 1 3.00e+01 1.11e-03 9.94e+00 ... (remaining 5324 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.028: 530 0.028 - 0.055: 242 0.055 - 0.083: 93 0.083 - 0.110: 32 0.110 - 0.138: 15 Chirality restraints: 912 Sorted by residual: chirality pdb=" CA VAL A 230 " pdb=" N VAL A 230 " pdb=" C VAL A 230 " pdb=" CB VAL A 230 " both_signs ideal model delta sigma weight residual False 2.44 2.58 -0.14 2.00e-01 2.50e+01 4.73e-01 chirality pdb=" CA PRO A 450 " pdb=" N PRO A 450 " pdb=" C PRO A 450 " pdb=" CB PRO A 450 " both_signs ideal model delta sigma weight residual False 2.72 2.59 0.13 2.00e-01 2.50e+01 4.17e-01 chirality pdb=" CA PRO A 367 " pdb=" N PRO A 367 " pdb=" C PRO A 367 " pdb=" CB PRO A 367 " both_signs ideal model delta sigma weight residual False 2.72 2.59 0.13 2.00e-01 2.50e+01 4.15e-01 ... (remaining 909 not shown) Planarity restraints: 1610 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C THR A 449 " 0.034 5.00e-02 4.00e+02 5.11e-02 4.18e+00 pdb=" N PRO A 450 " -0.088 5.00e-02 4.00e+02 pdb=" CA PRO A 450 " 0.026 5.00e-02 4.00e+02 pdb=" CD PRO A 450 " 0.029 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C LEU A 557 " -0.022 5.00e-02 4.00e+02 3.37e-02 1.82e+00 pdb=" N PRO A 558 " 0.058 5.00e-02 4.00e+02 pdb=" CA PRO A 558 " -0.017 5.00e-02 4.00e+02 pdb=" CD PRO A 558 " -0.019 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C GLY A 323 " 0.022 5.00e-02 4.00e+02 3.35e-02 1.80e+00 pdb=" N PRO A 324 " -0.058 5.00e-02 4.00e+02 pdb=" CA PRO A 324 " 0.017 5.00e-02 4.00e+02 pdb=" CD PRO A 324 " 0.019 5.00e-02 4.00e+02 ... (remaining 1607 not shown) Histogram of nonbonded interaction distances: 1.58 - 2.18: 552 2.18 - 2.79: 22910 2.79 - 3.39: 31979 3.39 - 4.00: 41178 4.00 - 4.60: 65160 Nonbonded interactions: 161779 Sorted by model distance: nonbonded pdb=" O GLN A 257 " pdb=" HG1 THR A 261 " model vdw 1.580 2.450 nonbonded pdb=" O ILE A 49 " pdb=" HG1 THR A 53 " model vdw 1.594 2.450 nonbonded pdb=" OD1 ASN A 418 " pdb=" H LYS A 420 " model vdw 1.597 2.450 nonbonded pdb=" HG SER A 322 " pdb=" O4 8X3 A 702 " model vdw 1.631 2.450 nonbonded pdb=" OE1 GLU A 340 " pdb="HH11 ARG A 341 " model vdw 1.635 2.450 ... (remaining 161774 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 5.750 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: 0.090 Extract box with map and model: 0.250 Check model and map are aligned: 0.030 Set scattering table: 0.030 Process input model: 12.450 Find NCS groups from input model: 0.020 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:6.450 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 25.090 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8213 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 : 0.005 0.052 5641 Z= 0.231 Angle : 0.529 5.943 7680 Z= 0.284 Chirality : 0.040 0.138 912 Planarity : 0.004 0.051 933 Dihedral : 13.857 134.526 1986 Min Nonbonded Distance : 1.945 Molprobity Statistics. All-atom Clashscore : 7.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.97 % Favored : 97.03 % Rotamer: Outliers : 0.00 % Allowed : 1.59 % Favored : 98.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.71 % 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: -0.21 (0.31), residues: 707 helix: 0.37 (0.23), residues: 465 sheet: -1.59 (0.69), residues: 50 loop : -0.69 (0.44), residues: 192 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 489 TYR 0.011 0.001 TYR A 478 PHE 0.016 0.001 PHE A 126 TRP 0.012 0.001 TRP B 420 HIS 0.003 0.001 HIS A 424 Details of bonding type rmsd/Z covalent geometry : bond 0.00536 / 0.23 ( 5640) covalent geometry : angle 0.52704 / 0.28 ( 7678) SS BOND : bond 0.00386 / 0.20 ( 1) SS BOND : angle 2.90885 / 1.62 ( 2) hydrogen bonds : bond 0.21607 / 14.53 ( 379) hydrogen bonds : angle 8.44916 / 6.19 ( 1119) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1414 Ramachandran restraints generated. 707 Oldfield, 0 Emsley, 707 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1414 Ramachandran restraints generated. 707 Oldfield, 0 Emsley, 707 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 70 residues out of total 566 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 70 time to evaluate : 0.292 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 142 LYS cc_start: 0.8191 (ttpt) cc_final: 0.7899 (mtpm) REVERT: A 297 MET cc_start: 0.8056 (mtp) cc_final: 0.7771 (mtm) outliers start: 0 outliers final: 0 residues processed: 70 average time/residue: 0.8630 time to fit residues: 64.4609 Evaluate side-chains 49 residues out of total 566 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 49 time to evaluate : 0.295 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 71 random chunks: chunk 49 optimal weight: 0.9980 chunk 53 optimal weight: 0.8980 chunk 5 optimal weight: 0.6980 chunk 33 optimal weight: 1.9990 chunk 65 optimal weight: 2.9990 chunk 62 optimal weight: 1.9990 chunk 51 optimal weight: 1.9990 chunk 38 optimal weight: 4.9990 chunk 61 optimal weight: 1.9990 chunk 45 optimal weight: 1.9990 chunk 27 optimal weight: 2.9990 overall best weight: 1.3184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 510 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3825 r_free = 0.3825 target = 0.109465 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3601 r_free = 0.3601 target = 0.095793 restraints weight = 32784.649| |-----------------------------------------------------------------------------| r_work (start): 0.3601 rms_B_bonded: 2.36 r_work: 0.3493 rms_B_bonded: 2.74 restraints_weight: 0.5000 r_work: 0.3393 rms_B_bonded: 4.57 restraints_weight: 0.2500 r_work (final): 0.3393 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8157 moved from start: 0.1281 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 5641 Z= 0.176 Angle : 0.561 5.786 7680 Z= 0.305 Chirality : 0.039 0.142 912 Planarity : 0.005 0.047 933 Dihedral : 8.839 116.111 828 Min Nonbonded Distance : 2.337 Molprobity Statistics. All-atom Clashscore : 6.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.98 % Favored : 98.02 % Rotamer: Outliers : 1.06 % Allowed : 8.48 % Favored : 90.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.71 % 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: 0.82 (0.31), residues: 707 helix: 1.28 (0.23), residues: 472 sheet: -0.93 (0.76), residues: 50 loop : -0.83 (0.46), residues: 185 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 289 TYR 0.017 0.001 TYR A 478 PHE 0.020 0.001 PHE A 126 TRP 0.006 0.001 TRP B 487 HIS 0.001 0.001 HIS A 569 Details of bonding type rmsd/Z covalent geometry : bond 0.00387 / 0.18 ( 5640) covalent geometry : angle 0.56062 / 0.30 ( 7678) SS BOND : bond 0.00188 / 0.10 ( 1) SS BOND : angle 1.44892 / 0.83 ( 2) hydrogen bonds : bond 0.06000 / 3.93 ( 379) hydrogen bonds : angle 5.28115 / 3.98 ( 1119) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1414 Ramachandran restraints generated. 707 Oldfield, 0 Emsley, 707 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1414 Ramachandran restraints generated. 707 Oldfield, 0 Emsley, 707 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 62 residues out of total 566 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 56 time to evaluate : 0.288 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 76 GLU cc_start: 0.8412 (OUTLIER) cc_final: 0.8087 (tm-30) REVERT: A 142 LYS cc_start: 0.7989 (ttpt) cc_final: 0.7717 (mtpm) REVERT: A 297 MET cc_start: 0.8066 (mtp) cc_final: 0.7719 (mtm) REVERT: A 610 LEU cc_start: 0.8213 (OUTLIER) cc_final: 0.7982 (mp) REVERT: A 615 LEU cc_start: 0.8727 (OUTLIER) cc_final: 0.8436 (mp) outliers start: 6 outliers final: 1 residues processed: 59 average time/residue: 0.8191 time to fit residues: 51.5632 Evaluate side-chains 56 residues out of total 566 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 52 time to evaluate : 0.307 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 61 ILE Chi-restraints excluded: chain A residue 76 GLU Chi-restraints excluded: chain A residue 610 LEU Chi-restraints excluded: chain A residue 615 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 71 random chunks: chunk 41 optimal weight: 2.9990 chunk 37 optimal weight: 4.9990 chunk 40 optimal weight: 0.6980 chunk 70 optimal weight: 0.8980 chunk 14 optimal weight: 2.9990 chunk 30 optimal weight: 2.9990 chunk 24 optimal weight: 4.9990 chunk 51 optimal weight: 0.5980 chunk 52 optimal weight: 2.9990 chunk 18 optimal weight: 2.9990 chunk 9 optimal weight: 2.9990 overall best weight: 1.6384 ------------------------------------------------------------------------------- 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 = 0.3660 r_free = 0.3660 target = 0.103485 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3449 r_free = 0.3449 target = 0.090596 restraints weight = 32882.984| |-----------------------------------------------------------------------------| r_work (start): 0.3446 rms_B_bonded: 2.34 r_work: 0.3341 rms_B_bonded: 2.78 restraints_weight: 0.5000 r_work: 0.3225 rms_B_bonded: 4.68 restraints_weight: 0.2500 r_work (final): 0.3225 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8103 moved from start: 0.1599 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.046 5641 Z= 0.186 Angle : 0.539 5.903 7680 Z= 0.289 Chirality : 0.039 0.142 912 Planarity : 0.005 0.049 933 Dihedral : 8.500 94.524 828 Min Nonbonded Distance : 2.417 Molprobity Statistics. All-atom Clashscore : 7.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.26 % Favored : 97.74 % Rotamer: Outliers : 1.77 % Allowed : 9.54 % Favored : 88.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.71 % 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: 0.80 (0.32), residues: 707 helix: 1.32 (0.23), residues: 474 sheet: -1.10 (0.75), residues: 50 loop : -0.95 (0.45), residues: 183 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG A 341 TYR 0.015 0.001 TYR A 478 PHE 0.020 0.001 PHE A 126 TRP 0.006 0.001 TRP B 487 HIS 0.001 0.001 HIS A 424 Details of bonding type rmsd/Z covalent geometry : bond 0.00425 / 0.19 ( 5640) covalent geometry : angle 0.53890 / 0.29 ( 7678) SS BOND : bond 0.00123 / 0.06 ( 1) SS BOND : angle 1.27935 / 0.72 ( 2) hydrogen bonds : bond 0.05202 / 3.39 ( 379) hydrogen bonds : angle 4.94550 / 3.74 ( 1119) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1414 Ramachandran restraints generated. 707 Oldfield, 0 Emsley, 707 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1414 Ramachandran restraints generated. 707 Oldfield, 0 Emsley, 707 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 61 residues out of total 566 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 51 time to evaluate : 0.308 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 76 GLU cc_start: 0.8452 (OUTLIER) cc_final: 0.8014 (tm-30) REVERT: A 142 LYS cc_start: 0.7906 (ttpt) cc_final: 0.7573 (mtpm) REVERT: A 615 LEU cc_start: 0.8610 (OUTLIER) cc_final: 0.8358 (mp) outliers start: 10 outliers final: 3 residues processed: 58 average time/residue: 0.7386 time to fit residues: 46.0909 Evaluate side-chains 54 residues out of total 566 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 49 time to evaluate : 0.300 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 61 ILE Chi-restraints excluded: chain A residue 76 GLU Chi-restraints excluded: chain A residue 426 VAL Chi-restraints excluded: chain A residue 538 ILE Chi-restraints excluded: chain A residue 615 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 71 random chunks: chunk 7 optimal weight: 0.0980 chunk 45 optimal weight: 1.9990 chunk 63 optimal weight: 0.9980 chunk 39 optimal weight: 1.9990 chunk 65 optimal weight: 0.6980 chunk 35 optimal weight: 0.9980 chunk 30 optimal weight: 1.9990 chunk 61 optimal weight: 0.9990 chunk 18 optimal weight: 2.9990 chunk 9 optimal weight: 2.9990 chunk 32 optimal weight: 0.1980 overall best weight: 0.5980 ------------------------------------------------------------------------------- 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 = 0.3694 r_free = 0.3694 target = 0.105493 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3482 r_free = 0.3482 target = 0.092464 restraints weight = 32481.063| |-----------------------------------------------------------------------------| r_work (start): 0.3492 rms_B_bonded: 2.38 r_work: 0.3395 rms_B_bonded: 2.79 restraints_weight: 0.5000 r_work: 0.3287 rms_B_bonded: 4.66 restraints_weight: 0.2500 r_work (final): 0.3287 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8064 moved from start: 0.1862 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 5641 Z= 0.117 Angle : 0.500 5.739 7680 Z= 0.263 Chirality : 0.038 0.141 912 Planarity : 0.004 0.048 933 Dihedral : 7.873 62.736 828 Min Nonbonded Distance : 2.493 Molprobity Statistics. All-atom Clashscore : 5.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.70 % Favored : 98.30 % Rotamer: Outliers : 1.06 % Allowed : 10.78 % Favored : 88.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.71 % 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: 1.17 (0.32), residues: 707 helix: 1.63 (0.24), residues: 474 sheet: -1.03 (0.75), residues: 50 loop : -0.90 (0.45), residues: 183 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 341 TYR 0.012 0.001 TYR A 478 PHE 0.015 0.001 PHE A 126 TRP 0.005 0.001 TRP B 487 HIS 0.001 0.000 HIS A 469 Details of bonding type rmsd/Z covalent geometry : bond 0.00250 / 0.12 ( 5640) covalent geometry : angle 0.50017 / 0.26 ( 7678) SS BOND : bond 0.00110 / 0.06 ( 1) SS BOND : angle 0.85163 / 0.47 ( 2) hydrogen bonds : bond 0.04446 / 2.91 ( 379) hydrogen bonds : angle 4.61081 / 3.49 ( 1119) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1414 Ramachandran restraints generated. 707 Oldfield, 0 Emsley, 707 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1414 Ramachandran restraints generated. 707 Oldfield, 0 Emsley, 707 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 60 residues out of total 566 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 54 time to evaluate : 0.296 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 76 GLU cc_start: 0.8439 (tt0) cc_final: 0.8098 (tm-30) REVERT: A 142 LYS cc_start: 0.7883 (ttpt) cc_final: 0.7554 (mtpm) REVERT: A 615 LEU cc_start: 0.8568 (OUTLIER) cc_final: 0.8331 (mp) outliers start: 6 outliers final: 2 residues processed: 57 average time/residue: 0.7693 time to fit residues: 46.9874 Evaluate side-chains 54 residues out of total 566 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 51 time to evaluate : 0.243 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 538 ILE Chi-restraints excluded: chain A residue 542 PHE Chi-restraints excluded: chain A residue 615 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 71 random chunks: chunk 1 optimal weight: 0.7980 chunk 37 optimal weight: 0.8980 chunk 64 optimal weight: 2.9990 chunk 52 optimal weight: 1.9990 chunk 17 optimal weight: 0.0870 chunk 19 optimal weight: 2.9990 chunk 12 optimal weight: 0.9980 chunk 70 optimal weight: 0.5980 chunk 3 optimal weight: 3.9990 chunk 32 optimal weight: 1.9990 chunk 40 optimal weight: 0.9990 overall best weight: 0.6758 ------------------------------------------------------------------------------- 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 = 0.3698 r_free = 0.3698 target = 0.105672 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3491 r_free = 0.3491 target = 0.092798 restraints weight = 32324.482| |-----------------------------------------------------------------------------| r_work (start): 0.3500 rms_B_bonded: 2.35 r_work: 0.3401 rms_B_bonded: 2.78 restraints_weight: 0.5000 r_work: 0.3291 rms_B_bonded: 4.65 restraints_weight: 0.2500 r_work (final): 0.3291 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8056 moved from start: 0.1980 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 5641 Z= 0.118 Angle : 0.498 5.720 7680 Z= 0.260 Chirality : 0.038 0.141 912 Planarity : 0.004 0.050 933 Dihedral : 7.450 57.614 828 Min Nonbonded Distance : 2.477 Molprobity Statistics. All-atom Clashscore : 5.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.56 % Favored : 98.44 % Rotamer: Outliers : 0.88 % Allowed : 12.01 % Favored : 87.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.71 % 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: 1.34 (0.32), residues: 707 helix: 1.77 (0.24), residues: 473 sheet: -1.05 (0.74), residues: 50 loop : -0.83 (0.45), residues: 184 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG A 288 TYR 0.012 0.001 TYR A 478 PHE 0.013 0.001 PHE A 126 TRP 0.005 0.001 TRP A 85 HIS 0.001 0.000 HIS A 469 Details of bonding type rmsd/Z covalent geometry : bond 0.00260 / 0.12 ( 5640) covalent geometry : angle 0.49665 / 0.26 ( 7678) SS BOND : bond 0.00403 / 0.21 ( 1) SS BOND : angle 2.11446 / 1.19 ( 2) hydrogen bonds : bond 0.04224 / 2.77 ( 379) hydrogen bonds : angle 4.50330 / 3.41 ( 1119) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1414 Ramachandran restraints generated. 707 Oldfield, 0 Emsley, 707 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1414 Ramachandran restraints generated. 707 Oldfield, 0 Emsley, 707 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 59 residues out of total 566 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 54 time to evaluate : 0.274 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 76 GLU cc_start: 0.8434 (tt0) cc_final: 0.8088 (tm-30) REVERT: A 142 LYS cc_start: 0.7876 (ttpt) cc_final: 0.7538 (mtpm) REVERT: A 434 MET cc_start: 0.7404 (tmm) cc_final: 0.7116 (tmm) REVERT: A 615 LEU cc_start: 0.8547 (OUTLIER) cc_final: 0.8309 (mp) outliers start: 5 outliers final: 2 residues processed: 56 average time/residue: 0.7565 time to fit residues: 45.3329 Evaluate side-chains 54 residues out of total 566 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 51 time to evaluate : 0.226 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 538 ILE Chi-restraints excluded: chain A residue 542 PHE Chi-restraints excluded: chain A residue 615 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 71 random chunks: chunk 47 optimal weight: 2.9990 chunk 66 optimal weight: 3.9990 chunk 3 optimal weight: 4.9990 chunk 40 optimal weight: 0.3980 chunk 15 optimal weight: 0.9980 chunk 27 optimal weight: 2.9990 chunk 22 optimal weight: 2.9990 chunk 20 optimal weight: 2.9990 chunk 11 optimal weight: 1.9990 chunk 41 optimal weight: 1.9990 chunk 51 optimal weight: 0.5980 overall best weight: 1.1984 ------------------------------------------------------------------------------- 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 = 0.3686 r_free = 0.3686 target = 0.104939 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3475 r_free = 0.3475 target = 0.092001 restraints weight = 32884.908| |-----------------------------------------------------------------------------| r_work (start): 0.3487 rms_B_bonded: 2.37 r_work: 0.3389 rms_B_bonded: 2.79 restraints_weight: 0.5000 r_work: 0.3281 rms_B_bonded: 4.67 restraints_weight: 0.2500 r_work (final): 0.3281 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8072 moved from start: 0.2016 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 5641 Z= 0.149 Angle : 0.515 5.780 7680 Z= 0.269 Chirality : 0.038 0.142 912 Planarity : 0.004 0.053 933 Dihedral : 7.293 56.320 828 Min Nonbonded Distance : 2.463 Molprobity Statistics. All-atom Clashscore : 5.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.84 % Favored : 98.16 % Rotamer: Outliers : 1.41 % Allowed : 11.31 % Favored : 87.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.71 % 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: 1.26 (0.32), residues: 707 helix: 1.73 (0.24), residues: 474 sheet: -1.05 (0.74), residues: 50 loop : -0.95 (0.45), residues: 183 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG A 288 TYR 0.014 0.001 TYR A 478 PHE 0.014 0.001 PHE A 126 TRP 0.008 0.001 TRP A 85 HIS 0.001 0.000 HIS A 469 Details of bonding type rmsd/Z covalent geometry : bond 0.00341 / 0.15 ( 5640) covalent geometry : angle 0.51404 / 0.27 ( 7678) SS BOND : bond 0.00191 / 0.10 ( 1) SS BOND : angle 2.11499 / 1.20 ( 2) hydrogen bonds : bond 0.04233 / 2.77 ( 379) hydrogen bonds : angle 4.49106 / 3.40 ( 1119) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1414 Ramachandran restraints generated. 707 Oldfield, 0 Emsley, 707 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1414 Ramachandran restraints generated. 707 Oldfield, 0 Emsley, 707 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 58 residues out of total 566 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 50 time to evaluate : 0.299 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 76 GLU cc_start: 0.8446 (tt0) cc_final: 0.8097 (tm-30) REVERT: A 142 LYS cc_start: 0.7866 (ttpt) cc_final: 0.7523 (mtpm) REVERT: A 615 LEU cc_start: 0.8564 (OUTLIER) cc_final: 0.8337 (mp) outliers start: 8 outliers final: 5 residues processed: 55 average time/residue: 0.7639 time to fit residues: 44.8099 Evaluate side-chains 55 residues out of total 566 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 49 time to evaluate : 0.273 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 143 MET Chi-restraints excluded: chain A residue 528 ILE Chi-restraints excluded: chain A residue 538 ILE Chi-restraints excluded: chain A residue 542 PHE Chi-restraints excluded: chain A residue 610 LEU Chi-restraints excluded: chain A residue 615 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 71 random chunks: chunk 10 optimal weight: 0.7980 chunk 54 optimal weight: 0.9990 chunk 68 optimal weight: 1.9990 chunk 9 optimal weight: 1.9990 chunk 35 optimal weight: 0.6980 chunk 60 optimal weight: 3.9990 chunk 40 optimal weight: 2.9990 chunk 18 optimal weight: 2.9990 chunk 52 optimal weight: 1.9990 chunk 65 optimal weight: 1.9990 chunk 29 optimal weight: 2.9990 overall best weight: 1.2986 ------------------------------------------------------------------------------- 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 = 0.3679 r_free = 0.3679 target = 0.104571 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 25)----------------| | r_work = 0.3467 r_free = 0.3467 target = 0.091567 restraints weight = 32430.294| |-----------------------------------------------------------------------------| r_work (start): 0.3484 rms_B_bonded: 2.36 r_work: 0.3387 rms_B_bonded: 2.77 restraints_weight: 0.5000 r_work: 0.3279 rms_B_bonded: 4.63 restraints_weight: 0.2500 r_work (final): 0.3279 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8072 moved from start: 0.2032 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 5641 Z= 0.154 Angle : 0.519 6.394 7680 Z= 0.272 Chirality : 0.038 0.141 912 Planarity : 0.005 0.053 933 Dihedral : 7.193 57.485 828 Min Nonbonded Distance : 2.453 Molprobity Statistics. All-atom Clashscore : 5.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.84 % Favored : 98.16 % Rotamer: Outliers : 1.24 % Allowed : 11.48 % Favored : 87.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.71 % 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: 1.22 (0.32), residues: 707 helix: 1.70 (0.24), residues: 474 sheet: -1.11 (0.74), residues: 50 loop : -0.92 (0.45), residues: 183 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG A 288 TYR 0.014 0.001 TYR A 478 PHE 0.014 0.001 PHE A 126 TRP 0.009 0.001 TRP A 85 HIS 0.001 0.000 HIS A 469 Details of bonding type rmsd/Z covalent geometry : bond 0.00353 / 0.15 ( 5640) covalent geometry : angle 0.51854 / 0.27 ( 7678) SS BOND : bond 0.00195 / 0.10 ( 1) SS BOND : angle 1.73866 / 0.98 ( 2) hydrogen bonds : bond 0.04228 / 2.76 ( 379) hydrogen bonds : angle 4.48010 / 3.38 ( 1119) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1414 Ramachandran restraints generated. 707 Oldfield, 0 Emsley, 707 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1414 Ramachandran restraints generated. 707 Oldfield, 0 Emsley, 707 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 56 residues out of total 566 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 49 time to evaluate : 0.304 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 76 GLU cc_start: 0.8459 (tt0) cc_final: 0.8104 (tm-30) REVERT: A 142 LYS cc_start: 0.7825 (ttpt) cc_final: 0.7525 (mtpm) REVERT: A 438 ILE cc_start: 0.7799 (OUTLIER) cc_final: 0.7445 (mp) REVERT: A 615 LEU cc_start: 0.8558 (OUTLIER) cc_final: 0.8325 (mp) outliers start: 7 outliers final: 5 residues processed: 53 average time/residue: 0.7909 time to fit residues: 44.7472 Evaluate side-chains 56 residues out of total 566 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 49 time to evaluate : 0.284 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 143 MET Chi-restraints excluded: chain A residue 289 ARG Chi-restraints excluded: chain A residue 438 ILE Chi-restraints excluded: chain A residue 538 ILE Chi-restraints excluded: chain A residue 542 PHE Chi-restraints excluded: chain A residue 610 LEU Chi-restraints excluded: chain A residue 615 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 71 random chunks: chunk 11 optimal weight: 1.9990 chunk 24 optimal weight: 4.9990 chunk 35 optimal weight: 0.9990 chunk 66 optimal weight: 3.9990 chunk 48 optimal weight: 0.8980 chunk 0 optimal weight: 5.9990 chunk 55 optimal weight: 2.9990 chunk 32 optimal weight: 0.9990 chunk 28 optimal weight: 0.7980 chunk 4 optimal weight: 1.9990 chunk 16 optimal weight: 4.9990 overall best weight: 1.1386 ------------------------------------------------------------------------------- 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 = 0.3684 r_free = 0.3684 target = 0.104843 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3476 r_free = 0.3476 target = 0.092037 restraints weight = 32548.922| |-----------------------------------------------------------------------------| r_work (start): 0.3481 rms_B_bonded: 2.29 r_work: 0.3385 rms_B_bonded: 2.70 restraints_weight: 0.5000 r_work: 0.3277 rms_B_bonded: 4.53 restraints_weight: 0.2500 r_work (final): 0.3277 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8028 moved from start: 0.2097 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 5641 Z= 0.142 Angle : 0.510 5.998 7680 Z= 0.266 Chirality : 0.038 0.145 912 Planarity : 0.004 0.054 933 Dihedral : 7.105 59.964 828 Min Nonbonded Distance : 2.448 Molprobity Statistics. All-atom Clashscore : 6.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.98 % Favored : 98.02 % Rotamer: Outliers : 1.24 % Allowed : 11.66 % Favored : 87.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.71 % 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 (0.32), residues: 707 helix: 1.73 (0.24), residues: 474 sheet: -1.08 (0.74), residues: 50 loop : -0.91 (0.45), residues: 183 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG A 288 TYR 0.013 0.001 TYR A 478 PHE 0.012 0.001 PHE A 126 TRP 0.009 0.001 TRP A 85 HIS 0.001 0.000 HIS A 469 Details of bonding type rmsd/Z covalent geometry : bond 0.00324 / 0.14 ( 5640) covalent geometry : angle 0.50894 / 0.27 ( 7678) SS BOND : bond 0.00168 / 0.09 ( 1) SS BOND : angle 1.56532 / 0.88 ( 2) hydrogen bonds : bond 0.04144 / 2.71 ( 379) hydrogen bonds : angle 4.44339 / 3.36 ( 1119) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1414 Ramachandran restraints generated. 707 Oldfield, 0 Emsley, 707 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1414 Ramachandran restraints generated. 707 Oldfield, 0 Emsley, 707 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 56 residues out of total 566 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 49 time to evaluate : 0.272 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 76 GLU cc_start: 0.8437 (tt0) cc_final: 0.8043 (tm-30) REVERT: A 142 LYS cc_start: 0.7761 (ttpt) cc_final: 0.7458 (mtpm) REVERT: A 615 LEU cc_start: 0.8516 (OUTLIER) cc_final: 0.8292 (mp) outliers start: 7 outliers final: 4 residues processed: 53 average time/residue: 0.8052 time to fit residues: 45.4871 Evaluate side-chains 54 residues out of total 566 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 49 time to evaluate : 0.209 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 143 MET Chi-restraints excluded: chain A residue 289 ARG Chi-restraints excluded: chain A residue 538 ILE Chi-restraints excluded: chain A residue 542 PHE Chi-restraints excluded: chain A residue 615 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 71 random chunks: chunk 4 optimal weight: 1.9990 chunk 27 optimal weight: 2.9990 chunk 23 optimal weight: 0.9980 chunk 25 optimal weight: 3.9990 chunk 46 optimal weight: 1.9990 chunk 15 optimal weight: 0.7980 chunk 37 optimal weight: 3.9990 chunk 33 optimal weight: 1.9990 chunk 1 optimal weight: 0.7980 chunk 18 optimal weight: 2.9990 chunk 32 optimal weight: 0.6980 overall best weight: 1.0582 ------------------------------------------------------------------------------- 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 = 0.3686 r_free = 0.3686 target = 0.104928 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3477 r_free = 0.3477 target = 0.092082 restraints weight = 32285.457| |-----------------------------------------------------------------------------| r_work (start): 0.3491 rms_B_bonded: 2.31 r_work: 0.3396 rms_B_bonded: 2.72 restraints_weight: 0.5000 r_work: 0.3288 rms_B_bonded: 4.55 restraints_weight: 0.2500 r_work (final): 0.3288 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8019 moved from start: 0.2117 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 5641 Z= 0.137 Angle : 0.511 5.750 7680 Z= 0.267 Chirality : 0.038 0.150 912 Planarity : 0.004 0.055 933 Dihedral : 6.995 57.722 828 Min Nonbonded Distance : 2.444 Molprobity Statistics. All-atom Clashscore : 6.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.12 % Favored : 97.88 % Rotamer: Outliers : 1.24 % Allowed : 11.48 % Favored : 87.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.71 % 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: 1.30 (0.32), residues: 707 helix: 1.75 (0.24), residues: 474 sheet: -1.06 (0.74), residues: 50 loop : -0.89 (0.45), residues: 183 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 341 TYR 0.013 0.001 TYR A 478 PHE 0.011 0.001 PHE A 126 TRP 0.011 0.001 TRP A 85 HIS 0.001 0.000 HIS A 469 Details of bonding type rmsd/Z covalent geometry : bond 0.00312 / 0.14 ( 5640) covalent geometry : angle 0.51060 / 0.27 ( 7678) SS BOND : bond 0.00144 / 0.08 ( 1) SS BOND : angle 1.47286 / 0.83 ( 2) hydrogen bonds : bond 0.04100 / 2.68 ( 379) hydrogen bonds : angle 4.42294 / 3.34 ( 1119) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1414 Ramachandran restraints generated. 707 Oldfield, 0 Emsley, 707 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1414 Ramachandran restraints generated. 707 Oldfield, 0 Emsley, 707 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 56 residues out of total 566 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 49 time to evaluate : 0.300 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 76 GLU cc_start: 0.8437 (tt0) cc_final: 0.8035 (tm-30) REVERT: A 142 LYS cc_start: 0.7759 (ttpt) cc_final: 0.7454 (mtpm) REVERT: A 305 MET cc_start: 0.7349 (mmm) cc_final: 0.6968 (tpt) REVERT: A 615 LEU cc_start: 0.8520 (OUTLIER) cc_final: 0.8292 (mp) outliers start: 7 outliers final: 4 residues processed: 53 average time/residue: 0.8376 time to fit residues: 47.4700 Evaluate side-chains 55 residues out of total 566 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 50 time to evaluate : 0.262 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 143 MET Chi-restraints excluded: chain A residue 289 ARG Chi-restraints excluded: chain A residue 538 ILE Chi-restraints excluded: chain A residue 542 PHE Chi-restraints excluded: chain A residue 615 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 71 random chunks: chunk 20 optimal weight: 0.7980 chunk 12 optimal weight: 0.9990 chunk 14 optimal weight: 0.1980 chunk 15 optimal weight: 0.7980 chunk 2 optimal weight: 0.5980 chunk 13 optimal weight: 0.7980 chunk 7 optimal weight: 0.7980 chunk 68 optimal weight: 0.7980 chunk 22 optimal weight: 1.9990 chunk 5 optimal weight: 0.3980 chunk 35 optimal weight: 1.9990 overall best weight: 0.5580 ------------------------------------------------------------------------------- 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 = 0.3708 r_free = 0.3708 target = 0.106294 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3505 r_free = 0.3505 target = 0.093642 restraints weight = 32415.685| |-----------------------------------------------------------------------------| r_work (start): 0.3513 rms_B_bonded: 2.29 r_work: 0.3417 rms_B_bonded: 2.72 restraints_weight: 0.5000 r_work: 0.3307 rms_B_bonded: 4.56 restraints_weight: 0.2500 r_work (final): 0.3307 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8044 moved from start: 0.2267 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.035 5641 Z= 0.109 Angle : 0.493 5.683 7680 Z= 0.256 Chirality : 0.038 0.162 912 Planarity : 0.004 0.056 933 Dihedral : 6.708 59.708 828 Min Nonbonded Distance : 2.440 Molprobity Statistics. All-atom Clashscore : 6.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.98 % Favored : 98.02 % Rotamer: Outliers : 0.88 % Allowed : 11.48 % Favored : 87.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.71 % 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 (0.32), residues: 707 helix: 1.95 (0.24), residues: 474 sheet: -1.01 (0.74), residues: 50 loop : -0.79 (0.46), residues: 183 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG B 408 TYR 0.012 0.001 TYR B 426 PHE 0.009 0.001 PHE A 542 TRP 0.010 0.001 TRP A 85 HIS 0.001 0.000 HIS A 469 Details of bonding type rmsd/Z covalent geometry : bond 0.00242 / 0.11 ( 5640) covalent geometry : angle 0.49294 / 0.26 ( 7678) SS BOND : bond 0.00137 / 0.07 ( 1) SS BOND : angle 1.23973 / 0.70 ( 2) hydrogen bonds : bond 0.03871 / 2.54 ( 379) hydrogen bonds : angle 4.31018 / 3.26 ( 1119) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1414 Ramachandran restraints generated. 707 Oldfield, 0 Emsley, 707 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1414 Ramachandran restraints generated. 707 Oldfield, 0 Emsley, 707 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 58 residues out of total 566 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 53 time to evaluate : 0.183 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 76 GLU cc_start: 0.8434 (tt0) cc_final: 0.8075 (tm-30) REVERT: A 142 LYS cc_start: 0.7770 (ttpt) cc_final: 0.7474 (mtpm) REVERT: A 305 MET cc_start: 0.7332 (mmm) cc_final: 0.6989 (tpt) REVERT: A 615 LEU cc_start: 0.8498 (OUTLIER) cc_final: 0.8280 (mp) outliers start: 5 outliers final: 3 residues processed: 55 average time/residue: 0.8714 time to fit residues: 51.1140 Evaluate side-chains 55 residues out of total 566 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 51 time to evaluate : 0.286 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 143 MET Chi-restraints excluded: chain A residue 538 ILE Chi-restraints excluded: chain A residue 542 PHE Chi-restraints excluded: chain A residue 615 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 71 random chunks: chunk 18 optimal weight: 2.9990 chunk 67 optimal weight: 0.8980 chunk 21 optimal weight: 3.9990 chunk 40 optimal weight: 1.9990 chunk 44 optimal weight: 3.9990 chunk 6 optimal weight: 1.9990 chunk 63 optimal weight: 0.6980 chunk 24 optimal weight: 4.9990 chunk 52 optimal weight: 2.9990 chunk 35 optimal weight: 0.4980 chunk 10 optimal weight: 1.9990 overall best weight: 1.2184 ------------------------------------------------------------------------------- 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 = 0.3685 r_free = 0.3685 target = 0.104898 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 28)----------------| | r_work = 0.3478 r_free = 0.3478 target = 0.092143 restraints weight = 32568.184| |-----------------------------------------------------------------------------| r_work (start): 0.3486 rms_B_bonded: 2.31 r_work: 0.3388 rms_B_bonded: 2.73 restraints_weight: 0.5000 r_work: 0.3277 rms_B_bonded: 4.58 restraints_weight: 0.2500 r_work (final): 0.3277 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8087 moved from start: 0.2206 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 5641 Z= 0.149 Angle : 0.518 5.725 7680 Z= 0.271 Chirality : 0.038 0.160 912 Planarity : 0.004 0.055 933 Dihedral : 6.765 63.215 828 Min Nonbonded Distance : 2.435 Molprobity Statistics. All-atom Clashscore : 6.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.26 % Favored : 97.74 % Rotamer: Outliers : 1.06 % Allowed : 11.48 % Favored : 87.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.71 % 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: 1.39 (0.32), residues: 707 helix: 1.83 (0.24), residues: 474 sheet: -1.02 (0.74), residues: 50 loop : -0.86 (0.46), residues: 183 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 289 TYR 0.013 0.001 TYR A 478 PHE 0.012 0.001 PHE A 126 TRP 0.014 0.001 TRP A 85 HIS 0.001 0.001 HIS A 469 Details of bonding type rmsd/Z covalent geometry : bond 0.00343 / 0.15 ( 5640) covalent geometry : angle 0.51711 / 0.27 ( 7678) SS BOND : bond 0.00147 / 0.08 ( 1) SS BOND : angle 1.45957 / 0.82 ( 2) hydrogen bonds : bond 0.04037 / 2.64 ( 379) hydrogen bonds : angle 4.37755 / 3.30 ( 1119) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3050.12 seconds wall clock time: 52 minutes 21.97 seconds (3141.97 seconds total)