Starting phenix.real_space_refine on Wed Feb 4 15:49:57 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9pym_72036/02_2026/9pym_72036_trim.cif Found real_map, /net/cci-nas-00/data/ceres_data/9pym_72036/02_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 { real_map_files = "/net/cci-nas-00/data/ceres_data/9pym_72036/02_2026/9pym_72036.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9pym_72036/02_2026/9pym_72036.map" model { file = "/net/cci-nas-00/data/ceres_data/9pym_72036/02_2026/9pym_72036_trim.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9pym_72036/02_2026/9pym_72036_trim.cif" } 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-2.0-5952/lib/python3.9/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, 93 Unusual residues: {' NA': 1, '8X3': 1, 'PTY': 3} Classifications: {'undetermined': 5} Link IDs: {None: 4} 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: 2.53, per 1000 atoms: 0.23 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: 1.20 Conformation dependent library (CDL) restraints added in 373.0 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: 0.17 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: 2.51 Time building geometry restraints manager: 1.55 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: 5.210 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: 0.080 Extract box with map and model: 0.190 Check model and map are aligned: 0.030 Set scattering table: 0.030 Process input model: 12.790 Find NCS groups from input model: 0.030 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:7.170 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 25.550 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8208 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 covalent geometry : bond 0.00536 ( 5640) covalent geometry : angle 0.52704 ( 7678) SS BOND : bond 0.00386 ( 1) SS BOND : angle 2.90885 ( 2) hydrogen bonds : bond 0.21607 ( 379) hydrogen bonds : angle 8.44916 ( 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 : 0.303 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: 0.9704 time to fit residues: 72.1468 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 : 0.278 ------------------------------------------------------------------------------- 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... Flipped N/Q/H residues before XYZ refinement: B 510 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3820 r_free = 0.3820 target = 0.109296 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 23)----------------| | r_work = 0.3596 r_free = 0.3596 target = 0.095787 restraints weight = 32929.332| |-----------------------------------------------------------------------------| r_work (start): 0.3597 rms_B_bonded: 2.35 r_work: 0.3488 rms_B_bonded: 2.74 restraints_weight: 0.5000 r_work: 0.3388 rms_B_bonded: 4.57 restraints_weight: 0.2500 r_work (final): 0.3388 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8138 moved from start: 0.1258 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= 0.177 Angle : 0.561 5.800 7680 Z= 0.305 Chirality : 0.039 0.142 912 Planarity : 0.005 0.047 933 Dihedral : 8.829 116.351 828 Min Nonbonded Distance : 2.094 Molprobity Statistics. All-atom Clashscore : 6.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.56 % Favored : 98.44 % 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: 0.83 (0.31), residues: 707 helix: 1.28 (0.23), residues: 472 sheet: -0.92 (0.76), residues: 50 loop : -0.78 (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 0.021 0.001 PHE A 126 TRP 0.006 0.001 TRP B 487 HIS 0.001 0.000 HIS A 569 Details of bonding type rmsd covalent geometry : bond 0.00389 ( 5640) covalent geometry : angle 0.56029 ( 7678) SS BOND : bond 0.00139 ( 1) SS BOND : angle 1.49531 ( 2) hydrogen bonds : bond 0.06080 ( 379) hydrogen bonds : angle 5.30594 ( 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 60 residues out of total 566 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 54 time to evaluate : 0.284 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 76 GLU cc_start: 0.8408 (OUTLIER) cc_final: 0.8073 (tm-30) REVERT: A 142 LYS cc_start: 0.7993 (ttpt) cc_final: 0.7717 (mtpm) REVERT: A 297 MET cc_start: 0.8073 (mtp) cc_final: 0.7727 (mtm) REVERT: A 610 LEU cc_start: 0.8218 (OUTLIER) cc_final: 0.7986 (mp) REVERT: A 615 LEU cc_start: 0.8722 (OUTLIER) cc_final: 0.8432 (mp) outliers start: 6 outliers final: 1 residues processed: 57 average time/residue: 0.9284 time to fit residues: 56.2793 Evaluate side-chains 54 residues out of total 566 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 50 time to evaluate : 0.285 ------------------------------------------------------------------------------- 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: 0.9990 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: 0.3980 chunk 52 optimal weight: 1.9990 chunk 18 optimal weight: 2.9990 chunk 9 optimal weight: 2.9990 overall best weight: 1.4586 ------------------------------------------------------------------------------- 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 = 0.3663 r_free = 0.3663 target = 0.103704 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3447 r_free = 0.3447 target = 0.090578 restraints weight = 32765.178| |-----------------------------------------------------------------------------| r_work (start): 0.3461 rms_B_bonded: 2.36 r_work: 0.3361 rms_B_bonded: 2.78 restraints_weight: 0.5000 r_work: 0.3251 rms_B_bonded: 4.66 restraints_weight: 0.2500 r_work (final): 0.3251 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8068 moved from start: 0.1603 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 5641 Z= 0.172 Angle : 0.531 5.892 7680 Z= 0.284 Chirality : 0.038 0.142 912 Planarity : 0.005 0.049 933 Dihedral : 8.416 92.120 828 Min Nonbonded Distance : 2.086 Molprobity Statistics. All-atom Clashscore : 6.94 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: 0.90 (0.32), residues: 707 helix: 1.38 (0.24), residues: 475 sheet: -1.08 (0.75), residues: 50 loop : -0.87 (0.46), residues: 182 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 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 covalent geometry : bond 0.00389 ( 5640) covalent geometry : angle 0.53103 ( 7678) SS BOND : bond 0.00130 ( 1) SS BOND : angle 1.29715 ( 2) hydrogen bonds : bond 0.05177 ( 379) hydrogen bonds : angle 4.91705 ( 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 : 0.271 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 76 GLU cc_start: 0.8441 (OUTLIER) cc_final: 0.8023 (tm-30) REVERT: A 142 LYS cc_start: 0.7922 (ttpt) cc_final: 0.7594 (mtpm) REVERT: A 615 LEU cc_start: 0.8605 (OUTLIER) cc_final: 0.8351 (mp) outliers start: 10 outliers final: 3 residues processed: 57 average time/residue: 0.8634 time to fit residues: 52.5171 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 : 0.305 ------------------------------------------------------------------------------- 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: 0.7980 chunk 45 optimal weight: 0.7980 chunk 63 optimal weight: 1.9990 chunk 39 optimal weight: 0.1980 chunk 65 optimal weight: 0.8980 chunk 35 optimal weight: 0.7980 chunk 30 optimal weight: 2.9990 chunk 61 optimal weight: 2.9990 chunk 18 optimal weight: 2.9990 chunk 9 optimal weight: 2.9990 chunk 32 optimal weight: 1.9990 overall best weight: 0.6980 ------------------------------------------------------------------------------- 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 = 0.3688 r_free = 0.3688 target = 0.105189 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3474 r_free = 0.3474 target = 0.092099 restraints weight = 32446.194| |-----------------------------------------------------------------------------| r_work (start): 0.3487 rms_B_bonded: 2.38 r_work: 0.3389 rms_B_bonded: 2.79 restraints_weight: 0.5000 r_work: 0.3280 rms_B_bonded: 4.66 restraints_weight: 0.2500 r_work (final): 0.3280 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8035 moved from start: 0.1832 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 5641 Z= 0.119 Angle : 0.499 5.741 7680 Z= 0.263 Chirality : 0.038 0.140 912 Planarity : 0.004 0.048 933 Dihedral : 7.855 62.384 828 Min Nonbonded Distance : 2.143 Molprobity Statistics. All-atom Clashscore : 5.78 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: 1.16 (0.32), residues: 707 helix: 1.64 (0.24), residues: 472 sheet: -1.06 (0.75), residues: 50 loop : -0.91 (0.45), residues: 185 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 341 TYR 0.012 0.001 TYR A 478 PHE 0.012 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 covalent geometry : bond 0.00259 ( 5640) covalent geometry : angle 0.49898 ( 7678) SS BOND : bond 0.00122 ( 1) SS BOND : angle 0.85930 ( 2) hydrogen bonds : bond 0.04463 ( 379) hydrogen bonds : angle 4.61990 ( 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 59 residues out of total 566 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 53 time to evaluate : 0.288 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 76 GLU cc_start: 0.8429 (tt0) cc_final: 0.8090 (tm-30) REVERT: A 142 LYS cc_start: 0.7888 (ttpt) cc_final: 0.7560 (mtpm) REVERT: A 615 LEU cc_start: 0.8550 (OUTLIER) cc_final: 0.8308 (mp) outliers start: 6 outliers final: 2 residues processed: 56 average time/residue: 0.9197 time to fit residues: 54.8520 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 : 0.277 ------------------------------------------------------------------------------- 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: 0.6980 chunk 37 optimal weight: 0.9980 chunk 64 optimal weight: 2.9990 chunk 52 optimal weight: 1.9990 chunk 17 optimal weight: 2.9990 chunk 19 optimal weight: 2.9990 chunk 12 optimal weight: 0.6980 chunk 70 optimal weight: 0.5980 chunk 3 optimal weight: 4.9990 chunk 32 optimal weight: 1.9990 chunk 40 optimal weight: 0.9990 overall best weight: 0.7982 ------------------------------------------------------------------------------- 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 = 0.3692 r_free = 0.3692 target = 0.105330 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3479 r_free = 0.3479 target = 0.092239 restraints weight = 32320.905| |-----------------------------------------------------------------------------| r_work (start): 0.3492 rms_B_bonded: 2.36 r_work: 0.3392 rms_B_bonded: 2.79 restraints_weight: 0.5000 r_work: 0.3283 rms_B_bonded: 4.67 restraints_weight: 0.2500 r_work (final): 0.3283 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8031 moved from start: 0.1939 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 5641 Z= 0.124 Angle : 0.500 5.732 7680 Z= 0.261 Chirality : 0.038 0.141 912 Planarity : 0.004 0.050 933 Dihedral : 7.497 57.579 828 Min Nonbonded Distance : 2.126 Molprobity Statistics. All-atom Clashscore : 5.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.41 % Favored : 98.59 % Rotamer: Outliers : 0.88 % Allowed : 11.84 % 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: 1.31 (0.32), residues: 707 helix: 1.76 (0.24), residues: 471 sheet: -1.07 (0.74), residues: 50 loop : -0.83 (0.45), residues: 186 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 0.013 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 covalent geometry : bond 0.00274 ( 5640) covalent geometry : angle 0.49908 ( 7678) SS BOND : bond 0.00236 ( 1) SS BOND : angle 2.26072 ( 2) hydrogen bonds : bond 0.04274 ( 379) hydrogen bonds : angle 4.53342 ( 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 : 0.304 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 76 GLU cc_start: 0.8433 (tt0) cc_final: 0.8089 (tm-30) REVERT: A 142 LYS cc_start: 0.7884 (ttpt) cc_final: 0.7548 (mtpm) REVERT: A 434 MET cc_start: 0.7403 (tmm) cc_final: 0.7116 (tmm) REVERT: A 615 LEU cc_start: 0.8522 (OUTLIER) cc_final: 0.8293 (mp) outliers start: 5 outliers final: 2 residues processed: 56 average time/residue: 0.9472 time to fit residues: 56.4681 Evaluate side-chains 53 residues out of total 566 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 50 time to evaluate : 0.290 ------------------------------------------------------------------------------- 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: 5.9990 chunk 40 optimal weight: 2.9990 chunk 15 optimal weight: 0.7980 chunk 27 optimal weight: 1.9990 chunk 22 optimal weight: 2.9990 chunk 20 optimal weight: 2.9990 chunk 11 optimal weight: 0.8980 chunk 41 optimal weight: 0.7980 chunk 51 optimal weight: 0.7980 overall best weight: 1.0582 ------------------------------------------------------------------------------- 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 = 0.3687 r_free = 0.3687 target = 0.105011 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3481 r_free = 0.3481 target = 0.092295 restraints weight = 32851.012| |-----------------------------------------------------------------------------| r_work (start): 0.3488 rms_B_bonded: 2.31 r_work: 0.3391 rms_B_bonded: 2.71 restraints_weight: 0.5000 r_work: 0.3283 rms_B_bonded: 4.56 restraints_weight: 0.2500 r_work (final): 0.3283 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7990 moved from start: 0.2007 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 5641 Z= 0.138 Angle : 0.509 5.755 7680 Z= 0.266 Chirality : 0.038 0.140 912 Planarity : 0.004 0.053 933 Dihedral : 7.293 58.000 828 Min Nonbonded Distance : 2.105 Molprobity Statistics. All-atom Clashscore : 5.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.70 % Favored : 98.30 % Rotamer: Outliers : 1.24 % Allowed : 11.31 % 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: 1.31 (0.32), residues: 707 helix: 1.75 (0.24), residues: 474 sheet: -1.05 (0.75), residues: 50 loop : -0.85 (0.46), 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 0.013 0.001 PHE A 126 TRP 0.007 0.001 TRP A 85 HIS 0.001 0.000 HIS A 469 Details of bonding type rmsd covalent geometry : bond 0.00315 ( 5640) covalent geometry : angle 0.50813 ( 7678) SS BOND : bond 0.00246 ( 1) SS BOND : angle 2.05667 ( 2) hydrogen bonds : bond 0.04209 ( 379) hydrogen bonds : angle 4.48110 ( 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 59 residues out of total 566 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 52 time to evaluate : 0.290 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: 0.8434 (tt0) cc_final: 0.8053 (tm-30) REVERT: A 142 LYS cc_start: 0.7833 (ttpt) cc_final: 0.7483 (mtpm) REVERT: A 615 LEU cc_start: 0.8475 (OUTLIER) cc_final: 0.8248 (mp) outliers start: 7 outliers final: 5 residues processed: 56 average time/residue: 0.9749 time to fit residues: 58.1726 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 : 0.298 ------------------------------------------------------------------------------- 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: 0.8980 chunk 54 optimal weight: 0.8980 chunk 68 optimal weight: 1.9990 chunk 9 optimal weight: 1.9990 chunk 35 optimal weight: 1.9990 chunk 60 optimal weight: 3.9990 chunk 40 optimal weight: 0.4980 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: 1.2584 ------------------------------------------------------------------------------- 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 = 0.3678 r_free = 0.3678 target = 0.104503 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3469 r_free = 0.3469 target = 0.091612 restraints weight = 32376.247| |-----------------------------------------------------------------------------| r_work (start): 0.3484 rms_B_bonded: 2.35 r_work: 0.3387 rms_B_bonded: 2.76 restraints_weight: 0.5000 r_work: 0.3279 rms_B_bonded: 4.61 restraints_weight: 0.2500 r_work (final): 0.3279 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8038 moved from start: 0.2021 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= 0.150 Angle : 0.514 6.508 7680 Z= 0.269 Chirality : 0.038 0.142 912 Planarity : 0.004 0.053 933 Dihedral : 7.174 58.515 828 Min Nonbonded Distance : 2.096 Molprobity Statistics. All-atom Clashscore : 5.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.56 % Favored : 98.44 % Rotamer: Outliers : 1.06 % Allowed : 11.66 % 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: 1.71 (0.24), residues: 474 sheet: -1.06 (0.75), residues: 50 loop : -0.86 (0.46), 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 0.001 HIS A 469 Details of bonding type rmsd covalent geometry : bond 0.00345 ( 5640) covalent geometry : angle 0.51302 ( 7678) SS BOND : bond 0.00171 ( 1) SS BOND : angle 1.69333 ( 2) hydrogen bonds : bond 0.04221 ( 379) hydrogen bonds : angle 4.47952 ( 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 55 residues out of total 566 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 49 time to evaluate : 0.311 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: 0.8449 (tt0) cc_final: 0.8099 (tm-30) REVERT: A 142 LYS cc_start: 0.7830 (ttpt) cc_final: 0.7530 (mtpm) REVERT: A 438 ILE cc_start: 0.7776 (OUTLIER) cc_final: 0.7422 (mp) REVERT: A 615 LEU cc_start: 0.8546 (OUTLIER) cc_final: 0.8310 (mp) outliers start: 6 outliers final: 4 residues processed: 52 average time/residue: 0.9736 time to fit residues: 53.8613 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 : 0.293 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 143 MET 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: 0.8980 chunk 24 optimal weight: 4.9990 chunk 35 optimal weight: 0.9990 chunk 66 optimal weight: 3.9990 chunk 48 optimal weight: 1.9990 chunk 0 optimal weight: 5.9990 chunk 55 optimal weight: 2.9990 chunk 32 optimal weight: 0.5980 chunk 28 optimal weight: 0.6980 chunk 4 optimal weight: 1.9990 chunk 16 optimal weight: 4.9990 overall best weight: 1.0384 ------------------------------------------------------------------------------- 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 = 0.3687 r_free = 0.3687 target = 0.105144 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3478 r_free = 0.3478 target = 0.092211 restraints weight = 32527.694| |-----------------------------------------------------------------------------| r_work (start): 0.3494 rms_B_bonded: 2.32 r_work: 0.3398 rms_B_bonded: 2.73 restraints_weight: 0.5000 r_work: 0.3290 rms_B_bonded: 4.57 restraints_weight: 0.2500 r_work (final): 0.3290 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7981 moved from start: 0.2107 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= 0.133 Angle : 0.497 5.704 7680 Z= 0.260 Chirality : 0.038 0.149 912 Planarity : 0.004 0.054 933 Dihedral : 6.987 57.127 828 Min Nonbonded Distance : 2.114 Molprobity Statistics. All-atom Clashscore : 6.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.70 % Favored : 98.30 % 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: 1.35 (0.32), residues: 707 helix: 1.80 (0.24), residues: 474 sheet: -1.09 (0.74), residues: 50 loop : -0.85 (0.46), 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 0.010 0.001 TRP A 85 HIS 0.001 0.000 HIS A 469 Details of bonding type rmsd covalent geometry : bond 0.00302 ( 5640) covalent geometry : angle 0.49640 ( 7678) SS BOND : bond 0.00166 ( 1) SS BOND : angle 1.53403 ( 2) hydrogen bonds : bond 0.04084 ( 379) hydrogen bonds : angle 4.41318 ( 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 : 0.291 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: 0.8433 (tt0) cc_final: 0.8035 (tm-30) REVERT: A 142 LYS cc_start: 0.7765 (ttpt) cc_final: 0.7454 (mtpm) REVERT: A 615 LEU cc_start: 0.8515 (OUTLIER) cc_final: 0.8288 (mp) outliers start: 7 outliers final: 4 residues processed: 53 average time/residue: 1.0389 time to fit residues: 58.3366 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 : 0.301 ------------------------------------------------------------------------------- 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: 1.9990 chunk 23 optimal weight: 0.9990 chunk 25 optimal weight: 2.9990 chunk 46 optimal weight: 1.9990 chunk 15 optimal weight: 2.9990 chunk 37 optimal weight: 4.9990 chunk 33 optimal weight: 0.5980 chunk 1 optimal weight: 0.6980 chunk 18 optimal weight: 2.9990 chunk 32 optimal weight: 0.7980 overall best weight: 1.0184 ------------------------------------------------------------------------------- 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 = 0.3686 r_free = 0.3686 target = 0.105050 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3478 r_free = 0.3478 target = 0.092177 restraints weight = 32268.295| |-----------------------------------------------------------------------------| r_work (start): 0.3489 rms_B_bonded: 2.31 r_work: 0.3391 rms_B_bonded: 2.73 restraints_weight: 0.5000 r_work: 0.3283 rms_B_bonded: 4.56 restraints_weight: 0.2500 r_work (final): 0.3283 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7984 moved from start: 0.2124 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= 0.133 Angle : 0.499 5.691 7680 Z= 0.261 Chirality : 0.038 0.152 912 Planarity : 0.004 0.055 933 Dihedral : 6.899 58.138 828 Min Nonbonded Distance : 2.112 Molprobity Statistics. All-atom Clashscore : 6.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.12 % Favored : 97.88 % Rotamer: Outliers : 1.06 % Allowed : 11.66 % 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: 1.38 (0.32), residues: 707 helix: 1.81 (0.24), residues: 474 sheet: -1.05 (0.74), residues: 50 loop : -0.84 (0.46), residues: 183 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 341 TYR 0.013 0.001 TYR A 478 PHE 0.011 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 covalent geometry : bond 0.00302 ( 5640) covalent geometry : angle 0.49819 ( 7678) SS BOND : bond 0.00154 ( 1) SS BOND : angle 1.43428 ( 2) hydrogen bonds : bond 0.04055 ( 379) hydrogen bonds : angle 4.39385 ( 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: 6 poor density : 50 time to evaluate : 0.312 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 76 GLU cc_start: 0.8447 (tt0) cc_final: 0.8050 (tm-30) REVERT: A 142 LYS cc_start: 0.7765 (ttpt) cc_final: 0.7458 (mtpm) REVERT: A 615 LEU cc_start: 0.8479 (OUTLIER) cc_final: 0.8265 (mp) outliers start: 6 outliers final: 4 residues processed: 53 average time/residue: 1.0303 time to fit residues: 57.9797 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 : 0.282 ------------------------------------------------------------------------------- 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: 0.9980 chunk 14 optimal weight: 2.9990 chunk 15 optimal weight: 0.0980 chunk 2 optimal weight: 0.9990 chunk 13 optimal weight: 0.6980 chunk 7 optimal weight: 0.6980 chunk 68 optimal weight: 0.9980 chunk 22 optimal weight: 2.9990 chunk 5 optimal weight: 0.8980 chunk 35 optimal weight: 1.9990 overall best weight: 0.6380 ------------------------------------------------------------------------------- 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 = 0.3703 r_free = 0.3703 target = 0.106122 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3497 r_free = 0.3497 target = 0.093239 restraints weight = 32465.429| |-----------------------------------------------------------------------------| r_work (start): 0.3505 rms_B_bonded: 2.33 r_work: 0.3408 rms_B_bonded: 2.74 restraints_weight: 0.5000 r_work: 0.3303 rms_B_bonded: 4.58 restraints_weight: 0.2500 r_work (final): 0.3303 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7956 moved from start: 0.2256 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.036 5641 Z= 0.109 Angle : 0.482 5.649 7680 Z= 0.251 Chirality : 0.038 0.162 912 Planarity : 0.004 0.056 933 Dihedral : 6.651 62.193 828 Min Nonbonded Distance : 2.154 Molprobity Statistics. All-atom Clashscore : 6.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.70 % Favored : 98.30 % 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: 1.66 (0.32), residues: 707 helix: 2.03 (0.24), residues: 473 sheet: -1.01 (0.74), residues: 50 loop : -0.71 (0.46), residues: 184 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG B 408 TYR 0.012 0.001 TYR A 478 PHE 0.009 0.001 PHE A 542 TRP 0.013 0.001 TRP A 85 HIS 0.001 0.000 HIS A 469 Details of bonding type rmsd covalent geometry : bond 0.00243 ( 5640) covalent geometry : angle 0.48150 ( 7678) SS BOND : bond 0.00150 ( 1) SS BOND : angle 1.26815 ( 2) hydrogen bonds : bond 0.03856 ( 379) hydrogen bonds : angle 4.28329 ( 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 57 residues out of total 566 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 51 time to evaluate : 0.304 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 76 GLU cc_start: 0.8433 (tt0) cc_final: 0.8031 (tm-30) REVERT: A 142 LYS cc_start: 0.7722 (ttpt) cc_final: 0.7415 (mtpm) outliers start: 6 outliers final: 4 residues processed: 54 average time/residue: 1.0111 time to fit residues: 58.0208 Evaluate side-chains 54 residues out of total 566 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 50 time to evaluate : 0.291 ------------------------------------------------------------------------------- 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 610 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: 0.6980 chunk 21 optimal weight: 3.9990 chunk 40 optimal weight: 2.9990 chunk 44 optimal weight: 3.9990 chunk 6 optimal weight: 2.9990 chunk 63 optimal weight: 0.3980 chunk 24 optimal weight: 4.9990 chunk 52 optimal weight: 2.9990 chunk 35 optimal weight: 0.9980 chunk 10 optimal weight: 1.9990 overall best weight: 1.4184 ------------------------------------------------------------------------------- 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 = 0.3681 r_free = 0.3681 target = 0.104614 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3473 r_free = 0.3473 target = 0.091716 restraints weight = 32711.588| |-----------------------------------------------------------------------------| r_work (start): 0.3484 rms_B_bonded: 2.33 r_work: 0.3386 rms_B_bonded: 2.74 restraints_weight: 0.5000 r_work: 0.3276 rms_B_bonded: 4.58 restraints_weight: 0.2500 r_work (final): 0.3276 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7989 moved from start: 0.2164 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 5641 Z= 0.161 Angle : 0.515 5.694 7680 Z= 0.270 Chirality : 0.038 0.158 912 Planarity : 0.005 0.055 933 Dihedral : 6.770 65.512 828 Min Nonbonded Distance : 2.082 Molprobity Statistics. All-atom Clashscore : 6.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.98 % Favored : 98.02 % 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: 1.42 (0.32), residues: 707 helix: 1.85 (0.23), residues: 474 sheet: -1.07 (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 0.014 0.001 TYR A 478 PHE 0.013 0.001 PHE A 126 TRP 0.016 0.001 TRP A 85 HIS 0.001 0.001 HIS A 469 Details of bonding type rmsd covalent geometry : bond 0.00371 ( 5640) covalent geometry : angle 0.51459 ( 7678) SS BOND : bond 0.00164 ( 1) SS BOND : angle 1.50406 ( 2) hydrogen bonds : bond 0.04094 ( 379) hydrogen bonds : angle 4.37600 ( 1119) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3469.63 seconds wall clock time: 59 minutes 42.83 seconds (3582.83 seconds total)