Starting phenix.real_space_refine on Wed Sep 17 05:29:23 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9cy4_46006/09_2025/9cy4_46006.cif Found real_map, /net/cci-nas-00/data/ceres_data/9cy4_46006/09_2025/9cy4_46006.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.41 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9cy4_46006/09_2025/9cy4_46006.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9cy4_46006/09_2025/9cy4_46006.map" model { file = "/net/cci-nas-00/data/ceres_data/9cy4_46006/09_2025/9cy4_46006.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9cy4_46006/09_2025/9cy4_46006.cif" } resolution = 3.41 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.024 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: 4 Type Number sf(0) Gaussians S 39 5.16 5 C 3390 2.51 5 N 838 2.21 5 O 916 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 2 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5805/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 5183 Number of models: 1 Model: "" Number of chains: 3 Chain: "A" Number of atoms: 4186 Number of conformers: 1 Conformer: "" Number of residues, atoms: 542, 4186 Classifications: {'peptide': 542} Incomplete info: {'truncation_to_alanine': 15} Link IDs: {'PTRANS': 20, 'TRANS': 521} Chain breaks: 5 Unresolved non-hydrogen bonds: 46 Unresolved non-hydrogen angles: 58 Unresolved non-hydrogen dihedrals: 37 Unresolved non-hydrogen chiralities: 7 Planarities with less than four sites: {'GLN:plan1': 1, 'ARG:plan': 1, 'TYR:plan': 1} Unresolved non-hydrogen planarities: 16 Chain: "B" Number of atoms: 912 Number of conformers: 1 Conformer: "" Number of residues, atoms: 120, 912 Classifications: {'peptide': 120} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'PTRANS': 3, 'TRANS': 116} Unresolved non-hydrogen bonds: 10 Unresolved non-hydrogen angles: 13 Unresolved non-hydrogen dihedrals: 7 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 1} Unresolved non-hydrogen planarities: 8 Chain: "L" Number of atoms: 85 Number of conformers: 1 Conformer: "" Number of residues, atoms: 11, 85 Classifications: {'peptide': 11} Modifications used: {'PEPT-D': 1} Link IDs: {'NMTRANS': 7, 'TRANS': 3} Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 16 Planarities with less than four sites: {'MLE:plan-1': 4, 'MVA:plan-1': 1, 'BMT:plan-1': 1, 'ABA:plan-1': 1, 'SAR:plan-1': 1} Unresolved non-hydrogen planarities: 8 Time building chain proxies: 1.49, per 1000 atoms: 0.29 Number of scatterers: 5183 At special positions: 0 Unit cell: (61.544, 102.207, 104.405, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 39 16.00 O 916 8.00 N 838 7.00 C 3390 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=8, symmetry=0 Simple disulfide: pdb=" SG CYS A 142 " - pdb=" SG CYS A 463 " distance=2.03 Simple disulfide: pdb=" SG CYS A 430 " - pdb=" SG CYS A 530 " distance=2.04 Simple disulfide: pdb=" SG CYS A 459 " - pdb=" SG CYS A 506 " distance=2.03 Simple disulfide: pdb=" SG CYS A 465 " - pdb=" SG CYS A 485 " distance=2.03 Simple disulfide: pdb=" SG CYS A 474 " - pdb=" SG CYS A 524 " distance=2.03 Simple disulfide: pdb=" SG CYS A 489 " - pdb=" SG CYS A 504 " distance=2.03 Simple disulfide: pdb=" SG CYS A 599 " - pdb=" SG CYS A 613 " distance=2.03 Simple disulfide: pdb=" SG CYS B 26 " - pdb=" SG CYS B 100 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Links applied TRANS " DAL L 1 " - " ALA L 11 " Time building additional restraints: 0.57 Conformation dependent library (CDL) restraints added in 128.6 milliseconds Enol-peptide restraints added in 715.3 nanoseconds 1296 Ramachandran restraints generated. 648 Oldfield, 0 Emsley, 648 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Skipped Input residue name is d-peptide pdb=" CB DAL L 1 " Number of C-beta restraints generated: 1218 Finding SS restraints... Secondary structure from input PDB file: 23 helices and 5 sheets defined 53.7% alpha, 7.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.15 Creating SS restraints... Processing helix chain 'A' and resid 26 through 51 removed outlier: 3.504A pdb=" N SER A 51 " --> pdb=" O ILE A 47 " (cutoff:3.500A) Processing helix chain 'A' and resid 51 through 60 removed outlier: 3.708A pdb=" N ILE A 55 " --> pdb=" O SER A 51 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N GLU A 60 " --> pdb=" O GLU A 56 " (cutoff:3.500A) Processing helix chain 'A' and resid 62 through 88 removed outlier: 4.238A pdb=" N PHE A 73 " --> pdb=" O ILE A 69 " (cutoff:3.500A) removed outlier: 4.602A pdb=" N GLU A 74 " --> pdb=" O ASP A 70 " (cutoff:3.500A) removed outlier: 4.017A pdb=" N VAL A 80 " --> pdb=" O GLY A 76 " (cutoff:3.500A) removed outlier: 5.343A pdb=" N VAL A 82 " --> pdb=" O LEU A 78 " (cutoff:3.500A) removed outlier: 5.488A pdb=" N PHE A 83 " --> pdb=" O LEU A 79 " (cutoff:3.500A) Processing helix chain 'A' and resid 92 through 113 removed outlier: 3.541A pdb=" N ALA A 112 " --> pdb=" O GLY A 108 " (cutoff:3.500A) Processing helix chain 'A' and resid 114 through 116 No H-bonds generated for 'chain 'A' and resid 114 through 116' Processing helix chain 'A' and resid 170 through 185 removed outlier: 3.939A pdb=" N VAL A 174 " --> pdb=" O MET A 170 " (cutoff:3.500A) Processing helix chain 'A' and resid 190 through 200 removed outlier: 3.743A pdb=" N PHE A 199 " --> pdb=" O TYR A 195 " (cutoff:3.500A) Processing helix chain 'A' and resid 204 through 216 Processing helix chain 'A' and resid 217 through 233 removed outlier: 3.943A pdb=" N ILE A 221 " --> pdb=" O MET A 217 " (cutoff:3.500A) removed outlier: 4.014A pdb=" N MET A 233 " --> pdb=" O LEU A 229 " (cutoff:3.500A) Processing helix chain 'A' and resid 241 through 245 removed outlier: 3.607A pdb=" N ILE A 245 " --> pdb=" O LEU A 242 " (cutoff:3.500A) Processing helix chain 'A' and resid 257 through 274 removed outlier: 4.155A pdb=" N ASN A 261 " --> pdb=" O ALA A 257 " (cutoff:3.500A) removed outlier: 3.629A pdb=" N PHE A 262 " --> pdb=" O TRP A 258 " (cutoff:3.500A) Processing helix chain 'A' and resid 325 through 334 Processing helix chain 'A' and resid 335 through 357 Processing helix chain 'A' and resid 358 through 366 Processing helix chain 'A' and resid 381 through 400 Processing helix chain 'A' and resid 403 through 423 Processing helix chain 'A' and resid 424 through 429 removed outlier: 3.647A pdb=" N PHE A 427 " --> pdb=" O LEU A 424 " (cutoff:3.500A) removed outlier: 3.589A pdb=" N ILE A 428 " --> pdb=" O TYR A 425 " (cutoff:3.500A) removed outlier: 4.138A pdb=" N LEU A 429 " --> pdb=" O PHE A 426 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 424 through 429' Processing helix chain 'A' and resid 530 through 552 Processing helix chain 'A' and resid 553 through 563 removed outlier: 4.142A pdb=" N ILE A 559 " --> pdb=" O HIS A 555 " (cutoff:3.500A) removed outlier: 4.106A pdb=" N VAL A 560 " --> pdb=" O VAL A 556 " (cutoff:3.500A) removed outlier: 4.141A pdb=" N LYS A 561 " --> pdb=" O MET A 557 " (cutoff:3.500A) Processing helix chain 'A' and resid 567 through 583 Processing helix chain 'A' and resid 585 through 597 removed outlier: 3.668A pdb=" N ILE A 589 " --> pdb=" O ILE A 585 " (cutoff:3.500A) Processing helix chain 'A' and resid 617 through 651 removed outlier: 3.824A pdb=" N SER A 629 " --> pdb=" O TYR A 625 " (cutoff:3.500A) Processing helix chain 'B' and resid 91 through 95 removed outlier: 3.696A pdb=" N THR B 95 " --> pdb=" O PRO B 92 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 435 through 436 removed outlier: 3.796A pdb=" N CYS A 474 " --> pdb=" O HIS A 520 " (cutoff:3.500A) removed outlier: 3.996A pdb=" N HIS A 520 " --> pdb=" O CYS A 474 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 491 through 492 removed outlier: 3.537A pdb=" N SER A 491 " --> pdb=" O TYR A 502 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 7 through 11 Processing sheet with id=AA4, first strand: chain 'B' and resid 16 through 17 removed outlier: 7.170A pdb=" N VAL B 16 " --> pdb=" O SER B 118 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA4 Processing sheet with id=AA5, first strand: chain 'B' and resid 63 through 64 removed outlier: 6.697A pdb=" N TRP B 40 " --> pdb=" O VAL B 52 " (cutoff:3.500A) removed outlier: 4.538A pdb=" N ALA B 54 " --> pdb=" O MET B 38 " (cutoff:3.500A) removed outlier: 6.565A pdb=" N MET B 38 " --> pdb=" O ALA B 54 " (cutoff:3.500A) 281 hydrogen bonds defined for protein. 822 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 0.80 Time building geometry restraints manager: 0.59 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 1200 1.33 - 1.46: 1329 1.46 - 1.58: 2722 1.58 - 1.70: 1 1.70 - 1.82: 58 Bond restraints: 5310 Sorted by residual: bond pdb=" C VAL A 189 " pdb=" N PRO A 190 " ideal model delta sigma weight residual 1.334 1.395 -0.061 2.34e-02 1.83e+03 6.82e+00 bond pdb=" C ILE A 274 " pdb=" N PRO A 275 " ideal model delta sigma weight residual 1.335 1.359 -0.024 9.40e-03 1.13e+04 6.53e+00 bond pdb=" C ARG A 93 " pdb=" N PRO A 94 " ideal model delta sigma weight residual 1.336 1.365 -0.029 1.25e-02 6.40e+03 5.42e+00 bond pdb=" C ILE A 383 " pdb=" N PRO A 384 " ideal model delta sigma weight residual 1.335 1.364 -0.029 1.28e-02 6.10e+03 5.31e+00 bond pdb=" C SAR L 7 " pdb=" O SAR L 7 " ideal model delta sigma weight residual 1.266 1.221 0.045 2.00e-02 2.50e+03 5.17e+00 ... (remaining 5305 not shown) Histogram of bond angle deviations from ideal: 0.00 - 3.23: 7006 3.23 - 6.45: 148 6.45 - 9.68: 32 9.68 - 12.91: 7 12.91 - 16.13: 3 Bond angle restraints: 7196 Sorted by residual: angle pdb=" C MLE L 2 " pdb=" N MLE L 3 " pdb=" CA MLE L 3 " ideal model delta sigma weight residual 121.70 134.36 -12.66 1.80e+00 3.09e-01 4.95e+01 angle pdb=" N BMT L 5 " pdb=" CA BMT L 5 " pdb=" CB BMT L 5 " ideal model delta sigma weight residual 111.50 123.22 -11.72 1.70e+00 3.46e-01 4.75e+01 angle pdb=" C VAL L 9 " pdb=" N MLE L 10 " pdb=" CA MLE L 10 " ideal model delta sigma weight residual 121.70 132.54 -10.84 1.80e+00 3.09e-01 3.63e+01 angle pdb=" C MLE L 3 " pdb=" N MVA L 4 " pdb=" CA MVA L 4 " ideal model delta sigma weight residual 121.70 130.83 -9.13 1.80e+00 3.09e-01 2.57e+01 angle pdb=" C MLE L 2 " pdb=" N MLE L 3 " pdb=" CN MLE L 3 " ideal model delta sigma weight residual 124.30 109.25 15.05 3.00e+00 1.11e-01 2.52e+01 ... (remaining 7191 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 22.37: 2859 22.37 - 44.75: 186 44.75 - 67.12: 17 67.12 - 89.50: 10 89.50 - 111.87: 4 Dihedral angle restraints: 3076 sinusoidal: 1156 harmonic: 1920 Sorted by residual: dihedral pdb=" CA MVA L 4 " pdb=" C MVA L 4 " pdb=" N BMT L 5 " pdb=" CA BMT L 5 " ideal model delta harmonic sigma weight residual 180.00 68.13 111.87 0 5.00e+00 4.00e-02 5.01e+02 dihedral pdb=" CA SAR L 7 " pdb=" C SAR L 7 " pdb=" N MLE L 8 " pdb=" CA MLE L 8 " ideal model delta harmonic sigma weight residual 180.00 68.90 111.10 0 5.00e+00 4.00e-02 4.94e+02 dihedral pdb=" CA MLE L 2 " pdb=" C MLE L 2 " pdb=" N MLE L 3 " pdb=" CA MLE L 3 " ideal model delta harmonic sigma weight residual 180.00 73.44 106.56 0 5.00e+00 4.00e-02 4.54e+02 ... (remaining 3073 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.212: 793 0.212 - 0.425: 8 0.425 - 0.637: 2 0.637 - 0.850: 2 0.850 - 1.062: 1 Chirality restraints: 806 Sorted by residual: chirality pdb=" CA MLE L 10 " pdb=" N MLE L 10 " pdb=" C MLE L 10 " pdb=" CB MLE L 10 " both_signs ideal model delta sigma weight residual False 2.51 1.45 1.06 2.00e-01 2.50e+01 2.82e+01 chirality pdb=" CA BMT L 5 " pdb=" N BMT L 5 " pdb=" C BMT L 5 " pdb=" CB BMT L 5 " both_signs ideal model delta sigma weight residual False 2.53 1.70 0.83 2.00e-01 2.50e+01 1.71e+01 chirality pdb=" CB ILE A 47 " pdb=" CA ILE A 47 " pdb=" CG1 ILE A 47 " pdb=" CG2 ILE A 47 " both_signs ideal model delta sigma weight residual False 2.64 1.97 0.67 2.00e-01 2.50e+01 1.13e+01 ... (remaining 803 not shown) Planarity restraints: 894 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C GLN A 369 " 0.083 5.00e-02 4.00e+02 1.24e-01 2.48e+01 pdb=" N PRO A 370 " -0.215 5.00e-02 4.00e+02 pdb=" CA PRO A 370 " 0.068 5.00e-02 4.00e+02 pdb=" CD PRO A 370 " 0.064 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C GLY A 219 " 0.051 5.00e-02 4.00e+02 7.69e-02 9.46e+00 pdb=" N PRO A 220 " -0.133 5.00e-02 4.00e+02 pdb=" CA PRO A 220 " 0.039 5.00e-02 4.00e+02 pdb=" CD PRO A 220 " 0.043 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C LEU A 113 " 0.050 5.00e-02 4.00e+02 7.43e-02 8.83e+00 pdb=" N PRO A 114 " -0.128 5.00e-02 4.00e+02 pdb=" CA PRO A 114 " 0.037 5.00e-02 4.00e+02 pdb=" CD PRO A 114 " 0.042 5.00e-02 4.00e+02 ... (remaining 891 not shown) Histogram of nonbonded interaction distances: 2.31 - 2.83: 1562 2.83 - 3.35: 4502 3.35 - 3.86: 8508 3.86 - 4.38: 9445 4.38 - 4.90: 16642 Nonbonded interactions: 40659 Sorted by model distance: nonbonded pdb=" OH TYR A 338 " pdb=" O ALA A 571 " model vdw 2.310 3.040 nonbonded pdb=" O ILE A 353 " pdb=" OG1 THR A 357 " model vdw 2.338 3.040 nonbonded pdb=" O SER A 457 " pdb=" OG SER A 461 " model vdw 2.399 3.040 nonbonded pdb=" OG SER B 56 " pdb=" N SER B 57 " model vdw 2.402 3.120 nonbonded pdb=" O ASN B 34 " pdb=" OG SER B 57 " model vdw 2.435 3.040 ... (remaining 40654 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: 0.940 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.000 Extract box with map and model: 0.080 Check model and map are aligned: 0.020 Set scattering table: 0.020 Process input model: 6.280 Find NCS groups from input model: 0.020 Set up NCS constraints: 0.000 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:1.320 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 8.690 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7205 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.097 5319 Z= 0.300 Angle : 1.214 16.132 7215 Z= 0.632 Chirality : 0.086 1.062 806 Planarity : 0.011 0.124 893 Dihedral : 15.135 111.873 1831 Min Nonbonded Distance : 2.310 Molprobity Statistics. All-atom Clashscore : 3.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.86 % Favored : 96.14 % Rotamer: Outliers : 0.00 % Allowed : 0.36 % Favored : 99.64 % Cbeta Deviations : 0.82 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 1.40 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -3.09 (0.26), residues: 648 helix: -2.09 (0.19), residues: 334 sheet: -1.22 (0.69), residues: 63 loop : -1.96 (0.33), residues: 251 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG A 122 TYR 0.039 0.002 TYR A 640 PHE 0.034 0.002 PHE A 68 TRP 0.009 0.001 TRP B 40 HIS 0.003 0.001 HIS B 61 Details of bonding type rmsd covalent geometry : bond 0.00570 ( 5310) covalent geometry : angle 1.21382 ( 7196) SS BOND : bond 0.00328 ( 8) SS BOND : angle 1.17756 ( 16) hydrogen bonds : bond 0.12880 ( 281) hydrogen bonds : angle 7.06872 ( 822) link_TRANS : bond 0.01675 ( 1) link_TRANS : angle 2.07806 ( 3) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1296 Ramachandran restraints generated. 648 Oldfield, 0 Emsley, 648 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1296 Ramachandran restraints generated. 648 Oldfield, 0 Emsley, 648 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 176 residues out of total 567 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 176 time to evaluate : 0.208 Fit side-chains revert: symmetry clash REVERT: A 34 LEU cc_start: 0.7922 (tp) cc_final: 0.6998 (mm) REVERT: A 270 ILE cc_start: 0.8005 (mt) cc_final: 0.7703 (mm) REVERT: A 446 ASN cc_start: 0.7945 (t0) cc_final: 0.7532 (p0) REVERT: A 541 GLN cc_start: 0.8024 (tp40) cc_final: 0.7535 (tt0) REVERT: B 43 GLN cc_start: 0.7289 (mt0) cc_final: 0.6540 (mp10) REVERT: B 94 ASP cc_start: 0.7678 (m-30) cc_final: 0.7139 (m-30) outliers start: 0 outliers final: 0 residues processed: 176 average time/residue: 0.0623 time to fit residues: 14.7888 Evaluate side-chains 119 residues out of total 567 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 119 time to evaluate : 0.116 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 67 random chunks: chunk 49 optimal weight: 0.0570 chunk 53 optimal weight: 1.9990 chunk 5 optimal weight: 0.8980 chunk 33 optimal weight: 0.8980 chunk 65 optimal weight: 0.0770 chunk 62 optimal weight: 5.9990 chunk 51 optimal weight: 1.9990 chunk 38 optimal weight: 20.0000 chunk 61 optimal weight: 0.6980 chunk 45 optimal weight: 0.8980 chunk 27 optimal weight: 2.9990 overall best weight: 0.5256 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 178 ASN ** A 204 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 213 ASN A 365 GLN B 43 GLN B 88 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4041 r_free = 0.4041 target = 0.173562 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3741 r_free = 0.3741 target = 0.146090 restraints weight = 7930.152| |-----------------------------------------------------------------------------| r_work (start): 0.3728 rms_B_bonded: 2.26 r_work: 0.3627 rms_B_bonded: 3.03 restraints_weight: 0.5000 r_work (final): 0.3627 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7596 moved from start: 0.2618 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.046 5319 Z= 0.159 Angle : 0.773 11.457 7215 Z= 0.369 Chirality : 0.047 0.348 806 Planarity : 0.010 0.156 893 Dihedral : 7.464 82.008 730 Min Nonbonded Distance : 2.458 Molprobity Statistics. All-atom Clashscore : 9.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.55 % Favored : 96.45 % Rotamer: Outliers : 2.55 % Allowed : 13.48 % Favored : 83.97 % Cbeta Deviations : 0.16 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.78 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.86 (0.30), residues: 648 helix: 0.40 (0.25), residues: 333 sheet: -1.46 (0.76), residues: 53 loop : -1.60 (0.33), residues: 262 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 103 TYR 0.022 0.001 TYR A 590 PHE 0.016 0.001 PHE A 30 TRP 0.005 0.001 TRP A 602 HIS 0.002 0.001 HIS A 92 Details of bonding type rmsd covalent geometry : bond 0.00353 ( 5310) covalent geometry : angle 0.76261 ( 7196) SS BOND : bond 0.00817 ( 8) SS BOND : angle 1.65436 ( 16) hydrogen bonds : bond 0.03718 ( 281) hydrogen bonds : angle 4.64141 ( 822) link_TRANS : bond 0.01333 ( 1) link_TRANS : angle 5.09416 ( 3) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1296 Ramachandran restraints generated. 648 Oldfield, 0 Emsley, 648 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1296 Ramachandran restraints generated. 648 Oldfield, 0 Emsley, 648 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 143 residues out of total 567 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 129 time to evaluate : 0.118 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 46 ILE cc_start: 0.7666 (mm) cc_final: 0.7371 (tp) REVERT: A 175 PHE cc_start: 0.8303 (t80) cc_final: 0.8011 (t80) REVERT: A 179 MET cc_start: 0.8396 (mmm) cc_final: 0.8171 (mtt) REVERT: A 440 MET cc_start: 0.7200 (ptm) cc_final: 0.6971 (ptm) REVERT: A 631 MET cc_start: 0.8356 (tpt) cc_final: 0.7196 (tmm) REVERT: A 640 TYR cc_start: 0.8514 (OUTLIER) cc_final: 0.7269 (t80) REVERT: B 43 GLN cc_start: 0.7356 (mt0) cc_final: 0.7076 (mp10) REVERT: B 93 GLU cc_start: 0.8081 (pp20) cc_final: 0.7624 (pp20) outliers start: 14 outliers final: 8 residues processed: 135 average time/residue: 0.0712 time to fit residues: 12.5994 Evaluate side-chains 123 residues out of total 567 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 114 time to evaluate : 0.132 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 250 THR Chi-restraints excluded: chain A residue 473 VAL Chi-restraints excluded: chain A residue 482 ILE Chi-restraints excluded: chain A residue 483 SER Chi-restraints excluded: chain A residue 553 THR Chi-restraints excluded: chain A residue 635 SER Chi-restraints excluded: chain A residue 640 TYR Chi-restraints excluded: chain A residue 645 TYR Chi-restraints excluded: chain B residue 52 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 67 random chunks: chunk 45 optimal weight: 1.9990 chunk 31 optimal weight: 1.9990 chunk 4 optimal weight: 0.7980 chunk 53 optimal weight: 0.6980 chunk 63 optimal weight: 2.9990 chunk 65 optimal weight: 0.7980 chunk 6 optimal weight: 2.9990 chunk 25 optimal weight: 0.7980 chunk 43 optimal weight: 0.7980 chunk 58 optimal weight: 0.2980 chunk 23 optimal weight: 1.9990 overall best weight: 0.6780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 204 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4012 r_free = 0.4012 target = 0.170033 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3700 r_free = 0.3700 target = 0.142266 restraints weight = 7810.678| |-----------------------------------------------------------------------------| r_work (start): 0.3681 rms_B_bonded: 2.23 r_work: 0.3574 rms_B_bonded: 3.04 restraints_weight: 0.5000 r_work (final): 0.3574 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7669 moved from start: 0.3184 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 5319 Z= 0.145 Angle : 0.703 11.666 7215 Z= 0.336 Chirality : 0.046 0.361 806 Planarity : 0.009 0.145 893 Dihedral : 7.346 82.274 730 Min Nonbonded Distance : 2.566 Molprobity Statistics. All-atom Clashscore : 8.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.32 % Favored : 95.68 % Rotamer: Outliers : 4.01 % Allowed : 14.57 % Favored : 81.42 % Cbeta Deviations : 0.16 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.62 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.12 (0.32), residues: 648 helix: 1.35 (0.27), residues: 331 sheet: -1.41 (0.76), residues: 53 loop : -1.24 (0.35), residues: 264 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B 49 TYR 0.024 0.001 TYR A 590 PHE 0.015 0.001 PHE A 68 TRP 0.005 0.001 TRP A 258 HIS 0.002 0.000 HIS A 451 Details of bonding type rmsd covalent geometry : bond 0.00328 ( 5310) covalent geometry : angle 0.69513 ( 7196) SS BOND : bond 0.00865 ( 8) SS BOND : angle 1.59744 ( 16) hydrogen bonds : bond 0.03585 ( 281) hydrogen bonds : angle 4.35511 ( 822) link_TRANS : bond 0.01009 ( 1) link_TRANS : angle 4.05484 ( 3) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1296 Ramachandran restraints generated. 648 Oldfield, 0 Emsley, 648 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1296 Ramachandran restraints generated. 648 Oldfield, 0 Emsley, 648 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 148 residues out of total 567 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 126 time to evaluate : 0.209 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 73 PHE cc_start: 0.9052 (t80) cc_final: 0.8570 (t80) REVERT: A 74 GLU cc_start: 0.8378 (mt-10) cc_final: 0.7958 (mm-30) REVERT: A 96 LEU cc_start: 0.8205 (OUTLIER) cc_final: 0.7936 (mp) REVERT: A 179 MET cc_start: 0.8555 (mmm) cc_final: 0.8346 (ttm) REVERT: A 440 MET cc_start: 0.7282 (OUTLIER) cc_final: 0.7036 (ptm) REVERT: A 640 TYR cc_start: 0.8539 (OUTLIER) cc_final: 0.7207 (t80) REVERT: B 86 GLN cc_start: 0.8149 (tp40) cc_final: 0.7522 (mm110) REVERT: B 87 MET cc_start: 0.7378 (ttm) cc_final: 0.7144 (ptp) REVERT: B 94 ASP cc_start: 0.7514 (m-30) cc_final: 0.6894 (m-30) outliers start: 22 outliers final: 15 residues processed: 134 average time/residue: 0.0685 time to fit residues: 12.2404 Evaluate side-chains 131 residues out of total 567 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 113 time to evaluate : 0.199 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 80 VAL Chi-restraints excluded: chain A residue 96 LEU Chi-restraints excluded: chain A residue 233 MET Chi-restraints excluded: chain A residue 237 ILE Chi-restraints excluded: chain A residue 250 THR Chi-restraints excluded: chain A residue 332 ILE Chi-restraints excluded: chain A residue 440 MET Chi-restraints excluded: chain A residue 463 CYS Chi-restraints excluded: chain A residue 464 ASN Chi-restraints excluded: chain A residue 473 VAL Chi-restraints excluded: chain A residue 482 ILE Chi-restraints excluded: chain A residue 483 SER Chi-restraints excluded: chain A residue 550 LEU Chi-restraints excluded: chain A residue 553 THR Chi-restraints excluded: chain A residue 640 TYR Chi-restraints excluded: chain A residue 645 TYR Chi-restraints excluded: chain B residue 26 CYS Chi-restraints excluded: chain B residue 52 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 67 random chunks: chunk 42 optimal weight: 2.9990 chunk 30 optimal weight: 0.6980 chunk 28 optimal weight: 0.7980 chunk 40 optimal weight: 0.7980 chunk 11 optimal weight: 0.5980 chunk 10 optimal weight: 0.9990 chunk 7 optimal weight: 0.9990 chunk 12 optimal weight: 0.0770 chunk 41 optimal weight: 0.0980 chunk 63 optimal weight: 7.9990 chunk 49 optimal weight: 0.8980 overall best weight: 0.4538 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 178 ASN ** A 204 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4024 r_free = 0.4024 target = 0.170898 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3701 r_free = 0.3701 target = 0.142450 restraints weight = 7751.165| |-----------------------------------------------------------------------------| r_work (start): 0.3685 rms_B_bonded: 2.25 r_work: 0.3582 rms_B_bonded: 3.03 restraints_weight: 0.5000 r_work (final): 0.3582 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7667 moved from start: 0.3540 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 5319 Z= 0.130 Angle : 0.670 9.429 7215 Z= 0.324 Chirality : 0.046 0.348 806 Planarity : 0.008 0.130 893 Dihedral : 6.917 85.904 730 Min Nonbonded Distance : 2.558 Molprobity Statistics. All-atom Clashscore : 8.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.17 % Favored : 95.83 % Rotamer: Outliers : 4.37 % Allowed : 15.66 % Favored : 79.96 % Cbeta Deviations : 0.16 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.47 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.59 (0.33), residues: 648 helix: 1.83 (0.28), residues: 331 sheet: -1.40 (0.75), residues: 53 loop : -1.10 (0.35), residues: 264 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 23 TYR 0.024 0.001 TYR A 590 PHE 0.020 0.001 PHE A 325 TRP 0.005 0.001 TRP A 602 HIS 0.002 0.001 HIS B 101 Details of bonding type rmsd covalent geometry : bond 0.00292 ( 5310) covalent geometry : angle 0.66208 ( 7196) SS BOND : bond 0.00503 ( 8) SS BOND : angle 1.36935 ( 16) hydrogen bonds : bond 0.03373 ( 281) hydrogen bonds : angle 4.17084 ( 822) link_TRANS : bond 0.01110 ( 1) link_TRANS : angle 4.33363 ( 3) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1296 Ramachandran restraints generated. 648 Oldfield, 0 Emsley, 648 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1296 Ramachandran restraints generated. 648 Oldfield, 0 Emsley, 648 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 147 residues out of total 567 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 123 time to evaluate : 0.224 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 34 LEU cc_start: 0.8261 (tp) cc_final: 0.8034 (mt) REVERT: A 46 ILE cc_start: 0.7833 (mm) cc_final: 0.7561 (tp) REVERT: A 96 LEU cc_start: 0.8213 (OUTLIER) cc_final: 0.7964 (mp) REVERT: A 179 MET cc_start: 0.8572 (mmm) cc_final: 0.8326 (mtt) REVERT: A 440 MET cc_start: 0.7254 (OUTLIER) cc_final: 0.7007 (ptm) REVERT: A 541 GLN cc_start: 0.8109 (tp40) cc_final: 0.7586 (tt0) REVERT: A 640 TYR cc_start: 0.8498 (OUTLIER) cc_final: 0.7383 (t80) REVERT: B 43 GLN cc_start: 0.7237 (mp10) cc_final: 0.6772 (mp10) REVERT: B 82 THR cc_start: 0.8338 (m) cc_final: 0.8103 (p) REVERT: B 94 ASP cc_start: 0.7306 (m-30) cc_final: 0.6678 (m-30) REVERT: B 114 GLN cc_start: 0.8022 (mm-40) cc_final: 0.7819 (mp10) outliers start: 24 outliers final: 12 residues processed: 134 average time/residue: 0.0640 time to fit residues: 11.6205 Evaluate side-chains 135 residues out of total 567 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 120 time to evaluate : 0.198 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 96 LEU Chi-restraints excluded: chain A residue 209 LEU Chi-restraints excluded: chain A residue 233 MET Chi-restraints excluded: chain A residue 248 THR Chi-restraints excluded: chain A residue 332 ILE Chi-restraints excluded: chain A residue 440 MET Chi-restraints excluded: chain A residue 473 VAL Chi-restraints excluded: chain A residue 482 ILE Chi-restraints excluded: chain A residue 483 SER Chi-restraints excluded: chain A residue 553 THR Chi-restraints excluded: chain A residue 640 TYR Chi-restraints excluded: chain A residue 645 TYR Chi-restraints excluded: chain B residue 9 VAL Chi-restraints excluded: chain B residue 22 LEU Chi-restraints excluded: chain B residue 26 CYS Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 67 random chunks: chunk 4 optimal weight: 0.5980 chunk 37 optimal weight: 3.9990 chunk 5 optimal weight: 0.6980 chunk 55 optimal weight: 9.9990 chunk 33 optimal weight: 0.8980 chunk 46 optimal weight: 0.5980 chunk 8 optimal weight: 3.9990 chunk 41 optimal weight: 6.9990 chunk 11 optimal weight: 0.5980 chunk 66 optimal weight: 4.9990 chunk 64 optimal weight: 1.9990 overall best weight: 0.6780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 204 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3993 r_free = 0.3993 target = 0.168648 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3660 r_free = 0.3660 target = 0.139462 restraints weight = 7815.608| |-----------------------------------------------------------------------------| r_work (start): 0.3646 rms_B_bonded: 2.24 r_work: 0.3540 rms_B_bonded: 3.03 restraints_weight: 0.5000 r_work (final): 0.3540 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7711 moved from start: 0.3787 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 5319 Z= 0.140 Angle : 0.662 9.457 7215 Z= 0.323 Chirality : 0.045 0.351 806 Planarity : 0.008 0.125 893 Dihedral : 6.899 84.386 730 Min Nonbonded Distance : 2.557 Molprobity Statistics. All-atom Clashscore : 9.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.32 % Favored : 95.68 % Rotamer: Outliers : 4.19 % Allowed : 15.85 % Favored : 79.96 % Cbeta Deviations : 0.16 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.47 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.80 (0.33), residues: 648 helix: 1.97 (0.28), residues: 331 sheet: -1.56 (0.71), residues: 56 loop : -0.88 (0.37), residues: 261 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 246 TYR 0.023 0.001 TYR A 590 PHE 0.014 0.002 PHE A 117 TRP 0.007 0.001 TRP B 40 HIS 0.002 0.001 HIS B 101 Details of bonding type rmsd covalent geometry : bond 0.00323 ( 5310) covalent geometry : angle 0.65215 ( 7196) SS BOND : bond 0.00643 ( 8) SS BOND : angle 1.63911 ( 16) hydrogen bonds : bond 0.03484 ( 281) hydrogen bonds : angle 4.16963 ( 822) link_TRANS : bond 0.01068 ( 1) link_TRANS : angle 4.37165 ( 3) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1296 Ramachandran restraints generated. 648 Oldfield, 0 Emsley, 648 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1296 Ramachandran restraints generated. 648 Oldfield, 0 Emsley, 648 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 141 residues out of total 567 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 118 time to evaluate : 0.207 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 46 ILE cc_start: 0.8017 (mm) cc_final: 0.7769 (tp) REVERT: A 96 LEU cc_start: 0.8296 (OUTLIER) cc_final: 0.8045 (mp) REVERT: A 440 MET cc_start: 0.7253 (OUTLIER) cc_final: 0.7028 (ptm) REVERT: A 541 GLN cc_start: 0.8064 (tp40) cc_final: 0.7615 (tt0) REVERT: A 640 TYR cc_start: 0.8519 (OUTLIER) cc_final: 0.7403 (t80) REVERT: B 82 THR cc_start: 0.8415 (m) cc_final: 0.8181 (p) REVERT: B 86 GLN cc_start: 0.8106 (tp40) cc_final: 0.7785 (tp40) REVERT: B 94 ASP cc_start: 0.7312 (m-30) cc_final: 0.6631 (m-30) outliers start: 23 outliers final: 16 residues processed: 131 average time/residue: 0.0647 time to fit residues: 11.3531 Evaluate side-chains 129 residues out of total 567 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 110 time to evaluate : 0.171 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 82 VAL Chi-restraints excluded: chain A residue 96 LEU Chi-restraints excluded: chain A residue 209 LEU Chi-restraints excluded: chain A residue 211 ILE Chi-restraints excluded: chain A residue 233 MET Chi-restraints excluded: chain A residue 248 THR Chi-restraints excluded: chain A residue 332 ILE Chi-restraints excluded: chain A residue 440 MET Chi-restraints excluded: chain A residue 464 ASN Chi-restraints excluded: chain A residue 473 VAL Chi-restraints excluded: chain A residue 482 ILE Chi-restraints excluded: chain A residue 483 SER Chi-restraints excluded: chain A residue 550 LEU Chi-restraints excluded: chain A residue 553 THR Chi-restraints excluded: chain A residue 640 TYR Chi-restraints excluded: chain A residue 645 TYR Chi-restraints excluded: chain B residue 9 VAL Chi-restraints excluded: chain B residue 22 LEU Chi-restraints excluded: chain B residue 26 CYS Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 67 random chunks: chunk 19 optimal weight: 0.3980 chunk 50 optimal weight: 6.9990 chunk 28 optimal weight: 0.9990 chunk 40 optimal weight: 5.9990 chunk 66 optimal weight: 0.9990 chunk 16 optimal weight: 0.7980 chunk 0 optimal weight: 4.9990 chunk 20 optimal weight: 0.6980 chunk 65 optimal weight: 5.9990 chunk 43 optimal weight: 1.9990 chunk 6 optimal weight: 0.9990 overall best weight: 0.7784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 204 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3981 r_free = 0.3981 target = 0.167198 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3635 r_free = 0.3635 target = 0.137293 restraints weight = 7749.917| |-----------------------------------------------------------------------------| r_work (start): 0.3626 rms_B_bonded: 2.26 r_work: 0.3524 rms_B_bonded: 2.98 restraints_weight: 0.5000 r_work (final): 0.3524 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7749 moved from start: 0.4060 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 5319 Z= 0.150 Angle : 0.676 10.737 7215 Z= 0.329 Chirality : 0.046 0.359 806 Planarity : 0.008 0.126 893 Dihedral : 6.876 84.673 730 Min Nonbonded Distance : 2.558 Molprobity Statistics. All-atom Clashscore : 9.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.94 % Favored : 95.06 % Rotamer: Outliers : 4.19 % Allowed : 16.94 % Favored : 78.87 % Cbeta Deviations : 0.16 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.47 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.94 (0.33), residues: 648 helix: 2.02 (0.28), residues: 332 sheet: -1.46 (0.72), residues: 56 loop : -0.72 (0.38), residues: 260 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 23 TYR 0.022 0.001 TYR A 590 PHE 0.016 0.002 PHE A 117 TRP 0.006 0.001 TRP A 602 HIS 0.002 0.001 HIS B 101 Details of bonding type rmsd covalent geometry : bond 0.00347 ( 5310) covalent geometry : angle 0.66649 ( 7196) SS BOND : bond 0.01037 ( 8) SS BOND : angle 1.61540 ( 16) hydrogen bonds : bond 0.03551 ( 281) hydrogen bonds : angle 4.21917 ( 822) link_TRANS : bond 0.01096 ( 1) link_TRANS : angle 4.33488 ( 3) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1296 Ramachandran restraints generated. 648 Oldfield, 0 Emsley, 648 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1296 Ramachandran restraints generated. 648 Oldfield, 0 Emsley, 648 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 142 residues out of total 567 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 119 time to evaluate : 0.199 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 96 LEU cc_start: 0.8337 (OUTLIER) cc_final: 0.8071 (mp) REVERT: A 170 MET cc_start: 0.8795 (mmt) cc_final: 0.8476 (mmt) REVERT: A 179 MET cc_start: 0.8834 (ttm) cc_final: 0.8525 (mtt) REVERT: A 268 PHE cc_start: 0.8723 (t80) cc_final: 0.8351 (t80) REVERT: A 440 MET cc_start: 0.7221 (OUTLIER) cc_final: 0.6997 (ptm) REVERT: A 577 MET cc_start: 0.8197 (OUTLIER) cc_final: 0.7975 (ttm) REVERT: A 640 TYR cc_start: 0.8520 (OUTLIER) cc_final: 0.7521 (t80) REVERT: B 82 THR cc_start: 0.8534 (m) cc_final: 0.8332 (p) REVERT: B 94 ASP cc_start: 0.7459 (m-30) cc_final: 0.6771 (m-30) outliers start: 23 outliers final: 15 residues processed: 131 average time/residue: 0.0659 time to fit residues: 11.5830 Evaluate side-chains 130 residues out of total 567 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 111 time to evaluate : 0.171 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 31 LEU Chi-restraints excluded: chain A residue 80 VAL Chi-restraints excluded: chain A residue 96 LEU Chi-restraints excluded: chain A residue 209 LEU Chi-restraints excluded: chain A residue 211 ILE Chi-restraints excluded: chain A residue 233 MET Chi-restraints excluded: chain A residue 248 THR Chi-restraints excluded: chain A residue 332 ILE Chi-restraints excluded: chain A residue 440 MET Chi-restraints excluded: chain A residue 473 VAL Chi-restraints excluded: chain A residue 482 ILE Chi-restraints excluded: chain A residue 483 SER Chi-restraints excluded: chain A residue 550 LEU Chi-restraints excluded: chain A residue 553 THR Chi-restraints excluded: chain A residue 577 MET Chi-restraints excluded: chain A residue 640 TYR Chi-restraints excluded: chain A residue 645 TYR Chi-restraints excluded: chain B residue 9 VAL Chi-restraints excluded: chain B residue 26 CYS Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 67 random chunks: chunk 29 optimal weight: 2.9990 chunk 60 optimal weight: 3.9990 chunk 48 optimal weight: 0.9990 chunk 32 optimal weight: 4.9990 chunk 0 optimal weight: 4.9990 chunk 5 optimal weight: 0.8980 chunk 24 optimal weight: 0.7980 chunk 27 optimal weight: 0.6980 chunk 13 optimal weight: 0.6980 chunk 34 optimal weight: 10.0000 chunk 17 optimal weight: 0.6980 overall best weight: 0.7580 ------------------------------------------------------------------------------- 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 = 0.3976 r_free = 0.3976 target = 0.166765 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3637 r_free = 0.3637 target = 0.137214 restraints weight = 7699.270| |-----------------------------------------------------------------------------| r_work (start): 0.3630 rms_B_bonded: 2.26 r_work: 0.3526 rms_B_bonded: 2.98 restraints_weight: 0.5000 r_work (final): 0.3526 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7755 moved from start: 0.4199 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 5319 Z= 0.148 Angle : 0.673 9.900 7215 Z= 0.330 Chirality : 0.046 0.358 806 Planarity : 0.008 0.125 893 Dihedral : 6.792 84.225 730 Min Nonbonded Distance : 2.564 Molprobity Statistics. All-atom Clashscore : 10.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.48 % Favored : 95.52 % Rotamer: Outliers : 4.01 % Allowed : 16.94 % Favored : 79.05 % Cbeta Deviations : 0.16 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.31 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.98 (0.33), residues: 648 helix: 2.01 (0.28), residues: 332 sheet: -1.30 (0.72), residues: 56 loop : -0.67 (0.38), residues: 260 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 23 TYR 0.022 0.001 TYR A 590 PHE 0.014 0.001 PHE A 117 TRP 0.005 0.001 TRP A 602 HIS 0.002 0.001 HIS A 115 Details of bonding type rmsd covalent geometry : bond 0.00342 ( 5310) covalent geometry : angle 0.66492 ( 7196) SS BOND : bond 0.00561 ( 8) SS BOND : angle 1.38356 ( 16) hydrogen bonds : bond 0.03650 ( 281) hydrogen bonds : angle 4.23354 ( 822) link_TRANS : bond 0.01082 ( 1) link_TRANS : angle 4.43059 ( 3) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1296 Ramachandran restraints generated. 648 Oldfield, 0 Emsley, 648 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1296 Ramachandran restraints generated. 648 Oldfield, 0 Emsley, 648 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 135 residues out of total 567 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 113 time to evaluate : 0.248 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 96 LEU cc_start: 0.8356 (OUTLIER) cc_final: 0.8076 (mp) REVERT: A 102 PHE cc_start: 0.8126 (t80) cc_final: 0.7875 (t80) REVERT: A 268 PHE cc_start: 0.8724 (t80) cc_final: 0.8402 (t80) REVERT: A 541 GLN cc_start: 0.8047 (tp40) cc_final: 0.7654 (tt0) REVERT: A 577 MET cc_start: 0.8196 (OUTLIER) cc_final: 0.7958 (ttm) REVERT: A 640 TYR cc_start: 0.8550 (OUTLIER) cc_final: 0.7490 (t80) REVERT: B 82 THR cc_start: 0.8540 (m) cc_final: 0.8338 (p) REVERT: B 94 ASP cc_start: 0.7271 (m-30) cc_final: 0.6704 (m-30) outliers start: 22 outliers final: 13 residues processed: 124 average time/residue: 0.0677 time to fit residues: 11.3854 Evaluate side-chains 125 residues out of total 567 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 109 time to evaluate : 0.183 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 80 VAL Chi-restraints excluded: chain A residue 82 VAL Chi-restraints excluded: chain A residue 96 LEU Chi-restraints excluded: chain A residue 209 LEU Chi-restraints excluded: chain A residue 233 MET Chi-restraints excluded: chain A residue 248 THR Chi-restraints excluded: chain A residue 332 ILE Chi-restraints excluded: chain A residue 464 ASN Chi-restraints excluded: chain A residue 473 VAL Chi-restraints excluded: chain A residue 550 LEU Chi-restraints excluded: chain A residue 553 THR Chi-restraints excluded: chain A residue 577 MET Chi-restraints excluded: chain A residue 640 TYR Chi-restraints excluded: chain A residue 645 TYR Chi-restraints excluded: chain B residue 9 VAL Chi-restraints excluded: chain B residue 26 CYS Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 67 random chunks: chunk 10 optimal weight: 7.9990 chunk 2 optimal weight: 0.7980 chunk 66 optimal weight: 0.9980 chunk 30 optimal weight: 0.6980 chunk 49 optimal weight: 1.9990 chunk 15 optimal weight: 0.8980 chunk 22 optimal weight: 0.7980 chunk 18 optimal weight: 5.9990 chunk 6 optimal weight: 0.8980 chunk 29 optimal weight: 1.9990 chunk 26 optimal weight: 0.7980 overall best weight: 0.7980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 43 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3967 r_free = 0.3967 target = 0.165978 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3631 r_free = 0.3631 target = 0.136888 restraints weight = 7682.483| |-----------------------------------------------------------------------------| r_work (start): 0.3619 rms_B_bonded: 2.21 r_work: 0.3518 rms_B_bonded: 2.92 restraints_weight: 0.5000 r_work: 0.3391 rms_B_bonded: 4.94 restraints_weight: 0.2500 r_work (final): 0.3391 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7868 moved from start: 0.4322 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.047 5319 Z= 0.152 Angle : 0.695 10.002 7215 Z= 0.339 Chirality : 0.046 0.365 806 Planarity : 0.008 0.124 893 Dihedral : 6.664 83.352 730 Min Nonbonded Distance : 2.569 Molprobity Statistics. All-atom Clashscore : 10.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.63 % Favored : 95.37 % Rotamer: Outliers : 4.19 % Allowed : 17.67 % Favored : 78.14 % Cbeta Deviations : 0.16 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.31 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.93 (0.33), residues: 648 helix: 1.94 (0.28), residues: 332 sheet: -1.30 (0.71), residues: 56 loop : -0.65 (0.38), residues: 260 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 103 TYR 0.022 0.001 TYR A 590 PHE 0.017 0.002 PHE A 117 TRP 0.006 0.001 TRP B 51 HIS 0.002 0.001 HIS A 115 Details of bonding type rmsd covalent geometry : bond 0.00351 ( 5310) covalent geometry : angle 0.68724 ( 7196) SS BOND : bond 0.00523 ( 8) SS BOND : angle 1.34172 ( 16) hydrogen bonds : bond 0.03713 ( 281) hydrogen bonds : angle 4.27322 ( 822) link_TRANS : bond 0.01076 ( 1) link_TRANS : angle 4.44319 ( 3) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1296 Ramachandran restraints generated. 648 Oldfield, 0 Emsley, 648 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1296 Ramachandran restraints generated. 648 Oldfield, 0 Emsley, 648 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 133 residues out of total 567 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 110 time to evaluate : 0.194 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 47 ILE cc_start: 0.8269 (OUTLIER) cc_final: 0.7684 (pt) REVERT: A 96 LEU cc_start: 0.8440 (OUTLIER) cc_final: 0.8134 (mp) REVERT: A 102 PHE cc_start: 0.8304 (t80) cc_final: 0.8034 (t80) REVERT: A 268 PHE cc_start: 0.8707 (t80) cc_final: 0.8397 (t80) REVERT: A 577 MET cc_start: 0.8353 (OUTLIER) cc_final: 0.8079 (ttm) REVERT: A 640 TYR cc_start: 0.8622 (OUTLIER) cc_final: 0.7525 (t80) REVERT: B 43 GLN cc_start: 0.7412 (mp10) cc_final: 0.6970 (mp10) REVERT: B 94 ASP cc_start: 0.7527 (m-30) cc_final: 0.6874 (m-30) outliers start: 23 outliers final: 17 residues processed: 126 average time/residue: 0.0719 time to fit residues: 12.0116 Evaluate side-chains 127 residues out of total 567 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 106 time to evaluate : 0.236 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 31 LEU Chi-restraints excluded: chain A residue 47 ILE Chi-restraints excluded: chain A residue 80 VAL Chi-restraints excluded: chain A residue 82 VAL Chi-restraints excluded: chain A residue 96 LEU Chi-restraints excluded: chain A residue 209 LEU Chi-restraints excluded: chain A residue 211 ILE Chi-restraints excluded: chain A residue 233 MET Chi-restraints excluded: chain A residue 248 THR Chi-restraints excluded: chain A residue 332 ILE Chi-restraints excluded: chain A residue 416 VAL Chi-restraints excluded: chain A residue 464 ASN Chi-restraints excluded: chain A residue 473 VAL Chi-restraints excluded: chain A residue 483 SER Chi-restraints excluded: chain A residue 550 LEU Chi-restraints excluded: chain A residue 553 THR Chi-restraints excluded: chain A residue 577 MET Chi-restraints excluded: chain A residue 640 TYR Chi-restraints excluded: chain A residue 645 TYR Chi-restraints excluded: chain B residue 9 VAL Chi-restraints excluded: chain B residue 26 CYS Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 67 random chunks: chunk 8 optimal weight: 0.7980 chunk 21 optimal weight: 0.0970 chunk 6 optimal weight: 0.7980 chunk 19 optimal weight: 0.8980 chunk 38 optimal weight: 2.9990 chunk 30 optimal weight: 0.5980 chunk 9 optimal weight: 0.8980 chunk 18 optimal weight: 2.9990 chunk 32 optimal weight: 7.9990 chunk 66 optimal weight: 5.9990 chunk 61 optimal weight: 2.9990 overall best weight: 0.6378 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 43 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3979 r_free = 0.3979 target = 0.167060 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3643 r_free = 0.3643 target = 0.137688 restraints weight = 7681.437| |-----------------------------------------------------------------------------| r_work (start): 0.3633 rms_B_bonded: 2.23 r_work: 0.3529 rms_B_bonded: 2.96 restraints_weight: 0.5000 r_work: 0.3403 rms_B_bonded: 4.99 restraints_weight: 0.2500 r_work (final): 0.3403 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7854 moved from start: 0.4417 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 5319 Z= 0.147 Angle : 0.718 15.041 7215 Z= 0.349 Chirality : 0.046 0.366 806 Planarity : 0.008 0.123 893 Dihedral : 6.527 82.908 730 Min Nonbonded Distance : 2.573 Molprobity Statistics. All-atom Clashscore : 10.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.48 % Favored : 95.52 % Rotamer: Outliers : 4.37 % Allowed : 18.03 % Favored : 77.60 % Cbeta Deviations : 0.16 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.31 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.01 (0.33), residues: 648 helix: 2.04 (0.28), residues: 332 sheet: -1.29 (0.69), residues: 56 loop : -0.67 (0.38), residues: 260 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 103 TYR 0.022 0.001 TYR A 590 PHE 0.025 0.002 PHE A 30 TRP 0.006 0.001 TRP B 51 HIS 0.002 0.001 HIS A 115 Details of bonding type rmsd covalent geometry : bond 0.00335 ( 5310) covalent geometry : angle 0.71124 ( 7196) SS BOND : bond 0.00472 ( 8) SS BOND : angle 1.21017 ( 16) hydrogen bonds : bond 0.03696 ( 281) hydrogen bonds : angle 4.31159 ( 822) link_TRANS : bond 0.01051 ( 1) link_TRANS : angle 4.36089 ( 3) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1296 Ramachandran restraints generated. 648 Oldfield, 0 Emsley, 648 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1296 Ramachandran restraints generated. 648 Oldfield, 0 Emsley, 648 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 134 residues out of total 567 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 110 time to evaluate : 0.207 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 47 ILE cc_start: 0.8244 (OUTLIER) cc_final: 0.7666 (pt) REVERT: A 96 LEU cc_start: 0.8395 (OUTLIER) cc_final: 0.8120 (mp) REVERT: A 102 PHE cc_start: 0.8344 (t80) cc_final: 0.7997 (t80) REVERT: A 179 MET cc_start: 0.8658 (mtp) cc_final: 0.8448 (mtt) REVERT: A 268 PHE cc_start: 0.8713 (t80) cc_final: 0.8420 (t80) REVERT: A 577 MET cc_start: 0.8317 (OUTLIER) cc_final: 0.8056 (ttm) REVERT: A 640 TYR cc_start: 0.8612 (OUTLIER) cc_final: 0.7545 (t80) REVERT: B 103 ARG cc_start: 0.7331 (ttt90) cc_final: 0.7068 (ttt-90) REVERT: B 111 GLN cc_start: 0.7998 (mt0) cc_final: 0.7107 (pt0) outliers start: 24 outliers final: 15 residues processed: 127 average time/residue: 0.0690 time to fit residues: 11.6750 Evaluate side-chains 123 residues out of total 567 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 104 time to evaluate : 0.206 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 31 LEU Chi-restraints excluded: chain A residue 34 LEU Chi-restraints excluded: chain A residue 47 ILE Chi-restraints excluded: chain A residue 80 VAL Chi-restraints excluded: chain A residue 82 VAL Chi-restraints excluded: chain A residue 96 LEU Chi-restraints excluded: chain A residue 209 LEU Chi-restraints excluded: chain A residue 233 MET Chi-restraints excluded: chain A residue 248 THR Chi-restraints excluded: chain A residue 332 ILE Chi-restraints excluded: chain A residue 416 VAL Chi-restraints excluded: chain A residue 464 ASN Chi-restraints excluded: chain A residue 483 SER Chi-restraints excluded: chain A residue 553 THR Chi-restraints excluded: chain A residue 577 MET Chi-restraints excluded: chain A residue 640 TYR Chi-restraints excluded: chain A residue 645 TYR Chi-restraints excluded: chain B residue 9 VAL Chi-restraints excluded: chain B residue 26 CYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 67 random chunks: chunk 45 optimal weight: 1.9990 chunk 53 optimal weight: 0.6980 chunk 18 optimal weight: 0.6980 chunk 38 optimal weight: 0.8980 chunk 24 optimal weight: 0.5980 chunk 46 optimal weight: 0.7980 chunk 15 optimal weight: 0.8980 chunk 12 optimal weight: 0.1980 chunk 13 optimal weight: 0.7980 chunk 48 optimal weight: 0.2980 chunk 61 optimal weight: 0.9990 overall best weight: 0.4980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 43 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3977 r_free = 0.3977 target = 0.167173 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3638 r_free = 0.3638 target = 0.137834 restraints weight = 7742.980| |-----------------------------------------------------------------------------| r_work (start): 0.3622 rms_B_bonded: 2.24 r_work: 0.3514 rms_B_bonded: 3.00 restraints_weight: 0.5000 r_work (final): 0.3514 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7733 moved from start: 0.4465 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.053 5319 Z= 0.139 Angle : 0.692 10.257 7215 Z= 0.340 Chirality : 0.046 0.368 806 Planarity : 0.008 0.123 893 Dihedral : 6.351 82.169 730 Min Nonbonded Distance : 2.581 Molprobity Statistics. All-atom Clashscore : 10.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.32 % Favored : 95.68 % Rotamer: Outliers : 3.64 % Allowed : 18.76 % Favored : 77.60 % Cbeta Deviations : 0.16 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.31 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.07 (0.33), residues: 648 helix: 2.10 (0.28), residues: 332 sheet: -1.17 (0.69), residues: 56 loop : -0.68 (0.38), residues: 260 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 103 TYR 0.022 0.001 TYR A 590 PHE 0.024 0.001 PHE A 30 TRP 0.007 0.001 TRP B 51 HIS 0.002 0.001 HIS B 101 Details of bonding type rmsd covalent geometry : bond 0.00314 ( 5310) covalent geometry : angle 0.68338 ( 7196) SS BOND : bond 0.00632 ( 8) SS BOND : angle 1.60783 ( 16) hydrogen bonds : bond 0.03435 ( 281) hydrogen bonds : angle 4.24025 ( 822) link_TRANS : bond 0.01031 ( 1) link_TRANS : angle 4.22303 ( 3) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1296 Ramachandran restraints generated. 648 Oldfield, 0 Emsley, 648 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1296 Ramachandran restraints generated. 648 Oldfield, 0 Emsley, 648 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 125 residues out of total 567 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 105 time to evaluate : 0.197 Fit side-chains revert: symmetry clash REVERT: A 96 LEU cc_start: 0.8280 (OUTLIER) cc_final: 0.8030 (mp) REVERT: A 268 PHE cc_start: 0.8642 (t80) cc_final: 0.8332 (t80) REVERT: A 541 GLN cc_start: 0.8081 (tp40) cc_final: 0.7810 (mm-40) REVERT: A 640 TYR cc_start: 0.8560 (OUTLIER) cc_final: 0.7536 (t80) REVERT: B 94 ASP cc_start: 0.7429 (m-30) cc_final: 0.7055 (m-30) REVERT: B 103 ARG cc_start: 0.7159 (ttt90) cc_final: 0.6931 (ttt-90) REVERT: B 111 GLN cc_start: 0.8122 (mt0) cc_final: 0.7256 (pt0) outliers start: 20 outliers final: 12 residues processed: 119 average time/residue: 0.0629 time to fit residues: 10.1948 Evaluate side-chains 118 residues out of total 567 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 104 time to evaluate : 0.193 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 31 LEU Chi-restraints excluded: chain A residue 47 ILE Chi-restraints excluded: chain A residue 80 VAL Chi-restraints excluded: chain A residue 96 LEU Chi-restraints excluded: chain A residue 209 LEU Chi-restraints excluded: chain A residue 233 MET Chi-restraints excluded: chain A residue 248 THR Chi-restraints excluded: chain A residue 332 ILE Chi-restraints excluded: chain A residue 483 SER Chi-restraints excluded: chain A residue 553 THR Chi-restraints excluded: chain A residue 640 TYR Chi-restraints excluded: chain A residue 645 TYR Chi-restraints excluded: chain B residue 9 VAL Chi-restraints excluded: chain B residue 26 CYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 67 random chunks: chunk 56 optimal weight: 9.9990 chunk 10 optimal weight: 8.9990 chunk 64 optimal weight: 0.9990 chunk 30 optimal weight: 0.5980 chunk 58 optimal weight: 0.9980 chunk 5 optimal weight: 0.9990 chunk 7 optimal weight: 1.9990 chunk 49 optimal weight: 0.6980 chunk 45 optimal weight: 2.9990 chunk 6 optimal weight: 0.5980 chunk 2 optimal weight: 0.9990 overall best weight: 0.7782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 43 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3971 r_free = 0.3971 target = 0.166242 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3630 r_free = 0.3630 target = 0.136837 restraints weight = 7776.227| |-----------------------------------------------------------------------------| r_work (start): 0.3617 rms_B_bonded: 2.24 r_work: 0.3514 rms_B_bonded: 2.96 restraints_weight: 0.5000 r_work: 0.3387 rms_B_bonded: 4.99 restraints_weight: 0.2500 r_work (final): 0.3387 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7872 moved from start: 0.4572 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.048 5319 Z= 0.153 Angle : 0.704 10.584 7215 Z= 0.346 Chirality : 0.047 0.385 806 Planarity : 0.008 0.123 893 Dihedral : 6.269 81.756 730 Min Nonbonded Distance : 2.574 Molprobity Statistics. All-atom Clashscore : 11.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.48 % Favored : 95.52 % Rotamer: Outliers : 2.55 % Allowed : 20.58 % Favored : 76.87 % Cbeta Deviations : 0.16 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.31 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.01 (0.33), residues: 648 helix: 2.01 (0.28), residues: 332 sheet: -1.10 (0.70), residues: 56 loop : -0.68 (0.38), residues: 260 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 103 TYR 0.022 0.001 TYR A 590 PHE 0.025 0.002 PHE A 30 TRP 0.005 0.001 TRP B 51 HIS 0.002 0.001 HIS A 115 Details of bonding type rmsd covalent geometry : bond 0.00355 ( 5310) covalent geometry : angle 0.69634 ( 7196) SS BOND : bond 0.00629 ( 8) SS BOND : angle 1.52450 ( 16) hydrogen bonds : bond 0.03583 ( 281) hydrogen bonds : angle 4.30915 ( 822) link_TRANS : bond 0.01001 ( 1) link_TRANS : angle 4.03279 ( 3) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1356.61 seconds wall clock time: 24 minutes 0.12 seconds (1440.12 seconds total)