Starting phenix.real_space_refine on Fri Jul 25 16:43:08 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9kgk_62321/07_2025/9kgk_62321.cif Found real_map, /net/cci-nas-00/data/ceres_data/9kgk_62321/07_2025/9kgk_62321.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.63 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9kgk_62321/07_2025/9kgk_62321.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9kgk_62321/07_2025/9kgk_62321.map" model { file = "/net/cci-nas-00/data/ceres_data/9kgk_62321/07_2025/9kgk_62321.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9kgk_62321/07_2025/9kgk_62321.cif" } resolution = 2.63 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } 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= 0.008 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: 4 Type Number sf(0) Gaussians S 41 5.16 5 C 4852 2.51 5 N 1263 2.21 5 O 1400 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 17 residue(s): 0.06s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5711/modules/chem_data/mon_lib" Total number of atoms: 7556 Number of models: 1 Model: "" Number of chains: 3 Chain: "A" Number of atoms: 5733 Number of conformers: 1 Conformer: "" Number of residues, atoms: 734, 5733 Classifications: {'peptide': 734} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 36, 'TRANS': 697} Chain breaks: 3 Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 3 Unresolved non-hydrogen dihedrals: 1 Unresolved non-hydrogen chiralities: 1 Chain: "E" Number of atoms: 876 Number of conformers: 1 Conformer: "" Number of residues, atoms: 114, 876 Classifications: {'peptide': 114} Link IDs: {'PTRANS': 3, 'TRANS': 110} Chain breaks: 1 Chain: "B" Number of atoms: 947 Number of conformers: 1 Conformer: "" Number of residues, atoms: 125, 947 Classifications: {'peptide': 125} Link IDs: {'PTRANS': 2, 'TRANS': 122} Time building chain proxies: 7.07, per 1000 atoms: 0.94 Number of scatterers: 7556 At special positions: 0 Unit cell: (78.183, 97.461, 168.147, 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 41 16.00 O 1400 8.00 N 1263 7.00 C 4852 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=7, symmetry=0 Simple disulfide: pdb=" SG CYS A 33 " - pdb=" SG CYS A 43 " distance=2.03 Simple disulfide: pdb=" SG CYS A 339 " - pdb=" SG CYS A 364 " distance=2.03 Simple disulfide: pdb=" SG CYS A 471 " - pdb=" SG CYS A 532 " distance=2.03 Simple disulfide: pdb=" SG CYS A 618 " - pdb=" SG CYS A 693 " distance=2.03 Simple disulfide: pdb=" SG CYS E 447 " - pdb=" SG CYS E 520 " distance=2.03 Simple disulfide: pdb=" SG CYS B 44 " - pdb=" SG CYS B 117 " distance=2.03 Simple disulfide: pdb=" SG CYS B 55 " - pdb=" SG CYS B 127 " 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: 3.26 Conformation dependent library (CDL) restraints added in 1.4 seconds 1918 Ramachandran restraints generated. 959 Oldfield, 0 Emsley, 959 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1820 Finding SS restraints... Secondary structure from input PDB file: 19 helices and 11 sheets defined 28.7% alpha, 14.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.96 Creating SS restraints... Processing helix chain 'A' and resid 170 through 175 Processing helix chain 'A' and resid 242 through 247 Processing helix chain 'A' and resid 335 through 339 removed outlier: 4.418A pdb=" N CYS A 339 " --> pdb=" O ASN A 336 " (cutoff:3.500A) Processing helix chain 'A' and resid 466 through 471 removed outlier: 3.902A pdb=" N CYS A 470 " --> pdb=" O TYR A 466 " (cutoff:3.500A) removed outlier: 3.819A pdb=" N CYS A 471 " --> pdb=" O ALA A 467 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 466 through 471' Processing helix chain 'A' and resid 472 through 474 No H-bonds generated for 'chain 'A' and resid 472 through 474' Processing helix chain 'A' and resid 538 through 565 Processing helix chain 'A' and resid 571 through 601 Processing helix chain 'A' and resid 604 through 615 removed outlier: 4.088A pdb=" N PHE A 608 " --> pdb=" O ARG A 604 " (cutoff:3.500A) removed outlier: 4.538A pdb=" N ILE A 610 " --> pdb=" O ALA A 606 " (cutoff:3.500A) removed outlier: 4.209A pdb=" N TRP A 611 " --> pdb=" O GLU A 607 " (cutoff:3.500A) Processing helix chain 'A' and resid 615 through 649 removed outlier: 4.068A pdb=" N LYS A 619 " --> pdb=" O GLY A 615 " (cutoff:3.500A) Processing helix chain 'A' and resid 658 through 683 Proline residue: A 680 - end of helix Processing helix chain 'A' and resid 704 through 732 Processing helix chain 'A' and resid 740 through 769 Proline residue: A 762 - end of helix Processing helix chain 'A' and resid 770 through 772 No H-bonds generated for 'chain 'A' and resid 770 through 772' Processing helix chain 'A' and resid 778 through 790 Processing helix chain 'A' and resid 791 through 805 Proline residue: A 798 - end of helix removed outlier: 3.725A pdb=" N ASN A 805 " --> pdb=" O TYR A 801 " (cutoff:3.500A) Processing helix chain 'A' and resid 805 through 820 removed outlier: 3.699A pdb=" N LYS A 809 " --> pdb=" O ASN A 805 " (cutoff:3.500A) Processing helix chain 'E' and resid 511 through 515 removed outlier: 3.780A pdb=" N THR E 515 " --> pdb=" O PRO E 512 " (cutoff:3.500A) Processing helix chain 'B' and resid 108 through 112 removed outlier: 3.582A pdb=" N THR B 112 " --> pdb=" O PRO B 109 " (cutoff:3.500A) Processing helix chain 'B' and resid 130 through 134 removed outlier: 3.575A pdb=" N TYR B 134 " --> pdb=" O GLU B 131 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 40 through 41 removed outlier: 7.035A pdb=" N LEU A 182 " --> pdb=" O HIS A 207 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 71 through 72 Processing sheet with id=AA3, first strand: chain 'A' and resid 191 through 192 Processing sheet with id=AA4, first strand: chain 'A' and resid 300 through 302 removed outlier: 6.416A pdb=" N LEU A 301 " --> pdb=" O THR A 325 " (cutoff:3.500A) removed outlier: 7.069A pdb=" N LEU A 324 " --> pdb=" O ASP A 349 " (cutoff:3.500A) removed outlier: 6.734A pdb=" N ILE A 370 " --> pdb=" O ASP A 395 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 379 through 380 Processing sheet with id=AA6, first strand: chain 'E' and resid 23 through 25 removed outlier: 4.096A pdb=" N THR E 502 " --> pdb=" O ASP E 497 " (cutoff:3.500A) removed outlier: 4.125A pdb=" N ASP E 497 " --> pdb=" O THR E 502 " (cutoff:3.500A) removed outlier: 4.003A pdb=" N GLN E 506 " --> pdb=" O THR E 493 " (cutoff:3.500A) removed outlier: 3.991A pdb=" N THR E 493 " --> pdb=" O GLN E 506 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'E' and resid 482 through 484 removed outlier: 5.626A pdb=" N GLY E 472 " --> pdb=" O ARG E 463 " (cutoff:3.500A) removed outlier: 6.606A pdb=" N ARG E 463 " --> pdb=" O GLY E 472 " (cutoff:3.500A) removed outlier: 3.844A pdb=" N ALA E 474 " --> pdb=" O TRP E 461 " (cutoff:3.500A) removed outlier: 3.624A pdb=" N PHE E 462 " --> pdb=" O TYR E 519 " (cutoff:3.500A) removed outlier: 3.542A pdb=" N MET E 517 " --> pdb=" O GLN E 464 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 27 through 29 Processing sheet with id=AA9, first strand: chain 'B' and resid 34 through 35 removed outlier: 6.734A pdb=" N VAL B 34 " --> pdb=" O SER B 146 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA9 Processing sheet with id=AB1, first strand: chain 'B' and resid 79 through 81 removed outlier: 6.678A pdb=" N TRP B 58 " --> pdb=" O ILE B 70 " (cutoff:3.500A) removed outlier: 4.552A pdb=" N THR B 72 " --> pdb=" O MET B 56 " (cutoff:3.500A) removed outlier: 6.828A pdb=" N MET B 56 " --> pdb=" O THR B 72 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'B' and resid 79 through 81 removed outlier: 6.678A pdb=" N TRP B 58 " --> pdb=" O ILE B 70 " (cutoff:3.500A) removed outlier: 4.552A pdb=" N THR B 72 " --> pdb=" O MET B 56 " (cutoff:3.500A) removed outlier: 6.828A pdb=" N MET B 56 " --> pdb=" O THR B 72 " (cutoff:3.500A) 281 hydrogen bonds defined for protein. 795 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: 2.76 Time building geometry restraints manager: 2.48 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 2415 1.34 - 1.46: 1776 1.46 - 1.58: 3479 1.58 - 1.70: 0 1.70 - 1.82: 56 Bond restraints: 7726 Sorted by residual: bond pdb=" C THR A 701 " pdb=" N PRO A 702 " ideal model delta sigma weight residual 1.334 1.359 -0.025 2.34e-02 1.83e+03 1.16e+00 bond pdb=" CA VAL A 168 " pdb=" CB VAL A 168 " ideal model delta sigma weight residual 1.537 1.525 0.012 1.29e-02 6.01e+03 8.93e-01 bond pdb=" CA ASN A 282 " pdb=" CB ASN A 282 " ideal model delta sigma weight residual 1.537 1.550 -0.013 1.38e-02 5.25e+03 8.84e-01 bond pdb=" CA CYS A 761 " pdb=" C CYS A 761 " ideal model delta sigma weight residual 1.520 1.532 -0.012 1.23e-02 6.61e+03 8.78e-01 bond pdb=" C GLN A 386 " pdb=" N GLY A 387 " ideal model delta sigma weight residual 1.331 1.317 0.013 1.46e-02 4.69e+03 8.25e-01 ... (remaining 7721 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.51: 10168 1.51 - 3.01: 263 3.01 - 4.52: 43 4.52 - 6.02: 12 6.02 - 7.53: 7 Bond angle restraints: 10493 Sorted by residual: angle pdb=" C ILE A 758 " pdb=" CA ILE A 758 " pdb=" CB ILE A 758 " ideal model delta sigma weight residual 111.97 108.16 3.81 1.28e+00 6.10e-01 8.86e+00 angle pdb=" CA GLY E 543 " pdb=" C GLY E 543 " pdb=" O GLY E 543 " ideal model delta sigma weight residual 122.22 120.48 1.74 6.50e-01 2.37e+00 7.21e+00 angle pdb=" N ASP A 137 " pdb=" CA ASP A 137 " pdb=" C ASP A 137 " ideal model delta sigma weight residual 111.24 114.51 -3.27 1.29e+00 6.01e-01 6.43e+00 angle pdb=" C PRO A 169 " pdb=" N VAL A 170 " pdb=" CA VAL A 170 " ideal model delta sigma weight residual 122.97 120.84 2.13 9.80e-01 1.04e+00 4.72e+00 angle pdb=" CA LEU A 728 " pdb=" CB LEU A 728 " pdb=" CG LEU A 728 " ideal model delta sigma weight residual 116.30 123.83 -7.53 3.50e+00 8.16e-02 4.62e+00 ... (remaining 10488 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.96: 4274 17.96 - 35.93: 262 35.93 - 53.89: 46 53.89 - 71.85: 4 71.85 - 89.81: 4 Dihedral angle restraints: 4590 sinusoidal: 1777 harmonic: 2813 Sorted by residual: dihedral pdb=" CB CYS A 471 " pdb=" SG CYS A 471 " pdb=" SG CYS A 532 " pdb=" CB CYS A 532 " ideal model delta sinusoidal sigma weight residual 93.00 143.67 -50.67 1 1.00e+01 1.00e-02 3.52e+01 dihedral pdb=" CB CYS A 618 " pdb=" SG CYS A 618 " pdb=" SG CYS A 693 " pdb=" CB CYS A 693 " ideal model delta sinusoidal sigma weight residual -86.00 -130.12 44.12 1 1.00e+01 1.00e-02 2.71e+01 dihedral pdb=" CA SER A 351 " pdb=" C SER A 351 " pdb=" N TYR A 352 " pdb=" CA TYR A 352 " ideal model delta harmonic sigma weight residual -180.00 -157.21 -22.79 0 5.00e+00 4.00e-02 2.08e+01 ... (remaining 4587 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.039: 821 0.039 - 0.077: 284 0.077 - 0.116: 86 0.116 - 0.154: 17 0.154 - 0.193: 2 Chirality restraints: 1210 Sorted by residual: chirality pdb=" CB THR A 183 " pdb=" CA THR A 183 " pdb=" OG1 THR A 183 " pdb=" CG2 THR A 183 " both_signs ideal model delta sigma weight residual False 2.55 2.36 0.19 2.00e-01 2.50e+01 9.27e-01 chirality pdb=" CB THR A 726 " pdb=" CA THR A 726 " pdb=" OG1 THR A 726 " pdb=" CG2 THR A 726 " both_signs ideal model delta sigma weight residual False 2.55 2.37 0.18 2.00e-01 2.50e+01 7.85e-01 chirality pdb=" CA ILE A 334 " pdb=" N ILE A 334 " pdb=" C ILE A 334 " pdb=" CB ILE A 334 " both_signs ideal model delta sigma weight residual False 2.43 2.58 -0.15 2.00e-01 2.50e+01 5.50e-01 ... (remaining 1207 not shown) Planarity restraints: 1330 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB PHE A 754 " 0.015 2.00e-02 2.50e+03 1.54e-02 4.13e+00 pdb=" CG PHE A 754 " -0.036 2.00e-02 2.50e+03 pdb=" CD1 PHE A 754 " 0.004 2.00e-02 2.50e+03 pdb=" CD2 PHE A 754 " 0.011 2.00e-02 2.50e+03 pdb=" CE1 PHE A 754 " 0.006 2.00e-02 2.50e+03 pdb=" CE2 PHE A 754 " -0.000 2.00e-02 2.50e+03 pdb=" CZ PHE A 754 " -0.000 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYR A 729 " 0.014 2.00e-02 2.50e+03 1.31e-02 3.42e+00 pdb=" CG TYR A 729 " -0.032 2.00e-02 2.50e+03 pdb=" CD1 TYR A 729 " 0.010 2.00e-02 2.50e+03 pdb=" CD2 TYR A 729 " 0.002 2.00e-02 2.50e+03 pdb=" CE1 TYR A 729 " -0.000 2.00e-02 2.50e+03 pdb=" CE2 TYR A 729 " 0.007 2.00e-02 2.50e+03 pdb=" CZ TYR A 729 " 0.000 2.00e-02 2.50e+03 pdb=" OH TYR A 729 " -0.001 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C SER E 455 " -0.027 5.00e-02 4.00e+02 4.05e-02 2.62e+00 pdb=" N PRO E 456 " 0.070 5.00e-02 4.00e+02 pdb=" CA PRO E 456 " -0.021 5.00e-02 4.00e+02 pdb=" CD PRO E 456 " -0.022 5.00e-02 4.00e+02 ... (remaining 1327 not shown) Histogram of nonbonded interaction distances: 2.14 - 2.69: 123 2.69 - 3.25: 7498 3.25 - 3.80: 11924 3.80 - 4.35: 15629 4.35 - 4.90: 26239 Nonbonded interactions: 61413 Sorted by model distance: nonbonded pdb=" O ASN A 353 " pdb=" ND2 ASN A 375 " model vdw 2.142 3.120 nonbonded pdb=" OG1 THR B 72 " pdb=" OG1 THR B 80 " model vdw 2.237 3.040 nonbonded pdb=" O ASN A 139 " pdb=" ND2 ASN A 163 " model vdw 2.277 3.120 nonbonded pdb=" O MET A 637 " pdb=" OG1 THR A 640 " model vdw 2.279 3.040 nonbonded pdb=" NE ARG A 542 " pdb=" OD2 ASP A 598 " model vdw 2.316 3.120 ... (remaining 61408 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: 34.560 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.020 Extract box with map and model: 0.350 Check model and map are aligned: 0.050 Set scattering table: 0.080 Process input model: 26.240 Find NCS groups from input model: 0.130 Set up NCS constraints: 0.060 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:17.870 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 79.370 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7854 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 : 0.003 0.030 7733 Z= 0.129 Angle : 0.613 7.527 10507 Z= 0.328 Chirality : 0.043 0.193 1210 Planarity : 0.004 0.040 1330 Dihedral : 12.007 89.813 2749 Min Nonbonded Distance : 2.142 Molprobity Statistics. All-atom Clashscore : 7.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.42 % Favored : 94.58 % Rotamer: Outliers : 0.00 % Allowed : 0.12 % Favored : 99.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.06 (0.28), residues: 959 helix: 2.53 (0.33), residues: 240 sheet: -1.16 (0.46), residues: 147 loop : -0.73 (0.26), residues: 572 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 159 HIS 0.004 0.001 HIS A 209 PHE 0.036 0.001 PHE A 754 TYR 0.032 0.002 TYR A 729 ARG 0.010 0.000 ARG E 525 Details of bonding type rmsd hydrogen bonds : bond 0.06564 ( 270) hydrogen bonds : angle 4.29934 ( 795) SS BOND : bond 0.00139 ( 7) SS BOND : angle 0.72202 ( 14) covalent geometry : bond 0.00261 ( 7726) covalent geometry : angle 0.61250 (10493) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1918 Ramachandran restraints generated. 959 Oldfield, 0 Emsley, 959 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1918 Ramachandran restraints generated. 959 Oldfield, 0 Emsley, 959 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 102 residues out of total 838 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 102 time to evaluate : 0.935 Fit side-chains REVERT: E 471 GLU cc_start: 0.8048 (mp0) cc_final: 0.7842 (mp0) REVERT: E 503 LEU cc_start: 0.8493 (mp) cc_final: 0.8247 (mp) outliers start: 0 outliers final: 0 residues processed: 102 average time/residue: 1.4867 time to fit residues: 161.5760 Evaluate side-chains 86 residues out of total 838 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 86 time to evaluate : 0.944 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 96 random chunks: chunk 81 optimal weight: 6.9990 chunk 72 optimal weight: 4.9990 chunk 40 optimal weight: 2.9990 chunk 24 optimal weight: 0.9980 chunk 49 optimal weight: 7.9990 chunk 38 optimal weight: 0.8980 chunk 75 optimal weight: 1.9990 chunk 29 optimal weight: 2.9990 chunk 45 optimal weight: 0.0980 chunk 56 optimal weight: 0.7980 chunk 87 optimal weight: 3.9990 overall best weight: 0.9582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 163 ASN ** A 209 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 375 ASN ** B 74 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3758 r_free = 0.3758 target = 0.108786 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3294 r_free = 0.3294 target = 0.078368 restraints weight = 14436.446| |-----------------------------------------------------------------------------| r_work (start): 0.3252 rms_B_bonded: 3.30 r_work: 0.3092 rms_B_bonded: 3.69 restraints_weight: 0.5000 r_work (final): 0.3092 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7682 moved from start: 0.1053 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.050 7733 Z= 0.186 Angle : 0.626 7.661 10507 Z= 0.315 Chirality : 0.045 0.184 1210 Planarity : 0.004 0.034 1330 Dihedral : 4.708 25.372 1030 Min Nonbonded Distance : 2.532 Molprobity Statistics. All-atom Clashscore : 6.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.47 % Favored : 93.53 % Rotamer: Outliers : 1.08 % Allowed : 8.48 % Favored : 90.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.01 (0.28), residues: 959 helix: 2.44 (0.33), residues: 240 sheet: -1.22 (0.44), residues: 154 loop : -0.74 (0.26), residues: 565 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 159 HIS 0.004 0.001 HIS A 256 PHE 0.012 0.001 PHE A 547 TYR 0.009 0.001 TYR E 457 ARG 0.005 0.000 ARG B 135 Details of bonding type rmsd hydrogen bonds : bond 0.03970 ( 270) hydrogen bonds : angle 4.15930 ( 795) SS BOND : bond 0.00194 ( 7) SS BOND : angle 0.82335 ( 14) covalent geometry : bond 0.00443 ( 7726) covalent geometry : angle 0.62524 (10493) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1918 Ramachandran restraints generated. 959 Oldfield, 0 Emsley, 959 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1918 Ramachandran restraints generated. 959 Oldfield, 0 Emsley, 959 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 96 residues out of total 838 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 87 time to evaluate : 0.943 Fit side-chains revert: symmetry clash REVERT: A 814 LEU cc_start: 0.8750 (tt) cc_final: 0.8408 (mp) REVERT: E 458 CYS cc_start: 0.8478 (t) cc_final: 0.7381 (p) REVERT: E 471 GLU cc_start: 0.8412 (mp0) cc_final: 0.7779 (mp0) REVERT: E 503 LEU cc_start: 0.7892 (mp) cc_final: 0.7675 (mp) REVERT: E 517 MET cc_start: 0.7704 (tpt) cc_final: 0.7376 (tpt) outliers start: 9 outliers final: 3 residues processed: 91 average time/residue: 0.9922 time to fit residues: 97.0440 Evaluate side-chains 86 residues out of total 838 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 83 time to evaluate : 0.808 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 523 THR Chi-restraints excluded: chain A residue 631 SER Chi-restraints excluded: chain E residue 493 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 96 random chunks: chunk 35 optimal weight: 2.9990 chunk 24 optimal weight: 0.9980 chunk 60 optimal weight: 6.9990 chunk 2 optimal weight: 2.9990 chunk 95 optimal weight: 0.7980 chunk 26 optimal weight: 1.9990 chunk 42 optimal weight: 3.9990 chunk 89 optimal weight: 0.9980 chunk 80 optimal weight: 7.9990 chunk 51 optimal weight: 0.8980 chunk 57 optimal weight: 8.9990 overall best weight: 1.1382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 209 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 = 0.3734 r_free = 0.3734 target = 0.107278 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3256 r_free = 0.3256 target = 0.076615 restraints weight = 14668.914| |-----------------------------------------------------------------------------| r_work (start): 0.3220 rms_B_bonded: 3.32 r_work: 0.3060 rms_B_bonded: 3.69 restraints_weight: 0.5000 r_work (final): 0.3060 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7706 moved from start: 0.1409 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.053 7733 Z= 0.211 Angle : 0.638 7.950 10507 Z= 0.322 Chirality : 0.045 0.205 1210 Planarity : 0.004 0.036 1330 Dihedral : 4.910 26.961 1030 Min Nonbonded Distance : 2.520 Molprobity Statistics. All-atom Clashscore : 6.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.26 % Favored : 93.74 % Rotamer: Outliers : 1.79 % Allowed : 10.51 % Favored : 87.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.10 (0.27), residues: 959 helix: 2.44 (0.33), residues: 240 sheet: -1.33 (0.43), residues: 154 loop : -0.82 (0.25), residues: 565 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 159 HIS 0.004 0.001 HIS A 256 PHE 0.013 0.001 PHE A 696 TYR 0.012 0.001 TYR A 234 ARG 0.005 0.000 ARG E 525 Details of bonding type rmsd hydrogen bonds : bond 0.04160 ( 270) hydrogen bonds : angle 4.23635 ( 795) SS BOND : bond 0.00214 ( 7) SS BOND : angle 0.82940 ( 14) covalent geometry : bond 0.00502 ( 7726) covalent geometry : angle 0.63745 (10493) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1918 Ramachandran restraints generated. 959 Oldfield, 0 Emsley, 959 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1918 Ramachandran restraints generated. 959 Oldfield, 0 Emsley, 959 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 101 residues out of total 838 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 86 time to evaluate : 0.870 Fit side-chains REVERT: A 814 LEU cc_start: 0.8786 (tt) cc_final: 0.8445 (mp) REVERT: E 459 MET cc_start: 0.7589 (ttm) cc_final: 0.7314 (ttt) REVERT: E 464 GLN cc_start: 0.7979 (OUTLIER) cc_final: 0.7356 (tp40) REVERT: E 468 LYS cc_start: 0.7377 (mppt) cc_final: 0.6992 (mppt) REVERT: E 471 GLU cc_start: 0.8616 (mp0) cc_final: 0.8032 (mp0) REVERT: E 517 MET cc_start: 0.7674 (OUTLIER) cc_final: 0.7313 (tpt) outliers start: 15 outliers final: 7 residues processed: 92 average time/residue: 0.9847 time to fit residues: 97.3992 Evaluate side-chains 89 residues out of total 838 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 80 time to evaluate : 0.925 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 329 THR Chi-restraints excluded: chain A residue 353 ASN Chi-restraints excluded: chain A residue 523 THR Chi-restraints excluded: chain A residue 631 SER Chi-restraints excluded: chain A residue 640 THR Chi-restraints excluded: chain A residue 675 VAL Chi-restraints excluded: chain E residue 464 GLN Chi-restraints excluded: chain E residue 493 THR Chi-restraints excluded: chain E residue 517 MET Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 96 random chunks: chunk 64 optimal weight: 4.9990 chunk 20 optimal weight: 0.9990 chunk 72 optimal weight: 3.9990 chunk 15 optimal weight: 0.8980 chunk 23 optimal weight: 0.7980 chunk 6 optimal weight: 0.9980 chunk 90 optimal weight: 0.9980 chunk 92 optimal weight: 0.6980 chunk 43 optimal weight: 0.0970 chunk 65 optimal weight: 3.9990 chunk 67 optimal weight: 4.9990 overall best weight: 0.6978 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 209 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 74 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3753 r_free = 0.3753 target = 0.108476 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3287 r_free = 0.3287 target = 0.078209 restraints weight = 14517.968| |-----------------------------------------------------------------------------| r_work (start): 0.3252 rms_B_bonded: 3.31 r_work: 0.3092 rms_B_bonded: 3.70 restraints_weight: 0.5000 r_work (final): 0.3092 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7686 moved from start: 0.1471 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 7733 Z= 0.147 Angle : 0.599 7.760 10507 Z= 0.300 Chirality : 0.044 0.226 1210 Planarity : 0.004 0.035 1330 Dihedral : 4.695 27.354 1030 Min Nonbonded Distance : 2.529 Molprobity Statistics. All-atom Clashscore : 7.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.15 % Favored : 93.85 % Rotamer: Outliers : 1.79 % Allowed : 11.83 % Favored : 86.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.05 (0.27), residues: 959 helix: 2.45 (0.33), residues: 240 sheet: -1.31 (0.43), residues: 154 loop : -0.76 (0.26), residues: 565 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A 612 HIS 0.003 0.001 HIS A 256 PHE 0.015 0.001 PHE A 696 TYR 0.012 0.001 TYR A 234 ARG 0.009 0.000 ARG E 525 Details of bonding type rmsd hydrogen bonds : bond 0.03766 ( 270) hydrogen bonds : angle 4.12741 ( 795) SS BOND : bond 0.00130 ( 7) SS BOND : angle 0.66305 ( 14) covalent geometry : bond 0.00348 ( 7726) covalent geometry : angle 0.59860 (10493) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1918 Ramachandran restraints generated. 959 Oldfield, 0 Emsley, 959 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1918 Ramachandran restraints generated. 959 Oldfield, 0 Emsley, 959 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 103 residues out of total 838 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 88 time to evaluate : 0.897 Fit side-chains REVERT: E 458 CYS cc_start: 0.8494 (t) cc_final: 0.8287 (m) REVERT: E 463 ARG cc_start: 0.8337 (ttp-170) cc_final: 0.8019 (ttp-170) REVERT: E 464 GLN cc_start: 0.7962 (OUTLIER) cc_final: 0.7385 (tp40) REVERT: E 468 LYS cc_start: 0.7392 (mppt) cc_final: 0.7019 (mppt) REVERT: E 471 GLU cc_start: 0.8666 (mp0) cc_final: 0.8038 (mp0) REVERT: E 517 MET cc_start: 0.7708 (OUTLIER) cc_final: 0.7249 (tpt) REVERT: B 28 GLU cc_start: 0.6592 (pm20) cc_final: 0.6358 (pm20) REVERT: B 110 GLU cc_start: 0.8673 (pp20) cc_final: 0.8432 (pp20) REVERT: B 139 GLN cc_start: 0.8718 (pm20) cc_final: 0.8272 (pm20) outliers start: 15 outliers final: 7 residues processed: 97 average time/residue: 0.9928 time to fit residues: 103.6336 Evaluate side-chains 92 residues out of total 838 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 83 time to evaluate : 0.915 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 329 THR Chi-restraints excluded: chain A residue 353 ASN Chi-restraints excluded: chain A residue 631 SER Chi-restraints excluded: chain A residue 640 THR Chi-restraints excluded: chain A residue 675 VAL Chi-restraints excluded: chain E residue 464 GLN Chi-restraints excluded: chain E residue 493 THR Chi-restraints excluded: chain E residue 517 MET Chi-restraints excluded: chain B residue 34 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 96 random chunks: chunk 56 optimal weight: 4.9990 chunk 39 optimal weight: 1.9990 chunk 33 optimal weight: 1.9990 chunk 74 optimal weight: 0.9980 chunk 92 optimal weight: 1.9990 chunk 76 optimal weight: 4.9990 chunk 85 optimal weight: 1.9990 chunk 52 optimal weight: 1.9990 chunk 81 optimal weight: 0.7980 chunk 14 optimal weight: 0.9990 chunk 73 optimal weight: 0.9990 overall best weight: 1.1586 ------------------------------------------------------------------------------- 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 = 0.3741 r_free = 0.3741 target = 0.107678 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3247 r_free = 0.3247 target = 0.076414 restraints weight = 14561.759| |-----------------------------------------------------------------------------| r_work (start): 0.3207 rms_B_bonded: 3.37 r_work: 0.3049 rms_B_bonded: 3.70 restraints_weight: 0.5000 r_work (final): 0.3049 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7698 moved from start: 0.1743 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.055 7733 Z= 0.215 Angle : 0.654 8.607 10507 Z= 0.326 Chirality : 0.046 0.245 1210 Planarity : 0.004 0.035 1330 Dihedral : 4.951 27.065 1030 Min Nonbonded Distance : 2.512 Molprobity Statistics. All-atom Clashscore : 7.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.36 % Favored : 93.64 % Rotamer: Outliers : 2.15 % Allowed : 13.02 % Favored : 84.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.13 (0.27), residues: 959 helix: 2.36 (0.33), residues: 240 sheet: -1.30 (0.43), residues: 154 loop : -0.83 (0.25), residues: 565 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 159 HIS 0.004 0.001 HIS A 256 PHE 0.015 0.001 PHE A 696 TYR 0.012 0.001 TYR A 234 ARG 0.003 0.000 ARG B 135 Details of bonding type rmsd hydrogen bonds : bond 0.04230 ( 270) hydrogen bonds : angle 4.23751 ( 795) SS BOND : bond 0.00183 ( 7) SS BOND : angle 0.81803 ( 14) covalent geometry : bond 0.00514 ( 7726) covalent geometry : angle 0.65338 (10493) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1918 Ramachandran restraints generated. 959 Oldfield, 0 Emsley, 959 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1918 Ramachandran restraints generated. 959 Oldfield, 0 Emsley, 959 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 105 residues out of total 838 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 87 time to evaluate : 0.814 Fit side-chains REVERT: A 279 LEU cc_start: 0.8500 (OUTLIER) cc_final: 0.8296 (pt) REVERT: E 458 CYS cc_start: 0.8541 (t) cc_final: 0.8076 (m) REVERT: E 463 ARG cc_start: 0.8401 (ttp-170) cc_final: 0.8097 (ttp-170) REVERT: E 464 GLN cc_start: 0.7930 (OUTLIER) cc_final: 0.7344 (tp40) REVERT: E 468 LYS cc_start: 0.7426 (mppt) cc_final: 0.7054 (mppt) REVERT: E 471 GLU cc_start: 0.8667 (mp0) cc_final: 0.8022 (mp0) REVERT: E 517 MET cc_start: 0.7667 (tpt) cc_final: 0.7299 (tpt) REVERT: B 125 ARG cc_start: 0.7388 (pmt170) cc_final: 0.6896 (pmt170) outliers start: 18 outliers final: 8 residues processed: 100 average time/residue: 0.9047 time to fit residues: 97.7394 Evaluate side-chains 97 residues out of total 838 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 87 time to evaluate : 0.890 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 183 THR Chi-restraints excluded: chain A residue 279 LEU Chi-restraints excluded: chain A residue 329 THR Chi-restraints excluded: chain A residue 353 ASN Chi-restraints excluded: chain A residue 631 SER Chi-restraints excluded: chain A residue 640 THR Chi-restraints excluded: chain A residue 675 VAL Chi-restraints excluded: chain E residue 464 GLN Chi-restraints excluded: chain E residue 493 THR Chi-restraints excluded: chain B residue 34 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 96 random chunks: chunk 54 optimal weight: 1.9990 chunk 46 optimal weight: 0.1980 chunk 4 optimal weight: 1.9990 chunk 55 optimal weight: 0.9980 chunk 78 optimal weight: 3.9990 chunk 32 optimal weight: 1.9990 chunk 37 optimal weight: 1.9990 chunk 79 optimal weight: 0.9980 chunk 20 optimal weight: 0.9990 chunk 92 optimal weight: 1.9990 chunk 66 optimal weight: 0.6980 overall best weight: 0.7782 ------------------------------------------------------------------------------- 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 = 0.3755 r_free = 0.3755 target = 0.108642 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3271 r_free = 0.3271 target = 0.077729 restraints weight = 14581.178| |-----------------------------------------------------------------------------| r_work (start): 0.3237 rms_B_bonded: 3.37 r_work: 0.3079 rms_B_bonded: 3.71 restraints_weight: 0.5000 r_work (final): 0.3079 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7680 moved from start: 0.1765 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 7733 Z= 0.158 Angle : 0.627 7.942 10507 Z= 0.313 Chirality : 0.044 0.253 1210 Planarity : 0.004 0.034 1330 Dihedral : 4.730 27.137 1030 Min Nonbonded Distance : 2.516 Molprobity Statistics. All-atom Clashscore : 8.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.94 % Favored : 94.06 % Rotamer: Outliers : 2.87 % Allowed : 13.98 % Favored : 83.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.04 (0.27), residues: 959 helix: 2.44 (0.33), residues: 240 sheet: -1.20 (0.43), residues: 154 loop : -0.79 (0.25), residues: 565 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 612 HIS 0.003 0.001 HIS A 256 PHE 0.017 0.001 PHE A 696 TYR 0.012 0.001 TYR A 234 ARG 0.002 0.000 ARG B 135 Details of bonding type rmsd hydrogen bonds : bond 0.03859 ( 270) hydrogen bonds : angle 4.14393 ( 795) SS BOND : bond 0.00142 ( 7) SS BOND : angle 0.74170 ( 14) covalent geometry : bond 0.00377 ( 7726) covalent geometry : angle 0.62646 (10493) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1918 Ramachandran restraints generated. 959 Oldfield, 0 Emsley, 959 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1918 Ramachandran restraints generated. 959 Oldfield, 0 Emsley, 959 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 113 residues out of total 838 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 89 time to evaluate : 0.833 Fit side-chains REVERT: A 424 GLU cc_start: 0.8465 (tm-30) cc_final: 0.8213 (tm-30) REVERT: A 814 LEU cc_start: 0.9044 (OUTLIER) cc_final: 0.8763 (tt) REVERT: E 458 CYS cc_start: 0.8465 (t) cc_final: 0.8163 (m) REVERT: E 463 ARG cc_start: 0.8430 (ttp-170) cc_final: 0.8086 (ttm170) REVERT: E 464 GLN cc_start: 0.7936 (OUTLIER) cc_final: 0.7340 (tp40) REVERT: E 468 LYS cc_start: 0.7512 (mppt) cc_final: 0.7142 (mppt) REVERT: E 471 GLU cc_start: 0.8706 (mp0) cc_final: 0.8079 (mp0) REVERT: E 517 MET cc_start: 0.7737 (OUTLIER) cc_final: 0.7220 (tpt) REVERT: B 110 GLU cc_start: 0.8779 (pp20) cc_final: 0.8568 (pp20) REVERT: B 125 ARG cc_start: 0.7311 (pmt170) cc_final: 0.6810 (pmt170) outliers start: 24 outliers final: 10 residues processed: 104 average time/residue: 1.0364 time to fit residues: 116.1413 Evaluate side-chains 96 residues out of total 838 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 83 time to evaluate : 0.843 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 329 THR Chi-restraints excluded: chain A residue 353 ASN Chi-restraints excluded: chain A residue 523 THR Chi-restraints excluded: chain A residue 631 SER Chi-restraints excluded: chain A residue 640 THR Chi-restraints excluded: chain A residue 675 VAL Chi-restraints excluded: chain A residue 707 THR Chi-restraints excluded: chain A residue 795 CYS Chi-restraints excluded: chain A residue 814 LEU Chi-restraints excluded: chain E residue 464 GLN Chi-restraints excluded: chain E residue 517 MET Chi-restraints excluded: chain E residue 520 CYS Chi-restraints excluded: chain B residue 34 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 96 random chunks: chunk 60 optimal weight: 4.9990 chunk 59 optimal weight: 0.8980 chunk 2 optimal weight: 2.9990 chunk 58 optimal weight: 3.9990 chunk 70 optimal weight: 0.6980 chunk 66 optimal weight: 0.5980 chunk 37 optimal weight: 0.0570 chunk 38 optimal weight: 2.9990 chunk 74 optimal weight: 0.9990 chunk 79 optimal weight: 0.9980 chunk 34 optimal weight: 0.7980 overall best weight: 0.6098 ------------------------------------------------------------------------------- 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 = 0.3767 r_free = 0.3767 target = 0.109520 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3287 r_free = 0.3287 target = 0.078604 restraints weight = 14479.458| |-----------------------------------------------------------------------------| r_work (start): 0.3254 rms_B_bonded: 3.38 r_work: 0.3097 rms_B_bonded: 3.73 restraints_weight: 0.5000 r_work (final): 0.3097 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7681 moved from start: 0.1750 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.050 7733 Z= 0.138 Angle : 0.618 7.724 10507 Z= 0.307 Chirality : 0.044 0.261 1210 Planarity : 0.003 0.032 1330 Dihedral : 4.590 27.152 1030 Min Nonbonded Distance : 2.517 Molprobity Statistics. All-atom Clashscore : 8.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.36 % Favored : 93.64 % Rotamer: Outliers : 1.79 % Allowed : 15.65 % Favored : 82.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.01 (0.28), residues: 959 helix: 2.38 (0.33), residues: 240 sheet: -1.13 (0.44), residues: 154 loop : -0.74 (0.26), residues: 565 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 474 HIS 0.003 0.001 HIS A 256 PHE 0.018 0.001 PHE A 696 TYR 0.012 0.001 TYR A 234 ARG 0.004 0.000 ARG B 135 Details of bonding type rmsd hydrogen bonds : bond 0.03643 ( 270) hydrogen bonds : angle 4.12653 ( 795) SS BOND : bond 0.00137 ( 7) SS BOND : angle 0.68288 ( 14) covalent geometry : bond 0.00327 ( 7726) covalent geometry : angle 0.61756 (10493) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1918 Ramachandran restraints generated. 959 Oldfield, 0 Emsley, 959 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1918 Ramachandran restraints generated. 959 Oldfield, 0 Emsley, 959 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 105 residues out of total 838 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 90 time to evaluate : 0.922 Fit side-chains revert: symmetry clash REVERT: A 814 LEU cc_start: 0.9119 (OUTLIER) cc_final: 0.8825 (tt) REVERT: E 458 CYS cc_start: 0.8519 (t) cc_final: 0.8081 (m) REVERT: E 463 ARG cc_start: 0.8421 (ttp-170) cc_final: 0.8184 (ttm170) REVERT: E 464 GLN cc_start: 0.7992 (tm-30) cc_final: 0.7386 (tp40) REVERT: E 471 GLU cc_start: 0.8723 (mp0) cc_final: 0.8093 (mp0) REVERT: E 517 MET cc_start: 0.7760 (OUTLIER) cc_final: 0.7225 (tpt) REVERT: B 125 ARG cc_start: 0.7326 (pmt170) cc_final: 0.6827 (pmt170) REVERT: B 139 GLN cc_start: 0.8639 (pm20) cc_final: 0.8430 (pm20) outliers start: 15 outliers final: 9 residues processed: 99 average time/residue: 1.0139 time to fit residues: 108.1008 Evaluate side-chains 95 residues out of total 838 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 84 time to evaluate : 0.839 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 353 ASN Chi-restraints excluded: chain A residue 598 ASP Chi-restraints excluded: chain A residue 631 SER Chi-restraints excluded: chain A residue 640 THR Chi-restraints excluded: chain A residue 675 VAL Chi-restraints excluded: chain A residue 707 THR Chi-restraints excluded: chain A residue 795 CYS Chi-restraints excluded: chain A residue 814 LEU Chi-restraints excluded: chain E residue 517 MET Chi-restraints excluded: chain E residue 520 CYS Chi-restraints excluded: chain B residue 34 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 96 random chunks: chunk 9 optimal weight: 0.0870 chunk 62 optimal weight: 0.6980 chunk 64 optimal weight: 0.8980 chunk 34 optimal weight: 0.9990 chunk 89 optimal weight: 0.9980 chunk 81 optimal weight: 0.8980 chunk 29 optimal weight: 1.9990 chunk 44 optimal weight: 0.5980 chunk 92 optimal weight: 1.9990 chunk 68 optimal weight: 1.9990 chunk 26 optimal weight: 2.9990 overall best weight: 0.6358 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 105 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3770 r_free = 0.3770 target = 0.109604 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3294 r_free = 0.3294 target = 0.078848 restraints weight = 14541.502| |-----------------------------------------------------------------------------| r_work (start): 0.3255 rms_B_bonded: 3.37 r_work: 0.3098 rms_B_bonded: 3.71 restraints_weight: 0.5000 r_work (final): 0.3098 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7681 moved from start: 0.1814 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.054 7733 Z= 0.146 Angle : 0.653 9.828 10507 Z= 0.325 Chirality : 0.045 0.332 1210 Planarity : 0.003 0.032 1330 Dihedral : 4.568 27.205 1030 Min Nonbonded Distance : 2.315 Molprobity Statistics. All-atom Clashscore : 8.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.36 % Favored : 93.64 % Rotamer: Outliers : 2.03 % Allowed : 16.37 % Favored : 81.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.06 (0.27), residues: 959 helix: 2.37 (0.33), residues: 240 sheet: -1.32 (0.44), residues: 147 loop : -0.74 (0.25), residues: 572 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 474 HIS 0.003 0.001 HIS A 402 PHE 0.018 0.001 PHE A 696 TYR 0.012 0.001 TYR A 234 ARG 0.004 0.000 ARG B 135 Details of bonding type rmsd hydrogen bonds : bond 0.03709 ( 270) hydrogen bonds : angle 4.10440 ( 795) SS BOND : bond 0.00132 ( 7) SS BOND : angle 0.68086 ( 14) covalent geometry : bond 0.00346 ( 7726) covalent geometry : angle 0.65302 (10493) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1918 Ramachandran restraints generated. 959 Oldfield, 0 Emsley, 959 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1918 Ramachandran restraints generated. 959 Oldfield, 0 Emsley, 959 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 106 residues out of total 838 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 89 time to evaluate : 0.925 Fit side-chains revert: symmetry clash REVERT: A 814 LEU cc_start: 0.9065 (OUTLIER) cc_final: 0.8808 (tt) REVERT: E 458 CYS cc_start: 0.8512 (t) cc_final: 0.8027 (m) REVERT: E 464 GLN cc_start: 0.7991 (OUTLIER) cc_final: 0.7373 (tp40) REVERT: E 471 GLU cc_start: 0.8722 (mp0) cc_final: 0.8087 (mp0) REVERT: E 517 MET cc_start: 0.7723 (OUTLIER) cc_final: 0.7194 (tpt) REVERT: B 125 ARG cc_start: 0.7389 (pmt170) cc_final: 0.6938 (pmt170) outliers start: 17 outliers final: 9 residues processed: 100 average time/residue: 0.9879 time to fit residues: 106.3298 Evaluate side-chains 96 residues out of total 838 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 84 time to evaluate : 0.816 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 353 ASN Chi-restraints excluded: chain A residue 598 ASP Chi-restraints excluded: chain A residue 631 SER Chi-restraints excluded: chain A residue 640 THR Chi-restraints excluded: chain A residue 675 VAL Chi-restraints excluded: chain A residue 707 THR Chi-restraints excluded: chain A residue 795 CYS Chi-restraints excluded: chain A residue 814 LEU Chi-restraints excluded: chain E residue 464 GLN Chi-restraints excluded: chain E residue 517 MET Chi-restraints excluded: chain E residue 520 CYS Chi-restraints excluded: chain B residue 34 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 96 random chunks: chunk 28 optimal weight: 1.9990 chunk 39 optimal weight: 0.0970 chunk 35 optimal weight: 0.9990 chunk 33 optimal weight: 1.9990 chunk 44 optimal weight: 0.8980 chunk 52 optimal weight: 1.9990 chunk 60 optimal weight: 3.9990 chunk 65 optimal weight: 9.9990 chunk 82 optimal weight: 2.9990 chunk 76 optimal weight: 2.9990 chunk 55 optimal weight: 0.9990 overall best weight: 0.9984 ------------------------------------------------------------------------------- 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 = 0.3742 r_free = 0.3742 target = 0.107744 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3254 r_free = 0.3254 target = 0.076741 restraints weight = 14839.459| |-----------------------------------------------------------------------------| r_work (start): 0.3215 rms_B_bonded: 3.38 r_work: 0.3057 rms_B_bonded: 3.72 restraints_weight: 0.5000 r_work (final): 0.3057 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7692 moved from start: 0.1975 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.062 7733 Z= 0.195 Angle : 0.695 11.379 10507 Z= 0.344 Chirality : 0.047 0.381 1210 Planarity : 0.004 0.034 1330 Dihedral : 4.838 28.903 1030 Min Nonbonded Distance : 2.485 Molprobity Statistics. All-atom Clashscore : 7.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.36 % Favored : 93.64 % Rotamer: Outliers : 1.91 % Allowed : 16.85 % Favored : 81.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.12 (0.27), residues: 959 helix: 2.29 (0.33), residues: 240 sheet: -1.17 (0.43), residues: 154 loop : -0.81 (0.25), residues: 565 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 159 HIS 0.004 0.001 HIS A 256 PHE 0.018 0.001 PHE A 696 TYR 0.011 0.001 TYR A 234 ARG 0.004 0.000 ARG B 135 Details of bonding type rmsd hydrogen bonds : bond 0.04103 ( 270) hydrogen bonds : angle 4.24883 ( 795) SS BOND : bond 0.00180 ( 7) SS BOND : angle 0.77780 ( 14) covalent geometry : bond 0.00468 ( 7726) covalent geometry : angle 0.69461 (10493) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1918 Ramachandran restraints generated. 959 Oldfield, 0 Emsley, 959 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1918 Ramachandran restraints generated. 959 Oldfield, 0 Emsley, 959 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 104 residues out of total 838 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 88 time to evaluate : 0.813 Fit side-chains revert: symmetry clash REVERT: E 458 CYS cc_start: 0.8634 (t) cc_final: 0.8066 (m) REVERT: E 464 GLN cc_start: 0.7953 (OUTLIER) cc_final: 0.7337 (tp40) REVERT: E 471 GLU cc_start: 0.8719 (mp0) cc_final: 0.8079 (mp0) REVERT: E 517 MET cc_start: 0.7703 (OUTLIER) cc_final: 0.7351 (tpt) REVERT: E 542 GLN cc_start: 0.8465 (mp10) cc_final: 0.7723 (pt0) outliers start: 16 outliers final: 9 residues processed: 97 average time/residue: 0.9502 time to fit residues: 99.1443 Evaluate side-chains 94 residues out of total 838 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 83 time to evaluate : 0.881 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 353 ASN Chi-restraints excluded: chain A residue 523 THR Chi-restraints excluded: chain A residue 598 ASP Chi-restraints excluded: chain A residue 631 SER Chi-restraints excluded: chain A residue 640 THR Chi-restraints excluded: chain A residue 675 VAL Chi-restraints excluded: chain A residue 795 CYS Chi-restraints excluded: chain E residue 464 GLN Chi-restraints excluded: chain E residue 517 MET Chi-restraints excluded: chain E residue 520 CYS Chi-restraints excluded: chain B residue 34 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 96 random chunks: chunk 48 optimal weight: 1.9990 chunk 77 optimal weight: 0.9980 chunk 92 optimal weight: 1.9990 chunk 8 optimal weight: 0.2980 chunk 6 optimal weight: 1.9990 chunk 79 optimal weight: 0.5980 chunk 54 optimal weight: 0.7980 chunk 36 optimal weight: 1.9990 chunk 84 optimal weight: 0.9990 chunk 41 optimal weight: 1.9990 chunk 20 optimal weight: 0.5980 overall best weight: 0.6580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 731 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3762 r_free = 0.3762 target = 0.109113 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3280 r_free = 0.3280 target = 0.078248 restraints weight = 14712.291| |-----------------------------------------------------------------------------| r_work (start): 0.3246 rms_B_bonded: 3.37 r_work: 0.3091 rms_B_bonded: 3.73 restraints_weight: 0.5000 r_work (final): 0.3091 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7684 moved from start: 0.1964 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.074 7733 Z= 0.151 Angle : 0.680 12.053 10507 Z= 0.336 Chirality : 0.046 0.376 1210 Planarity : 0.004 0.034 1330 Dihedral : 4.666 27.596 1030 Min Nonbonded Distance : 2.463 Molprobity Statistics. All-atom Clashscore : 8.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.94 % Favored : 94.06 % Rotamer: Outliers : 1.19 % Allowed : 17.92 % Favored : 80.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.14 (0.27), residues: 959 helix: 2.27 (0.33), residues: 241 sheet: -1.34 (0.43), residues: 147 loop : -0.80 (0.25), residues: 571 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP E 461 HIS 0.003 0.001 HIS A 256 PHE 0.019 0.001 PHE A 696 TYR 0.011 0.001 TYR A 234 ARG 0.004 0.000 ARG B 135 Details of bonding type rmsd hydrogen bonds : bond 0.03823 ( 270) hydrogen bonds : angle 4.20449 ( 795) SS BOND : bond 0.00143 ( 7) SS BOND : angle 0.67259 ( 14) covalent geometry : bond 0.00362 ( 7726) covalent geometry : angle 0.68001 (10493) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1918 Ramachandran restraints generated. 959 Oldfield, 0 Emsley, 959 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1918 Ramachandran restraints generated. 959 Oldfield, 0 Emsley, 959 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 95 residues out of total 838 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 85 time to evaluate : 0.858 Fit side-chains revert: symmetry clash REVERT: E 458 CYS cc_start: 0.8591 (t) cc_final: 0.8053 (m) REVERT: E 464 GLN cc_start: 0.7982 (tm-30) cc_final: 0.7366 (tp40) REVERT: E 471 GLU cc_start: 0.8707 (mp0) cc_final: 0.8055 (mp0) REVERT: E 517 MET cc_start: 0.7737 (OUTLIER) cc_final: 0.7342 (tpt) REVERT: E 542 GLN cc_start: 0.8452 (mp10) cc_final: 0.7734 (pt0) REVERT: B 125 ARG cc_start: 0.7551 (pmt170) cc_final: 0.7156 (pmt170) outliers start: 10 outliers final: 8 residues processed: 91 average time/residue: 1.0471 time to fit residues: 102.3319 Evaluate side-chains 93 residues out of total 838 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 84 time to evaluate : 0.839 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 353 ASN Chi-restraints excluded: chain A residue 598 ASP Chi-restraints excluded: chain A residue 631 SER Chi-restraints excluded: chain A residue 640 THR Chi-restraints excluded: chain A residue 675 VAL Chi-restraints excluded: chain A residue 795 CYS Chi-restraints excluded: chain E residue 517 MET Chi-restraints excluded: chain E residue 520 CYS Chi-restraints excluded: chain B residue 34 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 96 random chunks: chunk 82 optimal weight: 2.9990 chunk 30 optimal weight: 1.9990 chunk 87 optimal weight: 2.9990 chunk 19 optimal weight: 1.9990 chunk 4 optimal weight: 2.9990 chunk 12 optimal weight: 0.9980 chunk 49 optimal weight: 0.3980 chunk 45 optimal weight: 0.1980 chunk 9 optimal weight: 0.0170 chunk 54 optimal weight: 0.5980 chunk 31 optimal weight: 0.9980 overall best weight: 0.4418 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 731 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3780 r_free = 0.3780 target = 0.110456 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3307 r_free = 0.3307 target = 0.079723 restraints weight = 14461.613| |-----------------------------------------------------------------------------| r_work (start): 0.3276 rms_B_bonded: 3.37 r_work: 0.3119 rms_B_bonded: 3.75 restraints_weight: 0.5000 r_work (final): 0.3119 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7666 moved from start: 0.1944 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.075 7733 Z= 0.127 Angle : 0.661 12.177 10507 Z= 0.325 Chirality : 0.045 0.376 1210 Planarity : 0.003 0.037 1330 Dihedral : 4.465 27.609 1030 Min Nonbonded Distance : 2.501 Molprobity Statistics. All-atom Clashscore : 7.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.26 % Favored : 93.74 % Rotamer: Outliers : 1.08 % Allowed : 17.80 % Favored : 81.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.08 (0.27), residues: 959 helix: 2.30 (0.33), residues: 241 sheet: -1.33 (0.43), residues: 147 loop : -0.75 (0.26), residues: 571 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 474 HIS 0.003 0.000 HIS A 209 PHE 0.027 0.001 PHE A 696 TYR 0.011 0.001 TYR A 234 ARG 0.004 0.000 ARG B 135 Details of bonding type rmsd hydrogen bonds : bond 0.03522 ( 270) hydrogen bonds : angle 4.14581 ( 795) SS BOND : bond 0.00128 ( 7) SS BOND : angle 0.61127 ( 14) covalent geometry : bond 0.00304 ( 7726) covalent geometry : angle 0.66154 (10493) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5903.12 seconds wall clock time: 102 minutes 14.52 seconds (6134.52 seconds total)