Starting phenix.real_space_refine on Wed Sep 17 09:49:48 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9kgk_62321/09_2025/9kgk_62321.cif Found real_map, /net/cci-nas-00/data/ceres_data/9kgk_62321/09_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 { model { file = "/net/cci-nas-00/data/ceres_data/9kgk_62321/09_2025/9kgk_62321.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9kgk_62321/09_2025/9kgk_62321.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9kgk_62321/09_2025/9kgk_62321.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9kgk_62321/09_2025/9kgk_62321.map" } resolution = 2.63 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= 0.008 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): 0.01s 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: 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: 2.03, per 1000 atoms: 0.27 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: 0.55 Conformation dependent library (CDL) restraints added in 459.2 milliseconds Enol-peptide restraints added in 953.7 nanoseconds 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: 0.33 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: 1.44 Time building geometry restraints manager: 0.75 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: 4.390 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: 0.110 Check model and map are aligned: 0.020 Set scattering table: 0.030 Process input model: 8.930 Find NCS groups from input model: 0.030 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:9.190 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 22.720 ------------------------------------------------------------------------------- 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 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: 0.06 (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 ARG 0.010 0.000 ARG E 525 TYR 0.032 0.002 TYR A 729 PHE 0.036 0.001 PHE A 754 TRP 0.008 0.001 TRP A 159 HIS 0.004 0.001 HIS A 209 Details of bonding type rmsd covalent geometry : bond 0.00261 ( 7726) covalent geometry : angle 0.61250 (10493) SS BOND : bond 0.00139 ( 7) SS BOND : angle 0.72202 ( 14) hydrogen bonds : bond 0.06564 ( 270) hydrogen bonds : angle 4.29934 ( 795) *********************** 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 : 0.292 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: 0.5669 time to fit residues: 61.3564 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 : 0.307 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 96 random chunks: chunk 49 optimal weight: 6.9990 chunk 53 optimal weight: 2.9990 chunk 5 optimal weight: 2.9990 chunk 33 optimal weight: 3.9990 chunk 65 optimal weight: 8.9990 chunk 62 optimal weight: 0.7980 chunk 51 optimal weight: 0.9980 chunk 38 optimal weight: 0.0970 chunk 61 optimal weight: 3.9990 chunk 45 optimal weight: 0.0070 chunk 74 optimal weight: 7.9990 overall best weight: 0.9798 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 163 ASN 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 = 0.3757 r_free = 0.3757 target = 0.108775 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3294 r_free = 0.3294 target = 0.078404 restraints weight = 14496.792| |-----------------------------------------------------------------------------| r_work (start): 0.3251 rms_B_bonded: 3.31 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: 0.7683 moved from start: 0.1043 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.052 7733 Z= 0.189 Angle : 0.626 7.663 10507 Z= 0.315 Chirality : 0.045 0.223 1210 Planarity : 0.004 0.034 1330 Dihedral : 4.705 25.286 1030 Min Nonbonded Distance : 2.526 Molprobity Statistics. All-atom Clashscore : 6.43 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 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: -0.01 (0.28), residues: 959 helix: 2.46 (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 ARG 0.005 0.000 ARG B 135 TYR 0.010 0.001 TYR E 457 PHE 0.012 0.001 PHE A 547 TRP 0.008 0.001 TRP A 159 HIS 0.003 0.001 HIS A 256 Details of bonding type rmsd covalent geometry : bond 0.00452 ( 7726) covalent geometry : angle 0.62567 (10493) SS BOND : bond 0.00194 ( 7) SS BOND : angle 0.83264 ( 14) hydrogen bonds : bond 0.04000 ( 270) hydrogen bonds : angle 4.16287 ( 795) *********************** 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 : 0.314 Fit side-chains REVERT: A 814 LEU cc_start: 0.8750 (tt) cc_final: 0.8408 (mp) REVERT: E 458 CYS cc_start: 0.8488 (t) cc_final: 0.7415 (p) REVERT: E 468 LYS cc_start: 0.7288 (mppt) cc_final: 0.6969 (mppt) REVERT: E 471 GLU cc_start: 0.8409 (mp0) cc_final: 0.7779 (mp0) REVERT: E 503 LEU cc_start: 0.7899 (mp) cc_final: 0.7680 (mp) REVERT: E 517 MET cc_start: 0.7722 (tpt) cc_final: 0.7388 (tpt) outliers start: 9 outliers final: 3 residues processed: 91 average time/residue: 0.5189 time to fit residues: 50.4811 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 : 0.325 ------------------------------------------------------------------------------- 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 31 optimal weight: 1.9990 chunk 13 optimal weight: 0.6980 chunk 10 optimal weight: 0.5980 chunk 43 optimal weight: 0.2980 chunk 53 optimal weight: 1.9990 chunk 68 optimal weight: 5.9990 chunk 39 optimal weight: 0.9990 chunk 83 optimal weight: 2.9990 chunk 27 optimal weight: 1.9990 chunk 63 optimal weight: 4.9990 chunk 59 optimal weight: 0.5980 overall best weight: 0.6382 ------------------------------------------------------------------------------- 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 = 0.3772 r_free = 0.3772 target = 0.109837 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3305 r_free = 0.3305 target = 0.079201 restraints weight = 14409.724| |-----------------------------------------------------------------------------| r_work (start): 0.3268 rms_B_bonded: 3.33 r_work: 0.3109 rms_B_bonded: 3.73 restraints_weight: 0.5000 r_work (final): 0.3109 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7664 moved from start: 0.1120 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 7733 Z= 0.139 Angle : 0.584 9.444 10507 Z= 0.293 Chirality : 0.043 0.226 1210 Planarity : 0.004 0.034 1330 Dihedral : 4.567 27.170 1030 Min Nonbonded Distance : 2.534 Molprobity Statistics. All-atom Clashscore : 6.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.94 % Favored : 94.06 % Rotamer: Outliers : 1.31 % Allowed : 10.04 % Favored : 88.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.01 (0.27), residues: 959 helix: 2.47 (0.33), residues: 240 sheet: -1.27 (0.44), residues: 154 loop : -0.74 (0.26), residues: 565 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG E 525 TYR 0.012 0.001 TYR A 234 PHE 0.013 0.001 PHE A 696 TRP 0.006 0.001 TRP A 612 HIS 0.003 0.001 HIS A 256 Details of bonding type rmsd covalent geometry : bond 0.00325 ( 7726) covalent geometry : angle 0.58386 (10493) SS BOND : bond 0.00143 ( 7) SS BOND : angle 0.63421 ( 14) hydrogen bonds : bond 0.03643 ( 270) hydrogen bonds : angle 4.08133 ( 795) *********************** 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: 11 poor density : 90 time to evaluate : 0.315 Fit side-chains REVERT: A 787 LEU cc_start: 0.8795 (mt) cc_final: 0.8574 (mt) REVERT: E 459 MET cc_start: 0.7577 (ttm) cc_final: 0.7242 (ttt) REVERT: E 463 ARG cc_start: 0.8178 (ttm170) cc_final: 0.7969 (ttp-170) REVERT: E 464 GLN cc_start: 0.7945 (OUTLIER) cc_final: 0.7340 (tp40) REVERT: E 468 LYS cc_start: 0.7406 (mppt) cc_final: 0.7039 (mppt) REVERT: E 471 GLU cc_start: 0.8571 (mp0) cc_final: 0.7987 (mp0) REVERT: E 517 MET cc_start: 0.7681 (OUTLIER) cc_final: 0.7239 (tpt) REVERT: B 28 GLU cc_start: 0.6402 (pm20) cc_final: 0.5952 (pm20) REVERT: B 139 GLN cc_start: 0.8765 (pm20) cc_final: 0.8359 (pm20) outliers start: 11 outliers final: 4 residues processed: 96 average time/residue: 0.4915 time to fit residues: 50.5779 Evaluate side-chains 91 residues out of total 838 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 85 time to evaluate : 0.298 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 353 ASN Chi-restraints excluded: chain A residue 631 SER 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 85 optimal weight: 3.9990 chunk 64 optimal weight: 1.9990 chunk 83 optimal weight: 3.9990 chunk 58 optimal weight: 5.9990 chunk 72 optimal weight: 4.9990 chunk 40 optimal weight: 1.9990 chunk 56 optimal weight: 3.9990 chunk 32 optimal weight: 2.9990 chunk 2 optimal weight: 0.0070 chunk 28 optimal weight: 1.9990 chunk 73 optimal weight: 6.9990 overall best weight: 1.8006 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 74 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3711 r_free = 0.3711 target = 0.105654 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3211 r_free = 0.3211 target = 0.074465 restraints weight = 14728.913| |-----------------------------------------------------------------------------| r_work (start): 0.3171 rms_B_bonded: 3.33 r_work: 0.3011 rms_B_bonded: 3.67 restraints_weight: 0.5000 r_work (final): 0.3011 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7726 moved from start: 0.1860 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.089 7733 Z= 0.319 Angle : 0.741 10.994 10507 Z= 0.371 Chirality : 0.049 0.234 1210 Planarity : 0.004 0.040 1330 Dihedral : 5.334 31.467 1030 Min Nonbonded Distance : 2.475 Molprobity Statistics. All-atom Clashscore : 8.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.30 % Favored : 92.70 % Rotamer: Outliers : 1.67 % Allowed : 12.07 % Favored : 86.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.11 % 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: -0.30 (0.27), residues: 959 helix: 2.22 (0.33), residues: 241 sheet: -1.43 (0.42), residues: 155 loop : -0.94 (0.25), residues: 563 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG E 525 TYR 0.014 0.002 TYR E 457 PHE 0.016 0.002 PHE A 808 TRP 0.012 0.002 TRP A 159 HIS 0.005 0.001 HIS A 256 Details of bonding type rmsd covalent geometry : bond 0.00762 ( 7726) covalent geometry : angle 0.74015 (10493) SS BOND : bond 0.00292 ( 7) SS BOND : angle 1.08439 ( 14) hydrogen bonds : bond 0.04885 ( 270) hydrogen bonds : angle 4.43220 ( 795) *********************** 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 105 residues out of total 838 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 91 time to evaluate : 0.378 Fit side-chains REVERT: A 628 SER cc_start: 0.7640 (t) cc_final: 0.7347 (p) REVERT: A 814 LEU cc_start: 0.8389 (tt) cc_final: 0.8187 (mp) REVERT: E 443 LEU cc_start: 0.8748 (tm) cc_final: 0.8404 (mp) REVERT: E 464 GLN cc_start: 0.7913 (OUTLIER) cc_final: 0.7292 (tp40) REVERT: E 468 LYS cc_start: 0.7420 (mppt) cc_final: 0.7027 (mppt) REVERT: E 471 GLU cc_start: 0.8643 (mp0) cc_final: 0.8020 (mp0) REVERT: E 517 MET cc_start: 0.7540 (tpt) cc_final: 0.7143 (tpt) REVERT: B 125 ARG cc_start: 0.7443 (pmt170) cc_final: 0.6968 (pmt170) outliers start: 14 outliers final: 5 residues processed: 99 average time/residue: 0.4671 time to fit residues: 49.7473 Evaluate side-chains 86 residues out of total 838 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 80 time to evaluate : 0.308 ------------------------------------------------------------------------------- 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 631 SER Chi-restraints excluded: chain A residue 640 THR Chi-restraints excluded: chain E residue 464 GLN Chi-restraints excluded: chain E residue 493 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 96 random chunks: chunk 28 optimal weight: 0.6980 chunk 77 optimal weight: 0.9990 chunk 23 optimal weight: 0.9980 chunk 93 optimal weight: 0.6980 chunk 90 optimal weight: 0.5980 chunk 70 optimal weight: 0.5980 chunk 48 optimal weight: 0.6980 chunk 16 optimal weight: 0.9980 chunk 84 optimal weight: 0.6980 chunk 27 optimal weight: 0.6980 chunk 71 optimal weight: 0.9980 overall best weight: 0.6580 ------------------------------------------------------------------------------- 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 = 0.3764 r_free = 0.3764 target = 0.109084 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3284 r_free = 0.3284 target = 0.078333 restraints weight = 14595.907| |-----------------------------------------------------------------------------| r_work (start): 0.3242 rms_B_bonded: 3.36 r_work: 0.3083 rms_B_bonded: 3.71 restraints_weight: 0.5000 r_work (final): 0.3083 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7677 moved from start: 0.1669 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 7733 Z= 0.143 Angle : 0.621 9.066 10507 Z= 0.308 Chirality : 0.044 0.238 1210 Planarity : 0.004 0.034 1330 Dihedral : 4.802 27.450 1030 Min Nonbonded Distance : 2.527 Molprobity Statistics. All-atom Clashscore : 7.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.53 % Favored : 94.47 % Rotamer: Outliers : 2.27 % Allowed : 12.54 % Favored : 85.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.17 (0.27), residues: 959 helix: 2.32 (0.33), residues: 241 sheet: -1.31 (0.43), residues: 154 loop : -0.86 (0.25), residues: 564 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG E 525 TYR 0.013 0.001 TYR A 234 PHE 0.017 0.001 PHE A 696 TRP 0.007 0.001 TRP A 612 HIS 0.003 0.001 HIS A 256 Details of bonding type rmsd covalent geometry : bond 0.00336 ( 7726) covalent geometry : angle 0.62064 (10493) SS BOND : bond 0.00133 ( 7) SS BOND : angle 0.70146 ( 14) hydrogen bonds : bond 0.03833 ( 270) hydrogen bonds : angle 4.17389 ( 795) *********************** 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 108 residues out of total 838 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 89 time to evaluate : 0.234 Fit side-chains REVERT: E 464 GLN cc_start: 0.7936 (OUTLIER) cc_final: 0.7351 (tp40) REVERT: E 468 LYS cc_start: 0.7387 (mppt) cc_final: 0.7004 (mppt) REVERT: E 471 GLU cc_start: 0.8690 (mp0) cc_final: 0.8060 (mp0) REVERT: E 517 MET cc_start: 0.7708 (OUTLIER) cc_final: 0.7226 (tpt) REVERT: B 125 ARG cc_start: 0.7279 (pmt170) cc_final: 0.6872 (pmt170) outliers start: 19 outliers final: 3 residues processed: 103 average time/residue: 0.4302 time to fit residues: 47.8390 Evaluate side-chains 88 residues out of total 838 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 83 time to evaluate : 0.303 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 E residue 464 GLN Chi-restraints excluded: chain E residue 517 MET Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 96 random chunks: chunk 66 optimal weight: 0.8980 chunk 26 optimal weight: 1.9990 chunk 54 optimal weight: 1.9990 chunk 59 optimal weight: 2.9990 chunk 68 optimal weight: 4.9990 chunk 92 optimal weight: 2.9990 chunk 73 optimal weight: 9.9990 chunk 17 optimal weight: 1.9990 chunk 61 optimal weight: 0.1980 chunk 81 optimal weight: 3.9990 chunk 85 optimal weight: 3.9990 overall best weight: 1.4186 ------------------------------------------------------------------------------- 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 = 0.3719 r_free = 0.3719 target = 0.106242 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3224 r_free = 0.3224 target = 0.075135 restraints weight = 14791.413| |-----------------------------------------------------------------------------| r_work (start): 0.3183 rms_B_bonded: 3.37 r_work: 0.3023 rms_B_bonded: 3.70 restraints_weight: 0.5000 r_work (final): 0.3023 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7721 moved from start: 0.2005 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.070 7733 Z= 0.256 Angle : 0.714 10.401 10507 Z= 0.356 Chirality : 0.047 0.252 1210 Planarity : 0.004 0.038 1330 Dihedral : 5.151 28.553 1030 Min Nonbonded Distance : 2.499 Molprobity Statistics. All-atom Clashscore : 8.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.99 % Favored : 93.01 % Rotamer: Outliers : 1.67 % Allowed : 15.65 % Favored : 82.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.27 (0.27), residues: 959 helix: 2.26 (0.33), residues: 241 sheet: -1.28 (0.43), residues: 154 loop : -0.97 (0.25), residues: 564 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 135 TYR 0.011 0.001 TYR A 234 PHE 0.016 0.002 PHE A 696 TRP 0.011 0.001 TRP A 159 HIS 0.004 0.001 HIS A 256 Details of bonding type rmsd covalent geometry : bond 0.00612 ( 7726) covalent geometry : angle 0.71377 (10493) SS BOND : bond 0.00221 ( 7) SS BOND : angle 0.95662 ( 14) hydrogen bonds : bond 0.04515 ( 270) hydrogen bonds : angle 4.35142 ( 795) *********************** 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 99 residues out of total 838 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 85 time to evaluate : 0.339 Fit side-chains REVERT: A 814 LEU cc_start: 0.8399 (tt) cc_final: 0.8196 (mp) REVERT: E 464 GLN cc_start: 0.7943 (OUTLIER) cc_final: 0.7356 (tp40) REVERT: E 468 LYS cc_start: 0.7468 (mppt) cc_final: 0.7089 (mppt) REVERT: E 471 GLU cc_start: 0.8728 (mp0) cc_final: 0.8084 (mp0) REVERT: E 517 MET cc_start: 0.7675 (tpt) cc_final: 0.7336 (tpt) REVERT: B 131 GLU cc_start: 0.9110 (pt0) cc_final: 0.8902 (pt0) outliers start: 14 outliers final: 9 residues processed: 95 average time/residue: 0.4408 time to fit residues: 45.0469 Evaluate side-chains 91 residues out of total 838 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 81 time to evaluate : 0.237 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 55 LEU 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 707 THR Chi-restraints excluded: chain A residue 795 CYS Chi-restraints excluded: chain E residue 464 GLN Chi-restraints excluded: chain E residue 493 THR 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 57 optimal weight: 3.9990 chunk 62 optimal weight: 1.9990 chunk 45 optimal weight: 0.6980 chunk 6 optimal weight: 1.9990 chunk 81 optimal weight: 0.8980 chunk 89 optimal weight: 0.7980 chunk 80 optimal weight: 6.9990 chunk 88 optimal weight: 0.8980 chunk 74 optimal weight: 0.9990 chunk 55 optimal weight: 1.9990 chunk 19 optimal weight: 0.8980 overall best weight: 0.8380 ------------------------------------------------------------------------------- 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 = 0.3749 r_free = 0.3749 target = 0.108198 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3264 r_free = 0.3264 target = 0.077325 restraints weight = 14759.530| |-----------------------------------------------------------------------------| r_work (start): 0.3223 rms_B_bonded: 3.39 r_work: 0.3065 rms_B_bonded: 3.72 restraints_weight: 0.5000 r_work (final): 0.3065 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7694 moved from start: 0.1936 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= 0.169 Angle : 0.658 9.308 10507 Z= 0.327 Chirality : 0.045 0.280 1210 Planarity : 0.004 0.035 1330 Dihedral : 4.857 27.403 1030 Min Nonbonded Distance : 2.508 Molprobity Statistics. All-atom Clashscore : 8.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.26 % Favored : 93.74 % Rotamer: Outliers : 2.63 % Allowed : 15.53 % Favored : 81.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.19 (0.27), residues: 959 helix: 2.32 (0.33), residues: 241 sheet: -1.25 (0.43), residues: 154 loop : -0.91 (0.25), residues: 564 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 135 TYR 0.012 0.001 TYR A 234 PHE 0.018 0.001 PHE A 696 TRP 0.008 0.001 TRP A 612 HIS 0.004 0.001 HIS A 256 Details of bonding type rmsd covalent geometry : bond 0.00401 ( 7726) covalent geometry : angle 0.65825 (10493) SS BOND : bond 0.00145 ( 7) SS BOND : angle 0.73527 ( 14) hydrogen bonds : bond 0.03963 ( 270) hydrogen bonds : angle 4.24837 ( 795) *********************** 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 110 residues out of total 838 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 88 time to evaluate : 0.341 Fit side-chains REVERT: A 424 GLU cc_start: 0.8481 (tm-30) cc_final: 0.8190 (tm-30) REVERT: A 814 LEU cc_start: 0.8405 (tt) cc_final: 0.8097 (mp) REVERT: E 464 GLN cc_start: 0.7943 (OUTLIER) cc_final: 0.7358 (tp40) REVERT: E 471 GLU cc_start: 0.8730 (mp0) cc_final: 0.8086 (mp0) REVERT: E 517 MET cc_start: 0.7660 (OUTLIER) cc_final: 0.7267 (tpt) outliers start: 22 outliers final: 8 residues processed: 103 average time/residue: 0.4635 time to fit residues: 51.2692 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 : 0.286 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 64 ILE 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 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=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 96 random chunks: chunk 26 optimal weight: 1.9990 chunk 42 optimal weight: 3.9990 chunk 20 optimal weight: 0.9990 chunk 50 optimal weight: 0.9990 chunk 3 optimal weight: 3.9990 chunk 48 optimal weight: 0.6980 chunk 88 optimal weight: 0.2980 chunk 46 optimal weight: 0.6980 chunk 72 optimal weight: 2.9990 chunk 56 optimal weight: 1.9990 chunk 73 optimal weight: 8.9990 overall best weight: 0.7384 ------------------------------------------------------------------------------- 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 = 0.3754 r_free = 0.3754 target = 0.108620 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3268 r_free = 0.3268 target = 0.077619 restraints weight = 14644.934| |-----------------------------------------------------------------------------| r_work (start): 0.3233 rms_B_bonded: 3.38 r_work: 0.3073 rms_B_bonded: 3.74 restraints_weight: 0.5000 r_work (final): 0.3073 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7687 moved from start: 0.1961 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.049 7733 Z= 0.157 Angle : 0.664 8.919 10507 Z= 0.327 Chirality : 0.045 0.318 1210 Planarity : 0.004 0.035 1330 Dihedral : 4.764 27.385 1030 Min Nonbonded Distance : 2.490 Molprobity Statistics. All-atom Clashscore : 8.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.47 % Favored : 93.53 % 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 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: -0.13 (0.27), residues: 959 helix: 2.35 (0.33), residues: 241 sheet: -1.20 (0.43), residues: 154 loop : -0.87 (0.26), residues: 564 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 135 TYR 0.013 0.001 TYR A 234 PHE 0.018 0.001 PHE A 696 TRP 0.008 0.001 TRP A 474 HIS 0.003 0.001 HIS A 256 Details of bonding type rmsd covalent geometry : bond 0.00373 ( 7726) covalent geometry : angle 0.66376 (10493) SS BOND : bond 0.00163 ( 7) SS BOND : angle 0.75149 ( 14) hydrogen bonds : bond 0.03874 ( 270) hydrogen bonds : angle 4.20925 ( 795) *********************** 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 102 residues out of total 838 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 86 time to evaluate : 0.320 Fit side-chains revert: symmetry clash REVERT: A 424 GLU cc_start: 0.8455 (tm-30) cc_final: 0.8212 (tm-30) REVERT: E 464 GLN cc_start: 0.7978 (OUTLIER) cc_final: 0.7393 (tp40) REVERT: E 471 GLU cc_start: 0.8746 (mp0) cc_final: 0.8104 (mp0) REVERT: E 517 MET cc_start: 0.7676 (OUTLIER) cc_final: 0.7278 (tpt) REVERT: B 125 ARG cc_start: 0.7512 (pmt170) cc_final: 0.7095 (pmt170) REVERT: B 139 GLN cc_start: 0.8715 (pm20) cc_final: 0.8510 (pm20) outliers start: 16 outliers final: 9 residues processed: 96 average time/residue: 0.4778 time to fit residues: 49.2057 Evaluate side-chains 96 residues out of total 838 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 85 time to evaluate : 0.262 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 55 LEU 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 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=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 96 random chunks: chunk 8 optimal weight: 0.8980 chunk 63 optimal weight: 0.8980 chunk 33 optimal weight: 0.7980 chunk 85 optimal weight: 3.9990 chunk 76 optimal weight: 2.9990 chunk 83 optimal weight: 0.9990 chunk 71 optimal weight: 2.9990 chunk 37 optimal weight: 0.3980 chunk 32 optimal weight: 2.9990 chunk 53 optimal weight: 2.9990 chunk 18 optimal weight: 0.8980 overall best weight: 0.7780 ------------------------------------------------------------------------------- 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 = 0.108594 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3271 r_free = 0.3271 target = 0.077746 restraints weight = 14518.624| |-----------------------------------------------------------------------------| r_work (start): 0.3235 rms_B_bonded: 3.36 r_work: 0.3078 rms_B_bonded: 3.71 restraints_weight: 0.5000 r_work (final): 0.3078 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7689 moved from start: 0.1992 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.056 7733 Z= 0.162 Angle : 0.671 10.022 10507 Z= 0.330 Chirality : 0.046 0.372 1210 Planarity : 0.004 0.035 1330 Dihedral : 4.742 27.115 1030 Min Nonbonded Distance : 2.482 Molprobity Statistics. All-atom Clashscore : 8.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.15 % Favored : 93.85 % Rotamer: Outliers : 1.79 % Allowed : 17.32 % 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 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: -0.20 (0.27), residues: 959 helix: 2.29 (0.33), residues: 241 sheet: -1.41 (0.44), residues: 147 loop : -0.87 (0.25), residues: 571 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 135 TYR 0.013 0.001 TYR A 234 PHE 0.018 0.001 PHE A 696 TRP 0.008 0.001 TRP A 474 HIS 0.003 0.001 HIS A 256 Details of bonding type rmsd covalent geometry : bond 0.00387 ( 7726) covalent geometry : angle 0.67089 (10493) SS BOND : bond 0.00140 ( 7) SS BOND : angle 0.74875 ( 14) hydrogen bonds : bond 0.03871 ( 270) hydrogen bonds : angle 4.24552 ( 795) *********************** 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: 15 poor density : 89 time to evaluate : 0.379 Fit side-chains revert: symmetry clash REVERT: A 424 GLU cc_start: 0.8457 (tm-30) cc_final: 0.8212 (tm-30) REVERT: A 814 LEU cc_start: 0.8441 (tt) cc_final: 0.8217 (mp) REVERT: E 464 GLN cc_start: 0.8012 (OUTLIER) cc_final: 0.7458 (tp40) REVERT: E 471 GLU cc_start: 0.8774 (mp0) cc_final: 0.8121 (mp0) REVERT: E 517 MET cc_start: 0.7693 (OUTLIER) cc_final: 0.7300 (tpt) REVERT: B 125 ARG cc_start: 0.7510 (pmt170) cc_final: 0.7122 (pmt170) REVERT: B 139 GLN cc_start: 0.8637 (pm20) cc_final: 0.8356 (pm20) outliers start: 15 outliers final: 9 residues processed: 98 average time/residue: 0.4852 time to fit residues: 50.9489 Evaluate side-chains 96 residues out of total 838 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 85 time to evaluate : 0.308 ------------------------------------------------------------------------------- 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 63 optimal weight: 0.9990 chunk 25 optimal weight: 3.9990 chunk 55 optimal weight: 0.0980 chunk 64 optimal weight: 2.9990 chunk 14 optimal weight: 0.6980 chunk 59 optimal weight: 0.8980 chunk 16 optimal weight: 0.8980 chunk 0 optimal weight: 5.9990 chunk 2 optimal weight: 0.0570 chunk 48 optimal weight: 1.9990 chunk 50 optimal weight: 1.9990 overall best weight: 0.5298 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 731 ASN B 105 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3771 r_free = 0.3771 target = 0.109757 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3293 r_free = 0.3293 target = 0.078949 restraints weight = 14680.994| |-----------------------------------------------------------------------------| r_work (start): 0.3262 rms_B_bonded: 3.39 r_work: 0.3106 rms_B_bonded: 3.75 restraints_weight: 0.5000 r_work (final): 0.3106 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7682 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 : 0.003 0.065 7733 Z= 0.133 Angle : 0.656 11.920 10507 Z= 0.322 Chirality : 0.045 0.379 1210 Planarity : 0.004 0.034 1330 Dihedral : 4.578 27.319 1030 Min Nonbonded Distance : 2.471 Molprobity Statistics. All-atom Clashscore : 8.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.36 % Favored : 93.64 % Rotamer: Outliers : 1.43 % Allowed : 17.80 % Favored : 80.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.18 (0.27), residues: 959 helix: 2.26 (0.33), residues: 241 sheet: -1.40 (0.43), residues: 147 loop : -0.82 (0.26), residues: 571 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 135 TYR 0.013 0.001 TYR A 234 PHE 0.019 0.001 PHE A 696 TRP 0.009 0.001 TRP A 474 HIS 0.002 0.001 HIS A 256 Details of bonding type rmsd covalent geometry : bond 0.00316 ( 7726) covalent geometry : angle 0.65620 (10493) SS BOND : bond 0.00131 ( 7) SS BOND : angle 0.63874 ( 14) hydrogen bonds : bond 0.03629 ( 270) hydrogen bonds : angle 4.19235 ( 795) ********************** 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 100 residues out of total 838 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 88 time to evaluate : 0.328 Fit side-chains revert: symmetry clash REVERT: E 464 GLN cc_start: 0.7956 (tm-30) cc_final: 0.7400 (tp40) REVERT: E 471 GLU cc_start: 0.8779 (mp0) cc_final: 0.8139 (mp0) REVERT: E 517 MET cc_start: 0.7629 (OUTLIER) cc_final: 0.7140 (tpt) REVERT: E 542 GLN cc_start: 0.8429 (mp10) cc_final: 0.7732 (pt0) REVERT: B 28 GLU cc_start: 0.6756 (pm20) cc_final: 0.6546 (pm20) REVERT: B 125 ARG cc_start: 0.7440 (pmt170) cc_final: 0.7051 (pmt170) outliers start: 12 outliers final: 8 residues processed: 96 average time/residue: 0.4923 time to fit residues: 50.5864 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 : 0.301 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 64 ILE 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 Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 96 random chunks: chunk 66 optimal weight: 0.8980 chunk 92 optimal weight: 0.6980 chunk 25 optimal weight: 0.9980 chunk 83 optimal weight: 4.9990 chunk 61 optimal weight: 1.9990 chunk 81 optimal weight: 0.7980 chunk 30 optimal weight: 1.9990 chunk 31 optimal weight: 1.9990 chunk 86 optimal weight: 0.5980 chunk 49 optimal weight: 0.9990 chunk 63 optimal weight: 0.9980 overall best weight: 0.7980 ------------------------------------------------------------------------------- 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 = 0.3757 r_free = 0.3757 target = 0.108902 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3273 r_free = 0.3273 target = 0.077949 restraints weight = 14575.957| |-----------------------------------------------------------------------------| r_work (start): 0.3236 rms_B_bonded: 3.37 r_work: 0.3078 rms_B_bonded: 3.73 restraints_weight: 0.5000 r_work (final): 0.3078 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7684 moved from start: 0.2001 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= 0.170 Angle : 0.704 12.103 10507 Z= 0.347 Chirality : 0.046 0.383 1210 Planarity : 0.004 0.037 1330 Dihedral : 4.698 26.915 1030 Min Nonbonded Distance : 2.277 Molprobity Statistics. All-atom Clashscore : 8.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.47 % Favored : 93.53 % Rotamer: Outliers : 1.31 % Allowed : 18.04 % Favored : 80.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.20 (0.27), residues: 959 helix: 2.27 (0.33), residues: 241 sheet: -1.40 (0.43), residues: 147 loop : -0.85 (0.25), residues: 571 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B 135 TYR 0.012 0.001 TYR A 234 PHE 0.025 0.001 PHE A 696 TRP 0.009 0.001 TRP E 461 HIS 0.003 0.001 HIS A 256 Details of bonding type rmsd covalent geometry : bond 0.00410 ( 7726) covalent geometry : angle 0.70399 (10493) SS BOND : bond 0.00152 ( 7) SS BOND : angle 0.70824 ( 14) hydrogen bonds : bond 0.03866 ( 270) hydrogen bonds : angle 4.23405 ( 795) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2878.04 seconds wall clock time: 49 minutes 49.37 seconds (2989.37 seconds total)