Starting phenix.real_space_refine on Fri Aug 22 13:46:51 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8bw0_16279/08_2025/8bw0_16279.cif Found real_map, /net/cci-nas-00/data/ceres_data/8bw0_16279/08_2025/8bw0_16279.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.11 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/8bw0_16279/08_2025/8bw0_16279.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8bw0_16279/08_2025/8bw0_16279.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8bw0_16279/08_2025/8bw0_16279.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8bw0_16279/08_2025/8bw0_16279.map" } resolution = 3.11 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= 1.000 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 11 5.16 5 C 2004 2.51 5 N 525 2.21 5 O 661 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 3 residue(s): 0.00s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 3201 Number of models: 1 Model: "" Number of chains: 7 Chain: "H" Number of atoms: 884 Number of conformers: 1 Conformer: "" Number of residues, atoms: 117, 884 Classifications: {'peptide': 117} Link IDs: {'PTRANS': 5, 'TRANS': 111} Chain: "L" Number of atoms: 800 Number of conformers: 1 Conformer: "" Number of residues, atoms: 104, 800 Classifications: {'peptide': 104} Link IDs: {'PCIS': 1, 'PTRANS': 5, 'TRANS': 97} Chain: "C" Number of atoms: 1348 Number of conformers: 1 Conformer: "" Number of residues, atoms: 177, 1348 Classifications: {'peptide': 177} Link IDs: {'PTRANS': 15, 'TRANS': 161} Chain: "A" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "B" Number of atoms: 71 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 71 Unusual residues: {'BMA': 1, 'FUC': 1, 'MAN': 2, 'NAG': 2} Classifications: {'undetermined': 6} Link IDs: {None: 5} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 12 Unresolved non-hydrogen dihedrals: 18 Unresolved non-hydrogen chiralities: 6 Chain: "D" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "C" Number of atoms: 42 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 42 Unusual residues: {'NAG': 3} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Time building chain proxies: 0.98, per 1000 atoms: 0.31 Number of scatterers: 3201 At special positions: 0 Unit cell: (71.92, 92.8, 69.6, 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 11 16.00 O 661 8.00 N 525 7.00 C 2004 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=4, symmetry=0 Simple disulfide: pdb=" SG CYS H 22 " - pdb=" SG CYS H 96 " distance=2.03 Simple disulfide: pdb=" SG CYS L 23 " - pdb=" SG CYS L 88 " distance=2.03 Simple disulfide: pdb=" SG CYS C 523 " - pdb=" SG CYS C 571 " distance=2.04 Simple disulfide: pdb=" SG CYS C 615 " - pdb=" SG CYS C 655 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Links applied ALPHA1-3 " BMA B 3 " - " MAN B 4 " ALPHA1-6 " BMA B 3 " - " MAN B 5 " BETA1-4 " NAG A 1 " - " NAG A 2 " " NAG B 1 " - " NAG B 2 " " NAG B 2 " - " BMA B 3 " " NAG D 1 " - " NAG D 2 " BETA1-6 " NAG B 1 " - " FUC B 6 " ~> Even though FUC is an alpha isomer, a beta linkage is required... NAG-ASN " NAG A 1 " - " ASN C 508 " " NAG B 1 " - " ASN C 612 " " NAG C 701 " - " ASN C 553 " " NAG C 702 " - " ASN C 665 " " NAG C 703 " - " ASN C 560 " " NAG D 1 " - " ASN C 648 " Time building additional restraints: 0.38 Conformation dependent library (CDL) restraints added in 99.0 milliseconds Enol-peptide restraints added in 953.7 nanoseconds 784 Ramachandran restraints generated. 392 Oldfield, 0 Emsley, 392 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 734 Finding SS restraints... Secondary structure from input PDB file: 3 helices and 9 sheets defined 3.8% alpha, 37.9% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.14 Creating SS restraints... Processing helix chain 'H' and resid 87 through 91 removed outlier: 4.028A pdb=" N THR H 91 " --> pdb=" O SER H 88 " (cutoff:3.500A) Processing helix chain 'L' and resid 48 through 52 removed outlier: 3.705A pdb=" N THR L 51 " --> pdb=" O VAL L 48 " (cutoff:3.500A) removed outlier: 3.860A pdb=" N ARG L 52 " --> pdb=" O TYR L 49 " (cutoff:3.500A) No H-bonds generated for 'chain 'L' and resid 48 through 52' Processing helix chain 'C' and resid 562 through 566 removed outlier: 3.990A pdb=" N ALA C 566 " --> pdb=" O ARG C 563 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'H' and resid 3 through 7 Processing sheet with id=AA2, first strand: chain 'H' and resid 44 through 51 removed outlier: 6.375A pdb=" N TRP H 36 " --> pdb=" O VAL H 48 " (cutoff:3.500A) removed outlier: 4.996A pdb=" N TYR H 50 " --> pdb=" O MET H 34 " (cutoff:3.500A) removed outlier: 7.286A pdb=" N MET H 34 " --> pdb=" O TYR H 50 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'H' and resid 44 through 51 removed outlier: 6.375A pdb=" N TRP H 36 " --> pdb=" O VAL H 48 " (cutoff:3.500A) removed outlier: 4.996A pdb=" N TYR H 50 " --> pdb=" O MET H 34 " (cutoff:3.500A) removed outlier: 7.286A pdb=" N MET H 34 " --> pdb=" O TYR H 50 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'L' and resid 4 through 6 removed outlier: 5.672A pdb=" N THR L 69 " --> pdb=" O ALA L 25 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'L' and resid 45 through 47 Processing sheet with id=AA6, first strand: chain 'C' and resid 505 through 507 Processing sheet with id=AA7, first strand: chain 'C' and resid 539 through 540 removed outlier: 3.634A pdb=" N THR C 531 " --> pdb=" O GLN C 574 " (cutoff:3.500A) removed outlier: 3.951A pdb=" N ASN C 580 " --> pdb=" O ILE C 573 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'C' and resid 597 through 598 Processing sheet with id=AA9, first strand: chain 'C' and resid 632 through 635 removed outlier: 7.013A pdb=" N TRP C 627 " --> pdb=" O GLN C 634 " (cutoff:3.500A) 110 hydrogen bonds defined for protein. 273 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 0.45 Time building geometry restraints manager: 0.48 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: 999 1.34 - 1.46: 861 1.46 - 1.58: 1403 1.58 - 1.70: 1 1.70 - 1.82: 14 Bond restraints: 3278 Sorted by residual: bond pdb=" C1 NAG C 702 " pdb=" O5 NAG C 702 " ideal model delta sigma weight residual 1.406 1.487 -0.081 2.00e-02 2.50e+03 1.63e+01 bond pdb=" CB PRO C 545 " pdb=" CG PRO C 545 " ideal model delta sigma weight residual 1.492 1.591 -0.099 5.00e-02 4.00e+02 3.90e+00 bond pdb=" C1 NAG A 2 " pdb=" O5 NAG A 2 " ideal model delta sigma weight residual 1.406 1.442 -0.036 2.00e-02 2.50e+03 3.17e+00 bond pdb=" C1 MAN B 5 " pdb=" C2 MAN B 5 " ideal model delta sigma weight residual 1.526 1.561 -0.035 2.00e-02 2.50e+03 3.07e+00 bond pdb=" C1 NAG D 2 " pdb=" O5 NAG D 2 " ideal model delta sigma weight residual 1.406 1.439 -0.033 2.00e-02 2.50e+03 2.72e+00 ... (remaining 3273 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.26: 4359 2.26 - 4.53: 100 4.53 - 6.79: 14 6.79 - 9.05: 1 9.05 - 11.31: 1 Bond angle restraints: 4475 Sorted by residual: angle pdb=" CA PRO C 545 " pdb=" N PRO C 545 " pdb=" CD PRO C 545 " ideal model delta sigma weight residual 112.00 104.66 7.34 1.40e+00 5.10e-01 2.75e+01 angle pdb=" N GLU C 524 " pdb=" CA GLU C 524 " pdb=" C GLU C 524 " ideal model delta sigma weight residual 109.81 116.16 -6.35 2.21e+00 2.05e-01 8.27e+00 angle pdb=" C ASN L 50 " pdb=" N THR L 51 " pdb=" CA THR L 51 " ideal model delta sigma weight residual 123.91 128.41 -4.50 1.66e+00 3.63e-01 7.34e+00 angle pdb=" N PRO C 545 " pdb=" CA PRO C 545 " pdb=" CB PRO C 545 " ideal model delta sigma weight residual 103.30 100.73 2.57 1.12e+00 7.97e-01 5.26e+00 angle pdb=" CA GLU C 524 " pdb=" C GLU C 524 " pdb=" N PRO C 525 " ideal model delta sigma weight residual 118.44 122.02 -3.58 1.59e+00 3.96e-01 5.07e+00 ... (remaining 4470 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 23.08: 1934 23.08 - 46.16: 111 46.16 - 69.24: 27 69.24 - 92.32: 22 92.32 - 115.40: 15 Dihedral angle restraints: 2109 sinusoidal: 960 harmonic: 1149 Sorted by residual: dihedral pdb=" CB CYS C 523 " pdb=" SG CYS C 523 " pdb=" SG CYS C 571 " pdb=" CB CYS C 571 " ideal model delta sinusoidal sigma weight residual 93.00 24.34 68.66 1 1.00e+01 1.00e-02 6.11e+01 dihedral pdb=" CA GLU C 524 " pdb=" C GLU C 524 " pdb=" N PRO C 525 " pdb=" CA PRO C 525 " ideal model delta harmonic sigma weight residual -180.00 -156.52 -23.48 0 5.00e+00 4.00e-02 2.21e+01 dihedral pdb=" CA ASN C 665 " pdb=" C ASN C 665 " pdb=" N ASN C 666 " pdb=" CA ASN C 666 " ideal model delta harmonic sigma weight residual 180.00 156.72 23.28 0 5.00e+00 4.00e-02 2.17e+01 ... (remaining 2106 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.090: 490 0.090 - 0.181: 45 0.181 - 0.271: 2 0.271 - 0.361: 1 0.361 - 0.451: 1 Chirality restraints: 539 Sorted by residual: chirality pdb=" C1 NAG D 1 " pdb=" ND2 ASN C 648 " pdb=" C2 NAG D 1 " pdb=" O5 NAG D 1 " both_signs ideal model delta sigma weight residual False -2.40 -1.95 -0.45 2.00e-01 2.50e+01 5.09e+00 chirality pdb=" C5 BMA B 3 " pdb=" C4 BMA B 3 " pdb=" C6 BMA B 3 " pdb=" O5 BMA B 3 " both_signs ideal model delta sigma weight residual False -2.27 -2.56 0.29 2.00e-01 2.50e+01 2.05e+00 chirality pdb=" C1 NAG C 702 " pdb=" ND2 ASN C 665 " pdb=" C2 NAG C 702 " pdb=" O5 NAG C 702 " both_signs ideal model delta sigma weight residual False -2.40 -2.14 -0.26 2.00e-01 2.50e+01 1.64e+00 ... (remaining 536 not shown) Planarity restraints: 566 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C SER C 544 " 0.092 5.00e-02 4.00e+02 1.36e-01 2.94e+01 pdb=" N PRO C 545 " -0.234 5.00e-02 4.00e+02 pdb=" CA PRO C 545 " 0.071 5.00e-02 4.00e+02 pdb=" CD PRO C 545 " 0.071 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C PRO C 600 " -0.041 5.00e-02 4.00e+02 6.22e-02 6.19e+00 pdb=" N PRO C 601 " 0.108 5.00e-02 4.00e+02 pdb=" CA PRO C 601 " -0.032 5.00e-02 4.00e+02 pdb=" CD PRO C 601 " -0.034 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CB ASN C 508 " -0.017 2.00e-02 2.50e+03 1.58e-02 3.10e+00 pdb=" CG ASN C 508 " 0.021 2.00e-02 2.50e+03 pdb=" OD1 ASN C 508 " -0.003 2.00e-02 2.50e+03 pdb=" ND2 ASN C 508 " 0.016 2.00e-02 2.50e+03 pdb=" C1 NAG A 1 " -0.016 2.00e-02 2.50e+03 ... (remaining 563 not shown) Histogram of nonbonded interaction distances: 2.19 - 2.73: 193 2.73 - 3.27: 3100 3.27 - 3.82: 5125 3.82 - 4.36: 6008 4.36 - 4.90: 10269 Nonbonded interactions: 24695 Sorted by model distance: nonbonded pdb=" O4 NAG C 701 " pdb=" O7 NAG C 701 " model vdw 2.189 3.040 nonbonded pdb=" O4 NAG A 1 " pdb=" O7 NAG A 1 " model vdw 2.190 3.040 nonbonded pdb=" OG SER H 52 " pdb=" O GLY H 55 " model vdw 2.201 3.040 nonbonded pdb=" OG SER L 26 " pdb=" OE1 GLU L 27 " model vdw 2.241 3.040 nonbonded pdb=" O ALA C 527 " pdb=" OH TYR C 532 " model vdw 2.262 3.040 ... (remaining 24690 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 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'D' } 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: 1.150 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: 0.050 Check model and map are aligned: 0.000 Set scattering table: 0.010 Process input model: 4.890 Find NCS groups from input model: 0.020 Set up NCS constraints: 0.010 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.010 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.390 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 7.530 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7119 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.099 3295 Z= 0.208 Angle : 0.800 11.313 4522 Z= 0.361 Chirality : 0.055 0.451 539 Planarity : 0.008 0.136 560 Dihedral : 19.992 115.403 1363 Min Nonbonded Distance : 2.189 Molprobity Statistics. All-atom Clashscore : 10.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.10 % Favored : 94.90 % Rotamer: Outliers : 0.00 % Allowed : 0.59 % Favored : 99.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.85 % 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: 0.61 (0.45), residues: 392 helix: None (None), residues: 0 sheet: 1.21 (0.42), residues: 163 loop : -0.17 (0.45), residues: 229 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG H 67 TYR 0.025 0.001 TYR L 49 PHE 0.006 0.001 PHE C 521 TRP 0.005 0.001 TRP H 47 HIS 0.005 0.001 HIS L 91 Details of bonding type rmsd covalent geometry : bond 0.00451 ( 3278) covalent geometry : angle 0.76272 ( 4475) SS BOND : bond 0.00305 ( 4) SS BOND : angle 1.00451 ( 8) hydrogen bonds : bond 0.12594 ( 99) hydrogen bonds : angle 6.70789 ( 273) link_ALPHA1-3 : bond 0.00424 ( 1) link_ALPHA1-3 : angle 1.70992 ( 3) link_ALPHA1-6 : bond 0.00521 ( 1) link_ALPHA1-6 : angle 1.28752 ( 3) link_BETA1-4 : bond 0.00649 ( 4) link_BETA1-4 : angle 1.53124 ( 12) link_BETA1-6 : bond 0.00295 ( 1) link_BETA1-6 : angle 1.62210 ( 3) link_NAG-ASN : bond 0.00783 ( 6) link_NAG-ASN : angle 3.61287 ( 18) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 784 Ramachandran restraints generated. 392 Oldfield, 0 Emsley, 392 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 784 Ramachandran restraints generated. 392 Oldfield, 0 Emsley, 392 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 57 residues out of total 340 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 57 time to evaluate : 0.127 Fit side-chains REVERT: L 39 LYS cc_start: 0.7645 (mttm) cc_final: 0.7238 (mmmt) REVERT: C 524 GLU cc_start: 0.8089 (pp20) cc_final: 0.7658 (pp20) REVERT: C 525 PRO cc_start: 0.8949 (Cg_endo) cc_final: 0.8391 (Cg_exo) REVERT: C 575 ASN cc_start: 0.7667 (m-40) cc_final: 0.7382 (m-40) outliers start: 0 outliers final: 0 residues processed: 57 average time/residue: 0.0939 time to fit residues: 6.2529 Evaluate side-chains 44 residues out of total 340 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 44 time to evaluate : 0.095 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 38 random chunks: chunk 24 optimal weight: 5.9990 chunk 26 optimal weight: 1.9990 chunk 2 optimal weight: 3.9990 chunk 16 optimal weight: 2.9990 chunk 32 optimal weight: 2.9990 chunk 31 optimal weight: 0.0570 chunk 25 optimal weight: 7.9990 chunk 19 optimal weight: 2.9990 chunk 30 optimal weight: 1.9990 chunk 22 optimal weight: 2.9990 chunk 37 optimal weight: 2.9990 overall best weight: 2.0106 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 620 ASN C 659 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4152 r_free = 0.4152 target = 0.136668 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3738 r_free = 0.3738 target = 0.106992 restraints weight = 6319.562| |-----------------------------------------------------------------------------| r_work (start): 0.3747 rms_B_bonded: 3.20 r_work: 0.3612 rms_B_bonded: 3.50 restraints_weight: 0.5000 r_work (final): 0.3612 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7695 moved from start: 0.2091 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.069 3295 Z= 0.326 Angle : 0.941 10.218 4522 Z= 0.447 Chirality : 0.057 0.442 539 Planarity : 0.008 0.089 560 Dihedral : 16.405 93.415 693 Min Nonbonded Distance : 2.385 Molprobity Statistics. All-atom Clashscore : 13.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.12 % Favored : 93.88 % Rotamer: Outliers : 1.47 % Allowed : 10.00 % Favored : 88.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.85 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.27 % 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: 0.15 (0.44), residues: 392 helix: None (None), residues: 0 sheet: 0.77 (0.42), residues: 162 loop : -0.36 (0.44), residues: 230 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG L 24 TYR 0.021 0.003 TYR H 100 PHE 0.022 0.003 PHE L 83 TRP 0.014 0.004 TRP C 627 HIS 0.019 0.004 HIS L 91 Details of bonding type rmsd covalent geometry : bond 0.00764 ( 3278) covalent geometry : angle 0.90813 ( 4475) SS BOND : bond 0.00333 ( 4) SS BOND : angle 1.81521 ( 8) hydrogen bonds : bond 0.04429 ( 99) hydrogen bonds : angle 6.39746 ( 273) link_ALPHA1-3 : bond 0.00772 ( 1) link_ALPHA1-3 : angle 1.36317 ( 3) link_ALPHA1-6 : bond 0.00475 ( 1) link_ALPHA1-6 : angle 1.55366 ( 3) link_BETA1-4 : bond 0.00464 ( 4) link_BETA1-4 : angle 2.09186 ( 12) link_BETA1-6 : bond 0.00360 ( 1) link_BETA1-6 : angle 2.34183 ( 3) link_NAG-ASN : bond 0.00600 ( 6) link_NAG-ASN : angle 3.35187 ( 18) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 784 Ramachandran restraints generated. 392 Oldfield, 0 Emsley, 392 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 784 Ramachandran restraints generated. 392 Oldfield, 0 Emsley, 392 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 48 residues out of total 340 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 43 time to evaluate : 0.084 Fit side-chains REVERT: C 524 GLU cc_start: 0.8114 (pp20) cc_final: 0.7767 (pp20) outliers start: 5 outliers final: 5 residues processed: 46 average time/residue: 0.0797 time to fit residues: 4.3049 Evaluate side-chains 44 residues out of total 340 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 39 time to evaluate : 0.118 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 12 VAL Chi-restraints excluded: chain H residue 53 SER Chi-restraints excluded: chain L residue 85 THR Chi-restraints excluded: chain C residue 561 VAL Chi-restraints excluded: chain C residue 673 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 38 random chunks: chunk 2 optimal weight: 1.9990 chunk 24 optimal weight: 0.8980 chunk 23 optimal weight: 3.9990 chunk 21 optimal weight: 0.6980 chunk 32 optimal weight: 1.9990 chunk 0 optimal weight: 2.9990 chunk 15 optimal weight: 0.8980 chunk 36 optimal weight: 1.9990 chunk 4 optimal weight: 0.2980 chunk 30 optimal weight: 0.7980 chunk 7 optimal weight: 0.6980 overall best weight: 0.6780 ------------------------------------------------------------------------------- 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 = 0.4193 r_free = 0.4193 target = 0.139527 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3789 r_free = 0.3789 target = 0.110197 restraints weight = 6312.038| |-----------------------------------------------------------------------------| r_work (start): 0.3803 rms_B_bonded: 3.20 r_work: 0.3672 rms_B_bonded: 3.53 restraints_weight: 0.5000 r_work (final): 0.3672 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7623 moved from start: 0.2140 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.030 3295 Z= 0.157 Angle : 0.810 10.018 4522 Z= 0.373 Chirality : 0.052 0.406 539 Planarity : 0.006 0.073 560 Dihedral : 14.192 79.759 693 Min Nonbonded Distance : 2.403 Molprobity Statistics. All-atom Clashscore : 10.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.87 % Favored : 94.13 % Rotamer: Outliers : 1.76 % Allowed : 13.53 % Favored : 84.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.85 % 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 (0.45), residues: 392 helix: None (None), residues: 0 sheet: 0.86 (0.42), residues: 164 loop : -0.30 (0.44), residues: 228 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG L 52 TYR 0.011 0.001 TYR H 95 PHE 0.009 0.002 PHE H 27 TRP 0.007 0.002 TRP C 627 HIS 0.012 0.003 HIS L 91 Details of bonding type rmsd covalent geometry : bond 0.00351 ( 3278) covalent geometry : angle 0.77081 ( 4475) SS BOND : bond 0.00321 ( 4) SS BOND : angle 1.18084 ( 8) hydrogen bonds : bond 0.03364 ( 99) hydrogen bonds : angle 5.77842 ( 273) link_ALPHA1-3 : bond 0.01197 ( 1) link_ALPHA1-3 : angle 1.55788 ( 3) link_ALPHA1-6 : bond 0.00873 ( 1) link_ALPHA1-6 : angle 1.27007 ( 3) link_BETA1-4 : bond 0.00452 ( 4) link_BETA1-4 : angle 2.01707 ( 12) link_BETA1-6 : bond 0.00055 ( 1) link_BETA1-6 : angle 1.65260 ( 3) link_NAG-ASN : bond 0.00520 ( 6) link_NAG-ASN : angle 3.55917 ( 18) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 784 Ramachandran restraints generated. 392 Oldfield, 0 Emsley, 392 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 784 Ramachandran restraints generated. 392 Oldfield, 0 Emsley, 392 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 48 residues out of total 340 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 42 time to evaluate : 0.085 Fit side-chains REVERT: C 524 GLU cc_start: 0.8041 (pp20) cc_final: 0.7664 (pp20) outliers start: 6 outliers final: 6 residues processed: 46 average time/residue: 0.0730 time to fit residues: 3.9957 Evaluate side-chains 44 residues out of total 340 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 38 time to evaluate : 0.135 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 12 VAL Chi-restraints excluded: chain H residue 53 SER Chi-restraints excluded: chain H residue 78 THR Chi-restraints excluded: chain H residue 83 MET Chi-restraints excluded: chain L residue 85 THR Chi-restraints excluded: chain C residue 662 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 38 random chunks: chunk 6 optimal weight: 0.5980 chunk 10 optimal weight: 1.9990 chunk 7 optimal weight: 0.9990 chunk 33 optimal weight: 2.9990 chunk 17 optimal weight: 4.9990 chunk 16 optimal weight: 0.3980 chunk 0 optimal weight: 5.9990 chunk 24 optimal weight: 0.9990 chunk 25 optimal weight: 4.9990 chunk 12 optimal weight: 0.5980 chunk 1 optimal weight: 3.9990 overall best weight: 0.7184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 551 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4190 r_free = 0.4190 target = 0.141128 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3800 r_free = 0.3800 target = 0.112463 restraints weight = 6274.083| |-----------------------------------------------------------------------------| r_work (start): 0.3802 rms_B_bonded: 3.06 r_work: 0.3668 rms_B_bonded: 3.46 restraints_weight: 0.5000 r_work (final): 0.3668 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7642 moved from start: 0.2343 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 3295 Z= 0.162 Angle : 0.819 11.103 4522 Z= 0.378 Chirality : 0.051 0.405 539 Planarity : 0.006 0.066 560 Dihedral : 12.536 61.637 693 Min Nonbonded Distance : 2.168 Molprobity Statistics. All-atom Clashscore : 9.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.12 % Favored : 93.88 % Rotamer: Outliers : 2.94 % Allowed : 15.29 % Favored : 81.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.85 % 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: 0.30 (0.44), residues: 392 helix: None (None), residues: 0 sheet: 0.89 (0.41), residues: 164 loop : -0.29 (0.44), residues: 228 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG L 52 TYR 0.012 0.001 TYR H 95 PHE 0.010 0.001 PHE H 27 TRP 0.009 0.002 TRP C 627 HIS 0.011 0.002 HIS L 91 Details of bonding type rmsd covalent geometry : bond 0.00366 ( 3278) covalent geometry : angle 0.77726 ( 4475) SS BOND : bond 0.00242 ( 4) SS BOND : angle 1.05456 ( 8) hydrogen bonds : bond 0.03269 ( 99) hydrogen bonds : angle 5.70152 ( 273) link_ALPHA1-3 : bond 0.01230 ( 1) link_ALPHA1-3 : angle 1.69587 ( 3) link_ALPHA1-6 : bond 0.00974 ( 1) link_ALPHA1-6 : angle 1.28533 ( 3) link_BETA1-4 : bond 0.00388 ( 4) link_BETA1-4 : angle 2.15347 ( 12) link_BETA1-6 : bond 0.00108 ( 1) link_BETA1-6 : angle 1.70830 ( 3) link_NAG-ASN : bond 0.00519 ( 6) link_NAG-ASN : angle 3.69728 ( 18) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 784 Ramachandran restraints generated. 392 Oldfield, 0 Emsley, 392 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 784 Ramachandran restraints generated. 392 Oldfield, 0 Emsley, 392 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 49 residues out of total 340 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 39 time to evaluate : 0.140 Fit side-chains outliers start: 10 outliers final: 9 residues processed: 47 average time/residue: 0.0719 time to fit residues: 4.2043 Evaluate side-chains 47 residues out of total 340 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 38 time to evaluate : 0.121 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 12 VAL Chi-restraints excluded: chain H residue 53 SER Chi-restraints excluded: chain H residue 78 THR Chi-restraints excluded: chain H residue 83 MET Chi-restraints excluded: chain H residue 93 VAL Chi-restraints excluded: chain L residue 85 THR Chi-restraints excluded: chain C residue 662 THR Chi-restraints excluded: chain C residue 669 VAL Chi-restraints excluded: chain C residue 673 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 38 random chunks: chunk 34 optimal weight: 2.9990 chunk 24 optimal weight: 0.9980 chunk 20 optimal weight: 0.5980 chunk 21 optimal weight: 5.9990 chunk 27 optimal weight: 1.9990 chunk 25 optimal weight: 2.9990 chunk 18 optimal weight: 1.9990 chunk 14 optimal weight: 1.9990 chunk 6 optimal weight: 0.9980 chunk 17 optimal weight: 0.8980 chunk 5 optimal weight: 0.8980 overall best weight: 0.8780 ------------------------------------------------------------------------------- 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 = 0.4182 r_free = 0.4182 target = 0.140521 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3790 r_free = 0.3790 target = 0.111752 restraints weight = 6217.582| |-----------------------------------------------------------------------------| r_work (start): 0.3786 rms_B_bonded: 3.07 r_work: 0.3655 rms_B_bonded: 3.43 restraints_weight: 0.5000 r_work (final): 0.3655 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7652 moved from start: 0.2583 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.033 3295 Z= 0.176 Angle : 0.825 9.817 4522 Z= 0.383 Chirality : 0.051 0.408 539 Planarity : 0.006 0.064 560 Dihedral : 11.284 55.600 693 Min Nonbonded Distance : 2.353 Molprobity Statistics. All-atom Clashscore : 11.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.12 % Favored : 93.88 % Rotamer: Outliers : 4.71 % Allowed : 15.88 % Favored : 79.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.85 % 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: 0.33 (0.44), residues: 392 helix: None (None), residues: 0 sheet: 0.88 (0.42), residues: 161 loop : -0.23 (0.43), residues: 231 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG C 563 TYR 0.013 0.001 TYR H 95 PHE 0.012 0.002 PHE H 27 TRP 0.009 0.002 TRP C 627 HIS 0.011 0.002 HIS L 91 Details of bonding type rmsd covalent geometry : bond 0.00404 ( 3278) covalent geometry : angle 0.77671 ( 4475) SS BOND : bond 0.00219 ( 4) SS BOND : angle 1.00975 ( 8) hydrogen bonds : bond 0.03198 ( 99) hydrogen bonds : angle 5.49552 ( 273) link_ALPHA1-3 : bond 0.01155 ( 1) link_ALPHA1-3 : angle 1.66464 ( 3) link_ALPHA1-6 : bond 0.00941 ( 1) link_ALPHA1-6 : angle 1.34854 ( 3) link_BETA1-4 : bond 0.00390 ( 4) link_BETA1-4 : angle 2.22856 ( 12) link_BETA1-6 : bond 0.00072 ( 1) link_BETA1-6 : angle 1.71404 ( 3) link_NAG-ASN : bond 0.00569 ( 6) link_NAG-ASN : angle 3.98017 ( 18) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 784 Ramachandran restraints generated. 392 Oldfield, 0 Emsley, 392 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 784 Ramachandran restraints generated. 392 Oldfield, 0 Emsley, 392 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 58 residues out of total 340 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 42 time to evaluate : 0.126 Fit side-chains revert: symmetry clash REVERT: C 672 ILE cc_start: 0.8806 (OUTLIER) cc_final: 0.8574 (mp) outliers start: 16 outliers final: 8 residues processed: 53 average time/residue: 0.0598 time to fit residues: 3.9252 Evaluate side-chains 45 residues out of total 340 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 36 time to evaluate : 0.113 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 12 VAL Chi-restraints excluded: chain H residue 53 SER Chi-restraints excluded: chain H residue 78 THR Chi-restraints excluded: chain H residue 83 MET Chi-restraints excluded: chain H residue 93 VAL Chi-restraints excluded: chain L residue 85 THR Chi-restraints excluded: chain C residue 662 THR Chi-restraints excluded: chain C residue 672 ILE Chi-restraints excluded: chain C residue 673 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 38 random chunks: chunk 18 optimal weight: 2.9990 chunk 37 optimal weight: 0.0770 chunk 29 optimal weight: 6.9990 chunk 26 optimal weight: 0.9990 chunk 15 optimal weight: 2.9990 chunk 8 optimal weight: 3.9990 chunk 7 optimal weight: 0.9990 chunk 25 optimal weight: 0.0040 chunk 16 optimal weight: 0.6980 chunk 36 optimal weight: 0.6980 chunk 33 optimal weight: 0.5980 overall best weight: 0.4150 ------------------------------------------------------------------------------- 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 = 0.4216 r_free = 0.4216 target = 0.142942 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3828 r_free = 0.3828 target = 0.114197 restraints weight = 6254.096| |-----------------------------------------------------------------------------| r_work (start): 0.3820 rms_B_bonded: 3.09 r_work: 0.3684 rms_B_bonded: 3.50 restraints_weight: 0.5000 r_work (final): 0.3684 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7619 moved from start: 0.2649 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 3295 Z= 0.138 Angle : 0.818 9.952 4522 Z= 0.380 Chirality : 0.050 0.396 539 Planarity : 0.006 0.064 560 Dihedral : 10.603 56.435 693 Min Nonbonded Distance : 2.367 Molprobity Statistics. All-atom Clashscore : 10.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.87 % Favored : 94.13 % Rotamer: Outliers : 2.94 % Allowed : 17.65 % Favored : 79.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.85 % 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: 0.39 (0.44), residues: 392 helix: None (None), residues: 0 sheet: 0.93 (0.42), residues: 161 loop : -0.20 (0.43), residues: 231 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG H 67 TYR 0.010 0.001 TYR H 95 PHE 0.007 0.001 PHE H 107 TRP 0.007 0.001 TRP C 627 HIS 0.008 0.002 HIS L 91 Details of bonding type rmsd covalent geometry : bond 0.00300 ( 3278) covalent geometry : angle 0.76974 ( 4475) SS BOND : bond 0.00536 ( 4) SS BOND : angle 1.61870 ( 8) hydrogen bonds : bond 0.02909 ( 99) hydrogen bonds : angle 5.26297 ( 273) link_ALPHA1-3 : bond 0.01097 ( 1) link_ALPHA1-3 : angle 1.84165 ( 3) link_ALPHA1-6 : bond 0.01000 ( 1) link_ALPHA1-6 : angle 1.33649 ( 3) link_BETA1-4 : bond 0.00469 ( 4) link_BETA1-4 : angle 2.27031 ( 12) link_BETA1-6 : bond 0.00000 ( 1) link_BETA1-6 : angle 1.59632 ( 3) link_NAG-ASN : bond 0.00594 ( 6) link_NAG-ASN : angle 3.86329 ( 18) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 784 Ramachandran restraints generated. 392 Oldfield, 0 Emsley, 392 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 784 Ramachandran restraints generated. 392 Oldfield, 0 Emsley, 392 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 51 residues out of total 340 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 41 time to evaluate : 0.071 Fit side-chains revert: symmetry clash REVERT: C 672 ILE cc_start: 0.8768 (OUTLIER) cc_final: 0.8516 (mp) outliers start: 10 outliers final: 8 residues processed: 49 average time/residue: 0.0743 time to fit residues: 4.3189 Evaluate side-chains 46 residues out of total 340 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 37 time to evaluate : 0.109 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 12 VAL Chi-restraints excluded: chain H residue 53 SER Chi-restraints excluded: chain H residue 78 THR Chi-restraints excluded: chain H residue 83 MET Chi-restraints excluded: chain H residue 93 VAL Chi-restraints excluded: chain L residue 85 THR Chi-restraints excluded: chain C residue 522 THR Chi-restraints excluded: chain C residue 669 VAL Chi-restraints excluded: chain C residue 672 ILE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 38 random chunks: chunk 9 optimal weight: 4.9990 chunk 12 optimal weight: 3.9990 chunk 30 optimal weight: 0.9980 chunk 33 optimal weight: 0.4980 chunk 19 optimal weight: 0.1980 chunk 32 optimal weight: 0.7980 chunk 31 optimal weight: 1.9990 chunk 1 optimal weight: 1.9990 chunk 24 optimal weight: 5.9990 chunk 35 optimal weight: 0.9990 chunk 18 optimal weight: 0.5980 overall best weight: 0.6180 ------------------------------------------------------------------------------- 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 = 0.4204 r_free = 0.4204 target = 0.141542 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3803 r_free = 0.3803 target = 0.112428 restraints weight = 6219.989| |-----------------------------------------------------------------------------| r_work (start): 0.3807 rms_B_bonded: 3.08 r_work: 0.3673 rms_B_bonded: 3.47 restraints_weight: 0.5000 r_work (final): 0.3673 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7640 moved from start: 0.2757 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 3295 Z= 0.151 Angle : 0.821 9.879 4522 Z= 0.382 Chirality : 0.050 0.401 539 Planarity : 0.006 0.064 560 Dihedral : 10.191 55.985 693 Min Nonbonded Distance : 2.361 Molprobity Statistics. All-atom Clashscore : 9.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.87 % Favored : 94.13 % Rotamer: Outliers : 2.94 % Allowed : 18.24 % Favored : 78.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.85 % 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: 0.34 (0.44), residues: 392 helix: None (None), residues: 0 sheet: 0.91 (0.42), residues: 161 loop : -0.25 (0.42), residues: 231 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG L 24 TYR 0.012 0.001 TYR H 95 PHE 0.010 0.001 PHE H 27 TRP 0.008 0.001 TRP C 627 HIS 0.009 0.002 HIS L 91 Details of bonding type rmsd covalent geometry : bond 0.00337 ( 3278) covalent geometry : angle 0.77630 ( 4475) SS BOND : bond 0.00381 ( 4) SS BOND : angle 1.57492 ( 8) hydrogen bonds : bond 0.03073 ( 99) hydrogen bonds : angle 5.25266 ( 273) link_ALPHA1-3 : bond 0.01070 ( 1) link_ALPHA1-3 : angle 1.74909 ( 3) link_ALPHA1-6 : bond 0.00997 ( 1) link_ALPHA1-6 : angle 1.39749 ( 3) link_BETA1-4 : bond 0.00444 ( 4) link_BETA1-4 : angle 2.37052 ( 12) link_BETA1-6 : bond 0.00018 ( 1) link_BETA1-6 : angle 1.64605 ( 3) link_NAG-ASN : bond 0.00560 ( 6) link_NAG-ASN : angle 3.63160 ( 18) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 784 Ramachandran restraints generated. 392 Oldfield, 0 Emsley, 392 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 784 Ramachandran restraints generated. 392 Oldfield, 0 Emsley, 392 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 46 residues out of total 340 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 36 time to evaluate : 0.124 Fit side-chains REVERT: C 672 ILE cc_start: 0.8776 (OUTLIER) cc_final: 0.8527 (mp) outliers start: 10 outliers final: 9 residues processed: 44 average time/residue: 0.0627 time to fit residues: 3.4186 Evaluate side-chains 44 residues out of total 340 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 34 time to evaluate : 0.118 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 12 VAL Chi-restraints excluded: chain H residue 53 SER Chi-restraints excluded: chain H residue 78 THR Chi-restraints excluded: chain H residue 83 MET Chi-restraints excluded: chain H residue 93 VAL Chi-restraints excluded: chain L residue 85 THR Chi-restraints excluded: chain C residue 522 THR Chi-restraints excluded: chain C residue 662 THR Chi-restraints excluded: chain C residue 669 VAL Chi-restraints excluded: chain C residue 672 ILE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 38 random chunks: chunk 36 optimal weight: 0.0060 chunk 5 optimal weight: 0.9990 chunk 24 optimal weight: 2.9990 chunk 27 optimal weight: 0.9990 chunk 11 optimal weight: 0.5980 chunk 9 optimal weight: 4.9990 chunk 12 optimal weight: 0.0770 chunk 37 optimal weight: 0.9980 chunk 35 optimal weight: 0.6980 chunk 13 optimal weight: 1.9990 chunk 0 optimal weight: 5.9990 overall best weight: 0.4754 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 630 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4216 r_free = 0.4216 target = 0.142838 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3828 r_free = 0.3828 target = 0.114400 restraints weight = 6264.615| |-----------------------------------------------------------------------------| r_work (start): 0.3827 rms_B_bonded: 3.04 r_work: 0.3692 rms_B_bonded: 3.46 restraints_weight: 0.5000 r_work (final): 0.3692 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7620 moved from start: 0.2833 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 3295 Z= 0.138 Angle : 0.799 9.916 4522 Z= 0.371 Chirality : 0.050 0.396 539 Planarity : 0.006 0.063 560 Dihedral : 9.849 57.162 693 Min Nonbonded Distance : 2.371 Molprobity Statistics. All-atom Clashscore : 10.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.87 % Favored : 94.13 % Rotamer: Outliers : 3.24 % Allowed : 18.24 % Favored : 78.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.85 % 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: 0.32 (0.43), residues: 392 helix: None (None), residues: 0 sheet: 1.01 (0.42), residues: 155 loop : -0.31 (0.42), residues: 237 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG L 24 TYR 0.011 0.001 TYR H 95 PHE 0.007 0.001 PHE H 27 TRP 0.007 0.001 TRP C 627 HIS 0.008 0.002 HIS L 91 Details of bonding type rmsd covalent geometry : bond 0.00304 ( 3278) covalent geometry : angle 0.75483 ( 4475) SS BOND : bond 0.00450 ( 4) SS BOND : angle 1.69327 ( 8) hydrogen bonds : bond 0.02969 ( 99) hydrogen bonds : angle 5.15130 ( 273) link_ALPHA1-3 : bond 0.01012 ( 1) link_ALPHA1-3 : angle 1.75561 ( 3) link_ALPHA1-6 : bond 0.00993 ( 1) link_ALPHA1-6 : angle 1.42003 ( 3) link_BETA1-4 : bond 0.00494 ( 4) link_BETA1-4 : angle 2.45690 ( 12) link_BETA1-6 : bond 0.00008 ( 1) link_BETA1-6 : angle 1.59493 ( 3) link_NAG-ASN : bond 0.00544 ( 6) link_NAG-ASN : angle 3.50489 ( 18) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 784 Ramachandran restraints generated. 392 Oldfield, 0 Emsley, 392 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 784 Ramachandran restraints generated. 392 Oldfield, 0 Emsley, 392 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 49 residues out of total 340 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 38 time to evaluate : 0.153 Fit side-chains REVERT: C 672 ILE cc_start: 0.8762 (OUTLIER) cc_final: 0.8517 (mp) outliers start: 11 outliers final: 10 residues processed: 47 average time/residue: 0.0693 time to fit residues: 4.0223 Evaluate side-chains 46 residues out of total 340 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 35 time to evaluate : 0.121 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 12 VAL Chi-restraints excluded: chain H residue 53 SER Chi-restraints excluded: chain H residue 70 VAL Chi-restraints excluded: chain H residue 78 THR Chi-restraints excluded: chain H residue 83 MET Chi-restraints excluded: chain H residue 93 VAL Chi-restraints excluded: chain L residue 85 THR Chi-restraints excluded: chain C residue 505 ILE Chi-restraints excluded: chain C residue 522 THR Chi-restraints excluded: chain C residue 669 VAL Chi-restraints excluded: chain C residue 672 ILE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 38 random chunks: chunk 32 optimal weight: 4.9990 chunk 6 optimal weight: 1.9990 chunk 12 optimal weight: 4.9990 chunk 9 optimal weight: 4.9990 chunk 7 optimal weight: 0.7980 chunk 37 optimal weight: 0.8980 chunk 15 optimal weight: 1.9990 chunk 33 optimal weight: 2.9990 chunk 24 optimal weight: 1.9990 chunk 26 optimal weight: 0.9980 chunk 8 optimal weight: 0.5980 overall best weight: 1.0582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 650 ASN ** 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 = 0.4170 r_free = 0.4170 target = 0.139224 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3796 r_free = 0.3796 target = 0.111799 restraints weight = 6303.839| |-----------------------------------------------------------------------------| r_work (start): 0.3796 rms_B_bonded: 3.43 r_work: 0.3630 rms_B_bonded: 3.44 restraints_weight: 0.5000 r_work (final): 0.3630 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7694 moved from start: 0.3158 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.036 3295 Z= 0.198 Angle : 0.864 9.781 4522 Z= 0.413 Chirality : 0.052 0.415 539 Planarity : 0.006 0.064 560 Dihedral : 9.758 55.665 693 Min Nonbonded Distance : 2.334 Molprobity Statistics. All-atom Clashscore : 11.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.12 % Favored : 93.88 % Rotamer: Outliers : 3.24 % Allowed : 19.12 % Favored : 77.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.85 % 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: 0.21 (0.43), residues: 392 helix: None (None), residues: 0 sheet: 0.86 (0.42), residues: 155 loop : -0.33 (0.42), residues: 237 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG L 24 TYR 0.014 0.002 TYR H 95 PHE 0.014 0.002 PHE H 27 TRP 0.011 0.002 TRP C 627 HIS 0.012 0.003 HIS L 91 Details of bonding type rmsd covalent geometry : bond 0.00454 ( 3278) covalent geometry : angle 0.82234 ( 4475) SS BOND : bond 0.00479 ( 4) SS BOND : angle 1.95710 ( 8) hydrogen bonds : bond 0.03277 ( 99) hydrogen bonds : angle 5.53184 ( 273) link_ALPHA1-3 : bond 0.00930 ( 1) link_ALPHA1-3 : angle 1.48972 ( 3) link_ALPHA1-6 : bond 0.00906 ( 1) link_ALPHA1-6 : angle 1.46388 ( 3) link_BETA1-4 : bond 0.00400 ( 4) link_BETA1-4 : angle 2.57845 ( 12) link_BETA1-6 : bond 0.00155 ( 1) link_BETA1-6 : angle 1.76658 ( 3) link_NAG-ASN : bond 0.00555 ( 6) link_NAG-ASN : angle 3.46842 ( 18) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 784 Ramachandran restraints generated. 392 Oldfield, 0 Emsley, 392 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 784 Ramachandran restraints generated. 392 Oldfield, 0 Emsley, 392 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 50 residues out of total 340 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 39 time to evaluate : 0.107 Fit side-chains REVERT: H 89 GLU cc_start: 0.8042 (mp0) cc_final: 0.7788 (mp0) REVERT: C 672 ILE cc_start: 0.8800 (OUTLIER) cc_final: 0.8552 (mp) outliers start: 11 outliers final: 10 residues processed: 48 average time/residue: 0.0643 time to fit residues: 3.7847 Evaluate side-chains 48 residues out of total 340 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 37 time to evaluate : 0.100 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 12 VAL Chi-restraints excluded: chain H residue 53 SER Chi-restraints excluded: chain H residue 70 VAL Chi-restraints excluded: chain H residue 78 THR Chi-restraints excluded: chain H residue 83 MET Chi-restraints excluded: chain H residue 93 VAL Chi-restraints excluded: chain L residue 85 THR Chi-restraints excluded: chain C residue 505 ILE Chi-restraints excluded: chain C residue 522 THR Chi-restraints excluded: chain C residue 662 THR Chi-restraints excluded: chain C residue 672 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 38 random chunks: chunk 6 optimal weight: 0.6980 chunk 19 optimal weight: 0.6980 chunk 28 optimal weight: 0.2980 chunk 17 optimal weight: 3.9990 chunk 14 optimal weight: 0.4980 chunk 21 optimal weight: 1.9990 chunk 20 optimal weight: 0.5980 chunk 12 optimal weight: 1.9990 chunk 3 optimal weight: 2.9990 chunk 16 optimal weight: 0.1980 chunk 8 optimal weight: 0.8980 overall best weight: 0.4580 ------------------------------------------------------------------------------- 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 = 0.4205 r_free = 0.4205 target = 0.142053 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3818 r_free = 0.3818 target = 0.113628 restraints weight = 6191.847| |-----------------------------------------------------------------------------| r_work (start): 0.3813 rms_B_bonded: 3.01 r_work: 0.3677 rms_B_bonded: 3.44 restraints_weight: 0.5000 r_work (final): 0.3677 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7633 moved from start: 0.3107 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 3295 Z= 0.139 Angle : 0.823 9.971 4522 Z= 0.387 Chirality : 0.050 0.396 539 Planarity : 0.005 0.062 560 Dihedral : 9.486 57.609 693 Min Nonbonded Distance : 2.349 Molprobity Statistics. All-atom Clashscore : 10.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.61 % Favored : 94.39 % Rotamer: Outliers : 3.82 % Allowed : 19.12 % Favored : 77.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.85 % 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: 0.28 (0.44), residues: 392 helix: None (None), residues: 0 sheet: 0.94 (0.42), residues: 155 loop : -0.31 (0.42), residues: 237 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG L 24 TYR 0.011 0.001 TYR H 95 PHE 0.007 0.001 PHE H 29 TRP 0.007 0.001 TRP C 627 HIS 0.008 0.002 HIS L 91 Details of bonding type rmsd covalent geometry : bond 0.00303 ( 3278) covalent geometry : angle 0.78015 ( 4475) SS BOND : bond 0.00423 ( 4) SS BOND : angle 1.73680 ( 8) hydrogen bonds : bond 0.02891 ( 99) hydrogen bonds : angle 5.20352 ( 273) link_ALPHA1-3 : bond 0.00904 ( 1) link_ALPHA1-3 : angle 1.65276 ( 3) link_ALPHA1-6 : bond 0.00923 ( 1) link_ALPHA1-6 : angle 1.43470 ( 3) link_BETA1-4 : bond 0.00512 ( 4) link_BETA1-4 : angle 2.58997 ( 12) link_BETA1-6 : bond 0.00025 ( 1) link_BETA1-6 : angle 1.57872 ( 3) link_NAG-ASN : bond 0.00540 ( 6) link_NAG-ASN : angle 3.43859 ( 18) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 784 Ramachandran restraints generated. 392 Oldfield, 0 Emsley, 392 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 784 Ramachandran restraints generated. 392 Oldfield, 0 Emsley, 392 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 50 residues out of total 340 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 37 time to evaluate : 0.096 Fit side-chains REVERT: H 89 GLU cc_start: 0.8070 (mp0) cc_final: 0.7830 (mp0) REVERT: C 672 ILE cc_start: 0.8753 (OUTLIER) cc_final: 0.8504 (mp) outliers start: 13 outliers final: 12 residues processed: 48 average time/residue: 0.0592 time to fit residues: 3.4690 Evaluate side-chains 49 residues out of total 340 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 36 time to evaluate : 0.079 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 12 VAL Chi-restraints excluded: chain H residue 35 SER Chi-restraints excluded: chain H residue 53 SER Chi-restraints excluded: chain H residue 58 THR Chi-restraints excluded: chain H residue 70 VAL Chi-restraints excluded: chain H residue 78 THR Chi-restraints excluded: chain H residue 83 MET Chi-restraints excluded: chain H residue 93 VAL Chi-restraints excluded: chain L residue 85 THR Chi-restraints excluded: chain C residue 505 ILE Chi-restraints excluded: chain C residue 522 THR Chi-restraints excluded: chain C residue 662 THR Chi-restraints excluded: chain C residue 672 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 38 random chunks: chunk 37 optimal weight: 3.9990 chunk 25 optimal weight: 7.9990 chunk 20 optimal weight: 0.5980 chunk 28 optimal weight: 0.0170 chunk 29 optimal weight: 0.8980 chunk 27 optimal weight: 0.7980 chunk 16 optimal weight: 0.9980 chunk 2 optimal weight: 0.2980 chunk 22 optimal weight: 0.8980 chunk 3 optimal weight: 0.6980 chunk 18 optimal weight: 1.9990 overall best weight: 0.4818 ------------------------------------------------------------------------------- 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 = 0.4204 r_free = 0.4204 target = 0.142029 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3808 r_free = 0.3808 target = 0.112987 restraints weight = 6232.677| |-----------------------------------------------------------------------------| r_work (start): 0.3811 rms_B_bonded: 3.06 r_work: 0.3677 rms_B_bonded: 3.45 restraints_weight: 0.5000 r_work (final): 0.3677 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7632 moved from start: 0.3136 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 3295 Z= 0.141 Angle : 0.819 9.932 4522 Z= 0.384 Chirality : 0.050 0.394 539 Planarity : 0.005 0.064 560 Dihedral : 9.097 57.642 693 Min Nonbonded Distance : 2.368 Molprobity Statistics. All-atom Clashscore : 10.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.36 % Favored : 94.64 % Rotamer: Outliers : 3.82 % Allowed : 19.71 % Favored : 76.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.85 % 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: 0.30 (0.44), residues: 392 helix: None (None), residues: 0 sheet: 0.99 (0.42), residues: 155 loop : -0.33 (0.42), residues: 237 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG L 24 TYR 0.011 0.001 TYR H 95 PHE 0.009 0.001 PHE H 29 TRP 0.009 0.001 TRP C 627 HIS 0.008 0.002 HIS L 91 Details of bonding type rmsd covalent geometry : bond 0.00314 ( 3278) covalent geometry : angle 0.77648 ( 4475) SS BOND : bond 0.00416 ( 4) SS BOND : angle 1.76957 ( 8) hydrogen bonds : bond 0.02828 ( 99) hydrogen bonds : angle 5.11066 ( 273) link_ALPHA1-3 : bond 0.00891 ( 1) link_ALPHA1-3 : angle 1.54136 ( 3) link_ALPHA1-6 : bond 0.00952 ( 1) link_ALPHA1-6 : angle 1.43553 ( 3) link_BETA1-4 : bond 0.00490 ( 4) link_BETA1-4 : angle 2.61578 ( 12) link_BETA1-6 : bond 0.00009 ( 1) link_BETA1-6 : angle 1.62105 ( 3) link_NAG-ASN : bond 0.00528 ( 6) link_NAG-ASN : angle 3.36307 ( 18) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 997.77 seconds wall clock time: 17 minutes 43.97 seconds (1063.97 seconds total)