Starting phenix.real_space_refine on Wed Jun 4 16:48:37 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8bw0_16279/06_2025/8bw0_16279.cif Found real_map, /net/cci-nas-00/data/ceres_data/8bw0_16279/06_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 { real_map_files = "/net/cci-nas-00/data/ceres_data/8bw0_16279/06_2025/8bw0_16279.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8bw0_16279/06_2025/8bw0_16279.map" model { file = "/net/cci-nas-00/data/ceres_data/8bw0_16279/06_2025/8bw0_16279.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8bw0_16279/06_2025/8bw0_16279.cif" } resolution = 3.11 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 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): 0.01s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/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: 2.93, per 1000 atoms: 0.92 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: 0.98 Conformation dependent library (CDL) restraints added in 349.2 milliseconds 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: 0.38 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: 0.80 Time building geometry restraints manager: 1.13 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: 1.190 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: 0.120 Check model and map are aligned: 0.020 Set scattering table: 0.050 Process input model: 13.030 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:2.880 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 17.340 ------------------------------------------------------------------------------- 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.61 (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 TRP 0.005 0.001 TRP H 47 HIS 0.005 0.001 HIS L 91 PHE 0.006 0.001 PHE C 521 TYR 0.025 0.001 TYR L 49 ARG 0.001 0.000 ARG H 67 Details of bonding type rmsd link_NAG-ASN : bond 0.00783 ( 6) link_NAG-ASN : angle 3.61287 ( 18) 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_ALPHA1-3 : bond 0.00424 ( 1) link_ALPHA1-3 : angle 1.70992 ( 3) hydrogen bonds : bond 0.12594 ( 99) hydrogen bonds : angle 6.70789 ( 273) link_BETA1-6 : bond 0.00295 ( 1) link_BETA1-6 : angle 1.62210 ( 3) SS BOND : bond 0.00305 ( 4) SS BOND : angle 1.00451 ( 8) covalent geometry : bond 0.00451 ( 3278) covalent geometry : angle 0.76272 ( 4475) *********************** 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 : 0.350 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: 0.2116 time to fit residues: 14.4312 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 : 0.369 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 38 random chunks: chunk 32 optimal weight: 2.9990 chunk 28 optimal weight: 1.9990 chunk 15 optimal weight: 1.9990 chunk 9 optimal weight: 1.9990 chunk 19 optimal weight: 0.0770 chunk 29 optimal weight: 3.9990 chunk 11 optimal weight: 2.9990 chunk 18 optimal weight: 0.8980 chunk 22 optimal weight: 6.9990 chunk 34 optimal weight: 0.6980 chunk 10 optimal weight: 0.9980 overall best weight: 0.9340 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 620 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4231 r_free = 0.4231 target = 0.142339 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3839 r_free = 0.3839 target = 0.113248 restraints weight = 6162.033| |-----------------------------------------------------------------------------| r_work (start): 0.3852 rms_B_bonded: 3.21 r_work: 0.3722 rms_B_bonded: 3.54 restraints_weight: 0.5000 r_work (final): 0.3722 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7561 moved from start: 0.1463 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 3295 Z= 0.186 Angle : 0.827 10.896 4522 Z= 0.377 Chirality : 0.053 0.415 539 Planarity : 0.007 0.085 560 Dihedral : 15.782 84.008 693 Min Nonbonded Distance : 2.396 Molprobity Statistics. All-atom Clashscore : 9.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.10 % Favored : 94.90 % Rotamer: Outliers : 1.18 % Allowed : 7.94 % Favored : 90.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.85 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.53 (0.45), residues: 392 helix: None (None), residues: 0 sheet: 1.10 (0.42), residues: 163 loop : -0.18 (0.44), residues: 229 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.002 TRP H 47 HIS 0.012 0.003 HIS L 91 PHE 0.013 0.002 PHE L 83 TYR 0.015 0.002 TYR H 100 ARG 0.003 0.000 ARG L 24 Details of bonding type rmsd link_NAG-ASN : bond 0.00527 ( 6) link_NAG-ASN : angle 3.29180 ( 18) link_ALPHA1-6 : bond 0.00462 ( 1) link_ALPHA1-6 : angle 1.36479 ( 3) link_BETA1-4 : bond 0.00296 ( 4) link_BETA1-4 : angle 2.00359 ( 12) link_ALPHA1-3 : bond 0.01015 ( 1) link_ALPHA1-3 : angle 1.86239 ( 3) hydrogen bonds : bond 0.03606 ( 99) hydrogen bonds : angle 5.70627 ( 273) link_BETA1-6 : bond 0.00096 ( 1) link_BETA1-6 : angle 1.90720 ( 3) SS BOND : bond 0.00306 ( 4) SS BOND : angle 1.43951 ( 8) covalent geometry : bond 0.00424 ( 3278) covalent geometry : angle 0.79238 ( 4475) *********************** 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 47 residues out of total 340 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 43 time to evaluate : 0.338 Fit side-chains REVERT: L 39 LYS cc_start: 0.7761 (mttm) cc_final: 0.7350 (mmmt) REVERT: C 524 GLU cc_start: 0.8087 (pp20) cc_final: 0.7700 (pp20) REVERT: C 554 ARG cc_start: 0.7119 (tmt-80) cc_final: 0.6444 (tmt-80) REVERT: C 575 ASN cc_start: 0.7476 (m-40) cc_final: 0.7153 (m110) outliers start: 4 outliers final: 4 residues processed: 45 average time/residue: 0.2165 time to fit residues: 11.4777 Evaluate side-chains 42 residues out of total 340 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 38 time to evaluate : 0.352 ------------------------------------------------------------------------------- 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 673 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 38 random chunks: chunk 24 optimal weight: 6.9990 chunk 35 optimal weight: 0.0770 chunk 33 optimal weight: 1.9990 chunk 12 optimal weight: 0.9990 chunk 10 optimal weight: 0.8980 chunk 11 optimal weight: 4.9990 chunk 13 optimal weight: 0.5980 chunk 15 optimal weight: 0.9990 chunk 16 optimal weight: 1.9990 chunk 20 optimal weight: 0.8980 chunk 34 optimal weight: 1.9990 overall best weight: 0.6940 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 551 ASN C 574 GLN C 659 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4217 r_free = 0.4217 target = 0.141570 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3826 r_free = 0.3826 target = 0.112526 restraints weight = 6159.798| |-----------------------------------------------------------------------------| r_work (start): 0.3839 rms_B_bonded: 3.16 r_work: 0.3709 rms_B_bonded: 3.52 restraints_weight: 0.5000 r_work (final): 0.3709 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7571 moved from start: 0.1826 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.031 3295 Z= 0.157 Angle : 0.797 11.095 4522 Z= 0.363 Chirality : 0.051 0.403 539 Planarity : 0.006 0.071 560 Dihedral : 13.211 66.151 693 Min Nonbonded Distance : 2.235 Molprobity Statistics. All-atom Clashscore : 9.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.36 % Favored : 94.64 % Rotamer: Outliers : 2.06 % Allowed : 12.06 % Favored : 85.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.85 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.51 (0.45), residues: 392 helix: None (None), residues: 0 sheet: 1.07 (0.42), residues: 164 loop : -0.18 (0.44), residues: 228 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.002 TRP C 627 HIS 0.010 0.002 HIS L 91 PHE 0.010 0.002 PHE H 27 TYR 0.012 0.001 TYR H 95 ARG 0.002 0.000 ARG L 52 Details of bonding type rmsd link_NAG-ASN : bond 0.00531 ( 6) link_NAG-ASN : angle 3.53649 ( 18) link_ALPHA1-6 : bond 0.00768 ( 1) link_ALPHA1-6 : angle 1.24258 ( 3) link_BETA1-4 : bond 0.00522 ( 4) link_BETA1-4 : angle 2.08051 ( 12) link_ALPHA1-3 : bond 0.01231 ( 1) link_ALPHA1-3 : angle 1.49307 ( 3) hydrogen bonds : bond 0.03266 ( 99) hydrogen bonds : angle 5.50370 ( 273) link_BETA1-6 : bond 0.00046 ( 1) link_BETA1-6 : angle 1.62870 ( 3) SS BOND : bond 0.00247 ( 4) SS BOND : angle 1.04890 ( 8) covalent geometry : bond 0.00353 ( 3278) covalent geometry : angle 0.75701 ( 4475) *********************** 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 50 residues out of total 340 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 43 time to evaluate : 0.319 Fit side-chains REVERT: C 524 GLU cc_start: 0.8089 (pp20) cc_final: 0.7756 (pp20) REVERT: C 575 ASN cc_start: 0.7500 (m-40) cc_final: 0.7093 (m110) outliers start: 7 outliers final: 5 residues processed: 47 average time/residue: 0.1601 time to fit residues: 9.2623 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 : 0.366 ------------------------------------------------------------------------------- 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 669 VAL Chi-restraints excluded: chain C residue 673 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 38 random chunks: chunk 10 optimal weight: 1.9990 chunk 9 optimal weight: 1.9990 chunk 32 optimal weight: 0.6980 chunk 14 optimal weight: 1.9990 chunk 12 optimal weight: 0.5980 chunk 25 optimal weight: 4.9990 chunk 15 optimal weight: 0.8980 chunk 31 optimal weight: 0.6980 chunk 24 optimal weight: 3.9990 chunk 26 optimal weight: 0.9980 chunk 36 optimal weight: 0.8980 overall best weight: 0.7580 ------------------------------------------------------------------------------- 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 = 0.4208 r_free = 0.4208 target = 0.141199 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3825 r_free = 0.3825 target = 0.113071 restraints weight = 6283.085| |-----------------------------------------------------------------------------| r_work (start): 0.3822 rms_B_bonded: 3.13 r_work: 0.3689 rms_B_bonded: 3.51 restraints_weight: 0.5000 r_work (final): 0.3689 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7604 moved from start: 0.2106 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= 0.164 Angle : 0.797 9.962 4522 Z= 0.366 Chirality : 0.051 0.405 539 Planarity : 0.006 0.064 560 Dihedral : 11.523 57.803 693 Min Nonbonded Distance : 2.181 Molprobity Statistics. All-atom Clashscore : 9.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.36 % Favored : 94.64 % Rotamer: Outliers : 2.35 % Allowed : 13.53 % Favored : 84.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.85 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.49 (0.45), residues: 392 helix: None (None), residues: 0 sheet: 1.05 (0.42), residues: 164 loop : -0.18 (0.44), residues: 228 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.002 TRP C 627 HIS 0.010 0.002 HIS L 91 PHE 0.010 0.002 PHE H 27 TYR 0.013 0.001 TYR H 95 ARG 0.003 0.000 ARG C 554 Details of bonding type rmsd link_NAG-ASN : bond 0.00565 ( 6) link_NAG-ASN : angle 3.93693 ( 18) link_ALPHA1-6 : bond 0.00979 ( 1) link_ALPHA1-6 : angle 1.31135 ( 3) link_BETA1-4 : bond 0.00364 ( 4) link_BETA1-4 : angle 2.20510 ( 12) link_ALPHA1-3 : bond 0.01268 ( 1) link_ALPHA1-3 : angle 1.80072 ( 3) hydrogen bonds : bond 0.03199 ( 99) hydrogen bonds : angle 5.54785 ( 273) link_BETA1-6 : bond 0.00192 ( 1) link_BETA1-6 : angle 1.68470 ( 3) SS BOND : bond 0.00247 ( 4) SS BOND : angle 1.06195 ( 8) covalent geometry : bond 0.00371 ( 3278) covalent geometry : angle 0.74753 ( 4475) *********************** 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: 8 poor density : 41 time to evaluate : 0.332 Fit side-chains REVERT: C 524 GLU cc_start: 0.8073 (pp20) cc_final: 0.7870 (pp20) REVERT: C 575 ASN cc_start: 0.7581 (m-40) cc_final: 0.7177 (m-40) outliers start: 8 outliers final: 6 residues processed: 48 average time/residue: 0.1924 time to fit residues: 11.0194 Evaluate side-chains 45 residues out of total 340 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 39 time to evaluate : 0.349 ------------------------------------------------------------------------------- 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 93 VAL Chi-restraints excluded: chain L residue 85 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 27 optimal weight: 1.9990 chunk 35 optimal weight: 0.8980 chunk 32 optimal weight: 0.6980 chunk 13 optimal weight: 1.9990 chunk 4 optimal weight: 0.5980 chunk 24 optimal weight: 4.9990 chunk 2 optimal weight: 3.9990 chunk 30 optimal weight: 0.9980 chunk 36 optimal weight: 0.8980 chunk 26 optimal weight: 0.9980 chunk 34 optimal weight: 1.9990 overall best weight: 0.8180 ------------------------------------------------------------------------------- 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 = 0.141936 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3843 r_free = 0.3843 target = 0.114983 restraints weight = 6216.449| |-----------------------------------------------------------------------------| r_work (start): 0.3835 rms_B_bonded: 3.56 r_work: 0.3674 rms_B_bonded: 3.46 restraints_weight: 0.5000 r_work (final): 0.3674 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7637 moved from start: 0.2406 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 3295 Z= 0.171 Angle : 0.804 9.827 4522 Z= 0.377 Chirality : 0.050 0.405 539 Planarity : 0.006 0.064 560 Dihedral : 10.581 55.880 693 Min Nonbonded Distance : 2.359 Molprobity Statistics. All-atom Clashscore : 10.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.87 % Favored : 94.13 % Rotamer: Outliers : 2.94 % Allowed : 15.59 % Favored : 81.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.85 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.48 (0.45), residues: 392 helix: None (None), residues: 0 sheet: 1.04 (0.42), residues: 164 loop : -0.20 (0.44), residues: 228 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.002 TRP C 627 HIS 0.011 0.002 HIS L 91 PHE 0.012 0.002 PHE H 27 TYR 0.014 0.002 TYR H 95 ARG 0.008 0.001 ARG L 24 Details of bonding type rmsd link_NAG-ASN : bond 0.00578 ( 6) link_NAG-ASN : angle 3.73691 ( 18) link_ALPHA1-6 : bond 0.00996 ( 1) link_ALPHA1-6 : angle 1.38053 ( 3) link_BETA1-4 : bond 0.00431 ( 4) link_BETA1-4 : angle 2.33723 ( 12) link_ALPHA1-3 : bond 0.01087 ( 1) link_ALPHA1-3 : angle 1.65006 ( 3) hydrogen bonds : bond 0.03206 ( 99) hydrogen bonds : angle 5.57702 ( 273) link_BETA1-6 : bond 0.00026 ( 1) link_BETA1-6 : angle 1.72743 ( 3) SS BOND : bond 0.00263 ( 4) SS BOND : angle 1.05740 ( 8) covalent geometry : bond 0.00389 ( 3278) covalent geometry : angle 0.75804 ( 4475) *********************** 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 52 residues out of total 340 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 42 time to evaluate : 0.690 Fit side-chains REVERT: C 524 GLU cc_start: 0.8167 (pp20) cc_final: 0.7770 (pp20) REVERT: C 575 ASN cc_start: 0.7630 (m-40) cc_final: 0.7013 (m-40) outliers start: 10 outliers final: 7 residues processed: 51 average time/residue: 0.1760 time to fit residues: 11.3625 Evaluate side-chains 44 residues out of total 340 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 37 time to evaluate : 0.389 ------------------------------------------------------------------------------- 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 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=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 38 random chunks: chunk 4 optimal weight: 0.7980 chunk 24 optimal weight: 4.9990 chunk 21 optimal weight: 5.9990 chunk 16 optimal weight: 0.8980 chunk 27 optimal weight: 0.9980 chunk 7 optimal weight: 2.9990 chunk 23 optimal weight: 0.8980 chunk 17 optimal weight: 4.9990 chunk 14 optimal weight: 1.9990 chunk 13 optimal weight: 1.9990 chunk 25 optimal weight: 3.9990 overall best weight: 1.1182 ------------------------------------------------------------------------------- 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 = 0.4173 r_free = 0.4173 target = 0.139184 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3798 r_free = 0.3798 target = 0.111650 restraints weight = 6320.552| |-----------------------------------------------------------------------------| r_work (start): 0.3796 rms_B_bonded: 3.51 r_work: 0.3635 rms_B_bonded: 3.43 restraints_weight: 0.5000 r_work (final): 0.3635 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7689 moved from start: 0.2787 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.042 3295 Z= 0.206 Angle : 0.839 9.675 4522 Z= 0.401 Chirality : 0.052 0.418 539 Planarity : 0.006 0.064 560 Dihedral : 10.273 54.635 693 Min Nonbonded Distance : 2.114 Molprobity Statistics. All-atom Clashscore : 12.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.87 % Favored : 94.13 % Rotamer: Outliers : 3.53 % Allowed : 15.88 % Favored : 80.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.85 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.40 (0.45), residues: 392 helix: None (None), residues: 0 sheet: 0.92 (0.42), residues: 161 loop : -0.18 (0.44), residues: 231 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.002 TRP C 627 HIS 0.012 0.003 HIS L 91 PHE 0.016 0.002 PHE H 27 TYR 0.015 0.002 TYR H 95 ARG 0.003 0.000 ARG L 24 Details of bonding type rmsd link_NAG-ASN : bond 0.00559 ( 6) link_NAG-ASN : angle 3.56989 ( 18) link_ALPHA1-6 : bond 0.01004 ( 1) link_ALPHA1-6 : angle 1.43372 ( 3) link_BETA1-4 : bond 0.00377 ( 4) link_BETA1-4 : angle 2.47868 ( 12) link_ALPHA1-3 : bond 0.01081 ( 1) link_ALPHA1-3 : angle 1.63170 ( 3) hydrogen bonds : bond 0.03440 ( 99) hydrogen bonds : angle 5.72657 ( 273) link_BETA1-6 : bond 0.00168 ( 1) link_BETA1-6 : angle 1.80075 ( 3) SS BOND : bond 0.00514 ( 4) SS BOND : angle 1.38056 ( 8) covalent geometry : bond 0.00478 ( 3278) covalent geometry : angle 0.79696 ( 4475) *********************** 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 52 residues out of total 340 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 40 time to evaluate : 0.341 Fit side-chains REVERT: C 524 GLU cc_start: 0.8017 (pp20) cc_final: 0.7726 (pp20) REVERT: C 575 ASN cc_start: 0.7878 (m-40) cc_final: 0.7207 (m-40) REVERT: C 672 ILE cc_start: 0.8808 (OUTLIER) cc_final: 0.8582 (mp) outliers start: 12 outliers final: 7 residues processed: 50 average time/residue: 0.1658 time to fit residues: 10.1705 Evaluate side-chains 42 residues out of total 340 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 34 time to evaluate : 0.335 ------------------------------------------------------------------------------- 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 93 VAL Chi-restraints excluded: chain L residue 85 THR Chi-restraints excluded: chain C residue 533 LEU 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=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 38 random chunks: chunk 23 optimal weight: 0.6980 chunk 16 optimal weight: 0.6980 chunk 3 optimal weight: 0.7980 chunk 5 optimal weight: 1.9990 chunk 9 optimal weight: 0.0970 chunk 14 optimal weight: 1.9990 chunk 36 optimal weight: 0.6980 chunk 8 optimal weight: 3.9990 chunk 11 optimal weight: 0.6980 chunk 15 optimal weight: 0.8980 chunk 10 optimal weight: 0.5980 overall best weight: 0.5578 ------------------------------------------------------------------------------- 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 = 0.4197 r_free = 0.4197 target = 0.141020 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3798 r_free = 0.3798 target = 0.112185 restraints weight = 6148.482| |-----------------------------------------------------------------------------| r_work (start): 0.3804 rms_B_bonded: 3.05 r_work: 0.3672 rms_B_bonded: 3.40 restraints_weight: 0.5000 r_work (final): 0.3672 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7635 moved from start: 0.2810 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= 0.148 Angle : 0.821 9.906 4522 Z= 0.382 Chirality : 0.050 0.399 539 Planarity : 0.006 0.063 560 Dihedral : 9.913 56.627 693 Min Nonbonded Distance : 2.318 Molprobity Statistics. All-atom Clashscore : 10.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.12 % Favored : 93.88 % Rotamer: Outliers : 2.94 % Allowed : 16.76 % Favored : 80.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.85 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.40 (0.45), residues: 392 helix: None (None), residues: 0 sheet: 0.94 (0.42), residues: 161 loop : -0.20 (0.44), residues: 231 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP C 627 HIS 0.010 0.002 HIS L 91 PHE 0.008 0.001 PHE H 27 TYR 0.012 0.001 TYR H 95 ARG 0.003 0.000 ARG L 24 Details of bonding type rmsd link_NAG-ASN : bond 0.00527 ( 6) link_NAG-ASN : angle 3.54755 ( 18) link_ALPHA1-6 : bond 0.01000 ( 1) link_ALPHA1-6 : angle 1.42475 ( 3) link_BETA1-4 : bond 0.00480 ( 4) link_BETA1-4 : angle 2.52343 ( 12) link_ALPHA1-3 : bond 0.01031 ( 1) link_ALPHA1-3 : angle 1.75776 ( 3) hydrogen bonds : bond 0.03090 ( 99) hydrogen bonds : angle 5.30980 ( 273) link_BETA1-6 : bond 0.00012 ( 1) link_BETA1-6 : angle 1.63099 ( 3) SS BOND : bond 0.00453 ( 4) SS BOND : angle 1.48556 ( 8) covalent geometry : bond 0.00329 ( 3278) covalent geometry : angle 0.77701 ( 4475) *********************** 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 48 residues out of total 340 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 38 time to evaluate : 0.334 Fit side-chains REVERT: C 524 GLU cc_start: 0.7951 (pp20) cc_final: 0.7725 (pp20) REVERT: C 533 LEU cc_start: 0.8085 (OUTLIER) cc_final: 0.7447 (pp) REVERT: C 575 ASN cc_start: 0.7867 (m-40) cc_final: 0.7510 (m-40) REVERT: C 672 ILE cc_start: 0.8763 (OUTLIER) cc_final: 0.8539 (mp) outliers start: 10 outliers final: 8 residues processed: 46 average time/residue: 0.1715 time to fit residues: 9.6876 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 : 0.371 ------------------------------------------------------------------------------- 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 533 LEU Chi-restraints excluded: chain C residue 672 ILE Chi-restraints excluded: chain C residue 673 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 38 random chunks: chunk 1 optimal weight: 4.9990 chunk 25 optimal weight: 6.9990 chunk 5 optimal weight: 0.8980 chunk 2 optimal weight: 3.9990 chunk 29 optimal weight: 2.9990 chunk 0 optimal weight: 4.9990 chunk 30 optimal weight: 0.8980 chunk 32 optimal weight: 0.9990 chunk 13 optimal weight: 0.7980 chunk 8 optimal weight: 0.9980 chunk 31 optimal weight: 2.9990 overall best weight: 0.9182 ------------------------------------------------------------------------------- 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 = 0.4175 r_free = 0.4175 target = 0.139407 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3774 r_free = 0.3774 target = 0.110746 restraints weight = 6243.867| |-----------------------------------------------------------------------------| r_work (start): 0.3771 rms_B_bonded: 3.06 r_work: 0.3630 rms_B_bonded: 3.51 restraints_weight: 0.5000 r_work (final): 0.3630 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7685 moved from start: 0.3015 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 3295 Z= 0.179 Angle : 0.835 9.813 4522 Z= 0.391 Chirality : 0.051 0.410 539 Planarity : 0.006 0.065 560 Dihedral : 9.680 55.710 693 Min Nonbonded Distance : 2.324 Molprobity Statistics. All-atom Clashscore : 11.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.12 % Favored : 93.88 % Rotamer: Outliers : 3.24 % Allowed : 17.35 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.24 (0.44), residues: 392 helix: None (None), residues: 0 sheet: 0.80 (0.42), residues: 161 loop : -0.28 (0.43), residues: 231 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.002 TRP C 627 HIS 0.010 0.002 HIS L 91 PHE 0.012 0.002 PHE H 27 TYR 0.014 0.002 TYR H 95 ARG 0.003 0.000 ARG C 554 Details of bonding type rmsd link_NAG-ASN : bond 0.00601 ( 6) link_NAG-ASN : angle 3.49816 ( 18) link_ALPHA1-6 : bond 0.00979 ( 1) link_ALPHA1-6 : angle 1.46738 ( 3) link_BETA1-4 : bond 0.00424 ( 4) link_BETA1-4 : angle 2.61822 ( 12) link_ALPHA1-3 : bond 0.00957 ( 1) link_ALPHA1-3 : angle 1.54671 ( 3) hydrogen bonds : bond 0.03241 ( 99) hydrogen bonds : angle 5.41916 ( 273) link_BETA1-6 : bond 0.00113 ( 1) link_BETA1-6 : angle 1.74177 ( 3) SS BOND : bond 0.00382 ( 4) SS BOND : angle 1.55604 ( 8) covalent geometry : bond 0.00411 ( 3278) covalent geometry : angle 0.79257 ( 4475) *********************** 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 : 0.386 Fit side-chains REVERT: C 524 GLU cc_start: 0.7969 (pp20) cc_final: 0.7722 (pp20) REVERT: C 575 ASN cc_start: 0.7996 (m-40) cc_final: 0.7612 (m-40) REVERT: C 672 ILE cc_start: 0.8779 (OUTLIER) cc_final: 0.8525 (mp) outliers start: 11 outliers final: 10 residues processed: 47 average time/residue: 0.2171 time to fit residues: 12.6075 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 : 0.380 ------------------------------------------------------------------------------- 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 533 LEU 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=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 38 random chunks: chunk 32 optimal weight: 0.7980 chunk 5 optimal weight: 0.2980 chunk 9 optimal weight: 2.9990 chunk 34 optimal weight: 0.6980 chunk 28 optimal weight: 1.9990 chunk 23 optimal weight: 0.9990 chunk 35 optimal weight: 0.9990 chunk 31 optimal weight: 0.5980 chunk 10 optimal weight: 0.0980 chunk 33 optimal weight: 0.8980 chunk 24 optimal weight: 1.9990 overall best weight: 0.4980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 630 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4192 r_free = 0.4192 target = 0.139430 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3786 r_free = 0.3786 target = 0.110083 restraints weight = 6255.575| |-----------------------------------------------------------------------------| r_work (start): 0.3799 rms_B_bonded: 3.21 r_work: 0.3662 rms_B_bonded: 3.59 restraints_weight: 0.5000 r_work (final): 0.3662 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7639 moved from start: 0.2963 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 3295 Z= 0.138 Angle : 0.809 9.933 4522 Z= 0.375 Chirality : 0.050 0.396 539 Planarity : 0.006 0.062 560 Dihedral : 9.376 57.288 693 Min Nonbonded Distance : 2.334 Molprobity Statistics. All-atom Clashscore : 11.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.87 % Favored : 94.13 % Rotamer: Outliers : 3.24 % Allowed : 17.65 % Favored : 79.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.85 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.21 (0.44), residues: 392 helix: None (None), residues: 0 sheet: 0.80 (0.41), residues: 164 loop : -0.33 (0.44), residues: 228 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP C 627 HIS 0.009 0.002 HIS L 91 PHE 0.007 0.001 PHE H 27 TYR 0.012 0.001 TYR H 95 ARG 0.003 0.000 ARG C 554 Details of bonding type rmsd link_NAG-ASN : bond 0.00540 ( 6) link_NAG-ASN : angle 3.41493 ( 18) link_ALPHA1-6 : bond 0.00916 ( 1) link_ALPHA1-6 : angle 1.44387 ( 3) link_BETA1-4 : bond 0.00533 ( 4) link_BETA1-4 : angle 2.65095 ( 12) link_ALPHA1-3 : bond 0.00995 ( 1) link_ALPHA1-3 : angle 1.69425 ( 3) hydrogen bonds : bond 0.02933 ( 99) hydrogen bonds : angle 5.17613 ( 273) link_BETA1-6 : bond 0.00046 ( 1) link_BETA1-6 : angle 1.60828 ( 3) SS BOND : bond 0.00364 ( 4) SS BOND : angle 1.47102 ( 8) covalent geometry : bond 0.00307 ( 3278) covalent geometry : angle 0.76596 ( 4475) *********************** 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 51 residues out of total 340 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 40 time to evaluate : 0.337 Fit side-chains REVERT: C 524 GLU cc_start: 0.7963 (pp20) cc_final: 0.7663 (pp20) REVERT: C 533 LEU cc_start: 0.8170 (OUTLIER) cc_final: 0.7491 (pp) REVERT: C 534 TRP cc_start: 0.7284 (m100) cc_final: 0.7079 (m100) REVERT: C 575 ASN cc_start: 0.8028 (m-40) cc_final: 0.7637 (m-40) REVERT: C 672 ILE cc_start: 0.8745 (OUTLIER) cc_final: 0.8489 (mp) outliers start: 11 outliers final: 8 residues processed: 49 average time/residue: 0.1715 time to fit residues: 10.3255 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 : 0.367 ------------------------------------------------------------------------------- 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 93 VAL Chi-restraints excluded: chain L residue 85 THR Chi-restraints excluded: chain C residue 522 THR Chi-restraints excluded: chain C residue 533 LEU 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 25 optimal weight: 0.6980 chunk 32 optimal weight: 0.0370 chunk 20 optimal weight: 2.9990 chunk 1 optimal weight: 0.8980 chunk 30 optimal weight: 0.7980 chunk 2 optimal weight: 0.4980 chunk 29 optimal weight: 0.8980 chunk 28 optimal weight: 0.8980 chunk 13 optimal weight: 0.9990 chunk 18 optimal weight: 0.9980 chunk 12 optimal weight: 0.9990 overall best weight: 0.5858 ------------------------------------------------------------------------------- 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 = 0.4198 r_free = 0.4198 target = 0.141232 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3811 r_free = 0.3811 target = 0.113207 restraints weight = 6084.636| |-----------------------------------------------------------------------------| r_work (start): 0.3806 rms_B_bonded: 2.97 r_work: 0.3669 rms_B_bonded: 3.43 restraints_weight: 0.5000 r_work (final): 0.3669 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7640 moved from start: 0.3035 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 3295 Z= 0.146 Angle : 0.825 9.914 4522 Z= 0.380 Chirality : 0.050 0.397 539 Planarity : 0.006 0.065 560 Dihedral : 9.054 57.382 693 Min Nonbonded Distance : 2.345 Molprobity Statistics. All-atom Clashscore : 10.38 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.16 (0.44), residues: 392 helix: None (None), residues: 0 sheet: 0.79 (0.41), residues: 164 loop : -0.38 (0.44), residues: 228 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP C 627 HIS 0.009 0.002 HIS L 91 PHE 0.009 0.001 PHE H 27 TYR 0.012 0.001 TYR H 95 ARG 0.004 0.000 ARG C 554 Details of bonding type rmsd link_NAG-ASN : bond 0.00535 ( 6) link_NAG-ASN : angle 3.37859 ( 18) link_ALPHA1-6 : bond 0.00979 ( 1) link_ALPHA1-6 : angle 1.45246 ( 3) link_BETA1-4 : bond 0.00502 ( 4) link_BETA1-4 : angle 2.68016 ( 12) link_ALPHA1-3 : bond 0.00878 ( 1) link_ALPHA1-3 : angle 1.53765 ( 3) hydrogen bonds : bond 0.02947 ( 99) hydrogen bonds : angle 5.15604 ( 273) link_BETA1-6 : bond 0.00047 ( 1) link_BETA1-6 : angle 1.64509 ( 3) SS BOND : bond 0.00357 ( 4) SS BOND : angle 1.42669 ( 8) covalent geometry : bond 0.00327 ( 3278) covalent geometry : angle 0.78321 ( 4475) ********************** 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 51 residues out of total 340 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 41 time to evaluate : 0.338 Fit side-chains REVERT: H 89 GLU cc_start: 0.8026 (mp0) cc_final: 0.7821 (mp0) REVERT: C 524 GLU cc_start: 0.7864 (pp20) cc_final: 0.7620 (pp20) REVERT: C 533 LEU cc_start: 0.8157 (OUTLIER) cc_final: 0.7473 (pp) REVERT: C 575 ASN cc_start: 0.7983 (m-40) cc_final: 0.7620 (m-40) REVERT: C 672 ILE cc_start: 0.8753 (OUTLIER) cc_final: 0.8502 (mp) outliers start: 10 outliers final: 8 residues processed: 50 average time/residue: 0.1731 time to fit residues: 10.5812 Evaluate side-chains 48 residues out of total 340 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 38 time to evaluate : 0.434 ------------------------------------------------------------------------------- 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 93 VAL Chi-restraints excluded: chain L residue 85 THR Chi-restraints excluded: chain C residue 522 THR Chi-restraints excluded: chain C residue 533 LEU 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 26 optimal weight: 0.5980 chunk 12 optimal weight: 1.9990 chunk 15 optimal weight: 1.9990 chunk 14 optimal weight: 0.6980 chunk 11 optimal weight: 0.1980 chunk 5 optimal weight: 0.6980 chunk 8 optimal weight: 3.9990 chunk 29 optimal weight: 5.9990 chunk 37 optimal weight: 0.8980 chunk 28 optimal weight: 0.0000 chunk 3 optimal weight: 0.9990 overall best weight: 0.4384 ------------------------------------------------------------------------------- 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 = 0.4196 r_free = 0.4196 target = 0.139863 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3797 r_free = 0.3797 target = 0.110723 restraints weight = 6178.266| |-----------------------------------------------------------------------------| r_work (start): 0.3812 rms_B_bonded: 3.16 r_work: 0.3676 rms_B_bonded: 3.57 restraints_weight: 0.5000 r_work (final): 0.3676 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7625 moved from start: 0.3054 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 3295 Z= 0.136 Angle : 0.818 9.979 4522 Z= 0.375 Chirality : 0.050 0.393 539 Planarity : 0.006 0.063 560 Dihedral : 8.901 58.161 693 Min Nonbonded Distance : 2.373 Molprobity Statistics. All-atom Clashscore : 11.33 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.12 (0.44), residues: 392 helix: None (None), residues: 0 sheet: 0.79 (0.41), residues: 164 loop : -0.44 (0.43), residues: 228 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP C 534 HIS 0.008 0.002 HIS L 91 PHE 0.007 0.001 PHE H 27 TYR 0.010 0.001 TYR H 95 ARG 0.002 0.000 ARG L 24 Details of bonding type rmsd link_NAG-ASN : bond 0.00526 ( 6) link_NAG-ASN : angle 3.39162 ( 18) link_ALPHA1-6 : bond 0.00912 ( 1) link_ALPHA1-6 : angle 1.43065 ( 3) link_BETA1-4 : bond 0.00557 ( 4) link_BETA1-4 : angle 2.69705 ( 12) link_ALPHA1-3 : bond 0.00857 ( 1) link_ALPHA1-3 : angle 1.58557 ( 3) hydrogen bonds : bond 0.02859 ( 99) hydrogen bonds : angle 5.07307 ( 273) link_BETA1-6 : bond 0.00053 ( 1) link_BETA1-6 : angle 1.59701 ( 3) SS BOND : bond 0.00353 ( 4) SS BOND : angle 1.44081 ( 8) covalent geometry : bond 0.00303 ( 3278) covalent geometry : angle 0.77612 ( 4475) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2233.68 seconds wall clock time: 39 minutes 7.14 seconds (2347.14 seconds total)