Starting phenix.real_space_refine on Fri Dec 27 08:15:25 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8bw0_16279/12_2024/8bw0_16279.cif Found real_map, /net/cci-nas-00/data/ceres_data/8bw0_16279/12_2024/8bw0_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_16279/12_2024/8bw0_16279.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8bw0_16279/12_2024/8bw0_16279.map" model { file = "/net/cci-nas-00/data/ceres_data/8bw0_16279/12_2024/8bw0_16279.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8bw0_16279/12_2024/8bw0_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-5532/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: 3.01, per 1000 atoms: 0.94 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: 1.20 Conformation dependent library (CDL) restraints added in 398.7 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: 0.42 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: 0.85 Time building geometry restraints manager: 1.25 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: 0.790 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: 0.020 Extract box with map and model: 0.150 Check model and map are aligned: 0.020 Set scattering table: 0.040 Process input model: 13.580 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:3.080 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 17.730 ------------------------------------------------------------------------------- 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 3278 Z= 0.264 Angle : 0.763 11.313 4475 Z= 0.353 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 *********************** 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 : 0.338 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: 0.2358 time to fit residues: 15.6111 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 : 0.409 ------------------------------------------------------------------------------- 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: 0.0970 chunk 29 optimal weight: 3.9990 chunk 11 optimal weight: 0.0050 chunk 18 optimal weight: 1.9990 chunk 22 optimal weight: 6.9990 chunk 34 optimal weight: 0.6980 chunk 10 optimal weight: 0.9990 overall best weight: 0.7596 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7239 moved from start: 0.1330 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.033 3278 Z= 0.243 Angle : 0.770 11.080 4475 Z= 0.356 Chirality : 0.053 0.404 539 Planarity : 0.007 0.084 560 Dihedral : 15.889 83.562 693 Min Nonbonded Distance : 2.397 Molprobity Statistics. All-atom Clashscore : 9.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.10 % Favored : 94.90 % Rotamer: Outliers : 1.47 % Allowed : 7.35 % Favored : 91.18 % 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: 0.60 (0.45), residues: 392 helix: None (None), residues: 0 sheet: 1.16 (0.42), residues: 163 loop : -0.13 (0.44), residues: 229 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.002 TRP H 47 HIS 0.011 0.002 HIS L 91 PHE 0.011 0.002 PHE L 83 TYR 0.012 0.002 TYR H 100 ARG 0.002 0.000 ARG L 61 *********************** 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 : 0.386 Fit side-chains REVERT: L 39 LYS cc_start: 0.7635 (mttm) cc_final: 0.7270 (mmmt) REVERT: C 524 GLU cc_start: 0.8031 (pp20) cc_final: 0.7639 (pp20) REVERT: C 554 ARG cc_start: 0.7007 (tmt-80) cc_final: 0.6321 (tmt-80) REVERT: C 575 ASN cc_start: 0.7457 (m-40) cc_final: 0.7126 (m110) outliers start: 5 outliers final: 5 residues processed: 46 average time/residue: 0.2211 time to fit residues: 11.9835 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 : 0.384 ------------------------------------------------------------------------------- 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=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 38 random chunks: chunk 28 optimal weight: 1.9990 chunk 23 optimal weight: 1.9990 chunk 9 optimal weight: 1.9990 chunk 34 optimal weight: 0.8980 chunk 37 optimal weight: 4.9990 chunk 30 optimal weight: 0.6980 chunk 11 optimal weight: 3.9990 chunk 27 optimal weight: 0.8980 chunk 25 optimal weight: 4.9990 chunk 17 optimal weight: 4.9990 chunk 3 optimal weight: 0.5980 overall best weight: 1.0182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 551 ASN C 659 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7321 moved from start: 0.1997 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 3278 Z= 0.294 Angle : 0.788 11.064 4475 Z= 0.372 Chirality : 0.052 0.414 539 Planarity : 0.006 0.070 560 Dihedral : 13.193 65.708 693 Min Nonbonded Distance : 2.253 Molprobity Statistics. All-atom Clashscore : 11.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.36 % Favored : 94.64 % Rotamer: Outliers : 2.35 % Allowed : 12.06 % Favored : 85.59 % 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: 0.41 (0.45), residues: 392 helix: None (None), residues: 0 sheet: 0.98 (0.42), residues: 164 loop : -0.23 (0.44), residues: 228 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.002 TRP C 627 HIS 0.013 0.003 HIS L 91 PHE 0.014 0.002 PHE H 27 TYR 0.014 0.002 TYR H 95 ARG 0.002 0.000 ARG L 52 *********************** 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 52 residues out of total 340 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 44 time to evaluate : 0.353 Fit side-chains REVERT: C 524 GLU cc_start: 0.8006 (pp20) cc_final: 0.7627 (pp20) REVERT: C 575 ASN cc_start: 0.7567 (m-40) cc_final: 0.7157 (m110) outliers start: 8 outliers final: 6 residues processed: 49 average time/residue: 0.1638 time to fit residues: 9.8000 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 : 0.383 ------------------------------------------------------------------------------- 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=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 38 random chunks: chunk 16 optimal weight: 0.9980 chunk 23 optimal weight: 0.9990 chunk 34 optimal weight: 0.0020 chunk 36 optimal weight: 0.5980 chunk 18 optimal weight: 0.2980 chunk 32 optimal weight: 0.7980 chunk 9 optimal weight: 3.9990 chunk 30 optimal weight: 0.5980 chunk 20 optimal weight: 0.0980 chunk 0 optimal weight: 5.9990 chunk 27 optimal weight: 2.9990 overall best weight: 0.3188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 551 ASN C 659 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7256 moved from start: 0.1980 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 3278 Z= 0.186 Angle : 0.720 10.144 4475 Z= 0.340 Chirality : 0.049 0.390 539 Planarity : 0.005 0.063 560 Dihedral : 11.486 58.065 693 Min Nonbonded Distance : 2.215 Molprobity Statistics. All-atom Clashscore : 8.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.85 % Favored : 95.15 % Rotamer: Outliers : 1.76 % Allowed : 14.71 % Favored : 83.53 % 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: 0.55 (0.45), residues: 392 helix: None (None), residues: 0 sheet: 1.11 (0.42), residues: 164 loop : -0.17 (0.44), residues: 228 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP C 627 HIS 0.008 0.002 HIS L 91 PHE 0.012 0.001 PHE L 30 TYR 0.009 0.001 TYR H 95 ARG 0.001 0.000 ARG L 52 *********************** 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 47 residues out of total 340 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 41 time to evaluate : 0.386 Fit side-chains REVERT: C 524 GLU cc_start: 0.8001 (pp20) cc_final: 0.7793 (pp20) REVERT: C 575 ASN cc_start: 0.7581 (m-40) cc_final: 0.7189 (m-40) outliers start: 6 outliers final: 4 residues processed: 46 average time/residue: 0.2042 time to fit residues: 11.1898 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 : 0.398 ------------------------------------------------------------------------------- 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 Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 38 random chunks: chunk 15 optimal weight: 0.0870 chunk 31 optimal weight: 0.6980 chunk 25 optimal weight: 0.5980 chunk 0 optimal weight: 5.9990 chunk 18 optimal weight: 3.9990 chunk 32 optimal weight: 3.9990 chunk 9 optimal weight: 0.9990 chunk 12 optimal weight: 0.6980 chunk 33 optimal weight: 3.9990 chunk 7 optimal weight: 3.9990 chunk 21 optimal weight: 3.9990 overall best weight: 0.6160 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 659 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7298 moved from start: 0.2249 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 3278 Z= 0.226 Angle : 0.746 10.119 4475 Z= 0.358 Chirality : 0.050 0.401 539 Planarity : 0.006 0.064 560 Dihedral : 10.623 55.833 693 Min Nonbonded Distance : 2.359 Molprobity Statistics. All-atom Clashscore : 9.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.36 % Favored : 94.64 % Rotamer: Outliers : 2.35 % Allowed : 15.59 % Favored : 82.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.85 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: 0.56 (0.45), residues: 392 helix: None (None), residues: 0 sheet: 1.09 (0.42), residues: 164 loop : -0.13 (0.44), residues: 228 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.002 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 0.007 0.000 ARG L 24 *********************** 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 48 residues out of total 340 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 40 time to evaluate : 0.447 Fit side-chains REVERT: C 524 GLU cc_start: 0.8204 (pp20) cc_final: 0.7811 (pp20) REVERT: C 575 ASN cc_start: 0.7599 (m-40) cc_final: 0.6971 (m-40) outliers start: 8 outliers final: 5 residues processed: 47 average time/residue: 0.1811 time to fit residues: 10.4430 Evaluate side-chains 42 residues out of total 340 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 37 time to evaluate : 0.370 ------------------------------------------------------------------------------- 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 Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 38 random chunks: chunk 9 optimal weight: 4.9990 chunk 36 optimal weight: 0.9980 chunk 30 optimal weight: 0.8980 chunk 17 optimal weight: 5.9990 chunk 3 optimal weight: 0.9990 chunk 12 optimal weight: 0.9990 chunk 19 optimal weight: 0.5980 chunk 35 optimal weight: 0.9990 chunk 4 optimal weight: 0.6980 chunk 20 optimal weight: 0.0270 chunk 26 optimal weight: 9.9990 overall best weight: 0.6438 ------------------------------------------------------------------------------- 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 ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7308 moved from start: 0.2394 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 3278 Z= 0.226 Angle : 0.749 9.819 4475 Z= 0.358 Chirality : 0.050 0.402 539 Planarity : 0.006 0.063 560 Dihedral : 10.291 56.065 693 Min Nonbonded Distance : 2.279 Molprobity Statistics. All-atom Clashscore : 10.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.10 % Favored : 94.90 % 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 (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: 0.55 (0.45), residues: 392 helix: None (None), residues: 0 sheet: 1.07 (0.42), residues: 164 loop : -0.13 (0.45), residues: 228 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.002 TRP C 627 HIS 0.009 0.002 HIS L 91 PHE 0.009 0.001 PHE H 27 TYR 0.013 0.001 TYR H 95 ARG 0.005 0.000 ARG L 24 *********************** 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 49 residues out of total 340 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 39 time to evaluate : 0.380 Fit side-chains revert: symmetry clash REVERT: C 524 GLU cc_start: 0.8029 (pp20) cc_final: 0.7780 (pp20) REVERT: C 574 GLN cc_start: 0.7941 (mp10) cc_final: 0.7688 (mp10) REVERT: C 575 ASN cc_start: 0.7746 (m-40) cc_final: 0.7111 (m-40) REVERT: C 672 ILE cc_start: 0.8624 (OUTLIER) cc_final: 0.8367 (mp) outliers start: 10 outliers final: 8 residues processed: 47 average time/residue: 0.1765 time to fit residues: 10.2558 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 : 0.362 ------------------------------------------------------------------------------- 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 83 MET Chi-restraints excluded: chain L residue 78 LEU 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 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 20 optimal weight: 1.9990 chunk 30 optimal weight: 1.9990 chunk 36 optimal weight: 2.9990 chunk 22 optimal weight: 0.7980 chunk 16 optimal weight: 0.8980 chunk 14 optimal weight: 1.9990 chunk 21 optimal weight: 5.9990 chunk 11 optimal weight: 0.9980 chunk 7 optimal weight: 1.9990 chunk 23 optimal weight: 1.9990 chunk 24 optimal weight: 0.9980 overall best weight: 1.1382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 574 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7382 moved from start: 0.2858 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.041 3278 Z= 0.318 Angle : 0.791 9.499 4475 Z= 0.389 Chirality : 0.052 0.420 539 Planarity : 0.006 0.065 560 Dihedral : 10.015 54.971 693 Min Nonbonded Distance : 2.337 Molprobity Statistics. All-atom Clashscore : 12.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.38 % Favored : 93.62 % Rotamer: Outliers : 3.24 % Allowed : 15.59 % Favored : 81.18 % 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: 0.39 (0.45), residues: 392 helix: None (None), residues: 0 sheet: 1.00 (0.42), residues: 164 loop : -0.28 (0.44), residues: 228 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP C 627 HIS 0.012 0.003 HIS L 91 PHE 0.017 0.002 PHE H 27 TYR 0.015 0.002 TYR H 95 ARG 0.003 0.001 ARG L 24 *********************** 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 50 residues out of total 340 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 39 time to evaluate : 0.369 Fit side-chains REVERT: C 524 GLU cc_start: 0.7942 (pp20) cc_final: 0.7654 (pp20) REVERT: C 574 GLN cc_start: 0.7886 (mp10) cc_final: 0.7673 (mp10) REVERT: C 575 ASN cc_start: 0.7925 (m-40) cc_final: 0.7233 (m-40) REVERT: C 672 ILE cc_start: 0.8637 (OUTLIER) cc_final: 0.8378 (mp) outliers start: 11 outliers final: 8 residues processed: 47 average time/residue: 0.1690 time to fit residues: 9.7524 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 : 0.378 ------------------------------------------------------------------------------- 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 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=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 38 random chunks: chunk 18 optimal weight: 0.9980 chunk 3 optimal weight: 0.7980 chunk 28 optimal weight: 0.6980 chunk 33 optimal weight: 1.9990 chunk 35 optimal weight: 0.0070 chunk 32 optimal weight: 3.9990 chunk 34 optimal weight: 2.9990 chunk 20 optimal weight: 0.7980 chunk 14 optimal weight: 0.8980 chunk 26 optimal weight: 6.9990 chunk 10 optimal weight: 0.9980 overall best weight: 0.6398 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 574 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7344 moved from start: 0.2870 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 3278 Z= 0.221 Angle : 0.757 9.591 4475 Z= 0.364 Chirality : 0.050 0.403 539 Planarity : 0.006 0.063 560 Dihedral : 9.721 56.587 693 Min Nonbonded Distance : 2.341 Molprobity Statistics. All-atom Clashscore : 10.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.87 % Favored : 94.13 % Rotamer: Outliers : 2.94 % Allowed : 16.47 % 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: 0.36 (0.45), residues: 392 helix: None (None), residues: 0 sheet: 0.93 (0.42), residues: 164 loop : -0.25 (0.44), residues: 228 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP C 627 HIS 0.009 0.002 HIS L 91 PHE 0.009 0.001 PHE H 27 TYR 0.014 0.001 TYR H 95 ARG 0.005 0.000 ARG C 554 *********************** 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: 10 poor density : 39 time to evaluate : 0.358 Fit side-chains REVERT: C 524 GLU cc_start: 0.7929 (pp20) cc_final: 0.7614 (pp20) REVERT: C 575 ASN cc_start: 0.7937 (m-40) cc_final: 0.7282 (m-40) REVERT: C 672 ILE cc_start: 0.8576 (OUTLIER) cc_final: 0.8319 (mp) outliers start: 10 outliers final: 8 residues processed: 47 average time/residue: 0.1825 time to fit residues: 10.5128 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 : 0.353 ------------------------------------------------------------------------------- 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 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 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 30 optimal weight: 0.9980 chunk 32 optimal weight: 0.7980 chunk 34 optimal weight: 0.5980 chunk 22 optimal weight: 0.0370 chunk 36 optimal weight: 0.6980 chunk 17 optimal weight: 3.9990 chunk 25 optimal weight: 10.0000 chunk 37 optimal weight: 0.9980 chunk 3 optimal weight: 2.9990 chunk 23 optimal weight: 0.5980 chunk 18 optimal weight: 0.9980 overall best weight: 0.5458 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7333 moved from start: 0.2884 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 3278 Z= 0.207 Angle : 0.766 9.620 4475 Z= 0.365 Chirality : 0.050 0.398 539 Planarity : 0.006 0.064 560 Dihedral : 9.374 57.002 693 Min Nonbonded Distance : 2.349 Molprobity Statistics. All-atom Clashscore : 10.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.61 % Favored : 94.39 % Rotamer: Outliers : 2.94 % Allowed : 16.47 % 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: 0.32 (0.44), residues: 392 helix: None (None), residues: 0 sheet: 0.91 (0.42), residues: 164 loop : -0.29 (0.44), residues: 228 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP C 627 HIS 0.009 0.002 HIS L 91 PHE 0.008 0.001 PHE H 27 TYR 0.012 0.001 TYR H 95 ARG 0.004 0.000 ARG C 554 *********************** 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: 10 poor density : 41 time to evaluate : 0.373 Fit side-chains REVERT: C 524 GLU cc_start: 0.7855 (pp20) cc_final: 0.7606 (pp20) REVERT: C 575 ASN cc_start: 0.8020 (m-40) cc_final: 0.7649 (m-40) REVERT: C 672 ILE cc_start: 0.8572 (OUTLIER) cc_final: 0.8319 (mp) outliers start: 10 outliers final: 9 residues processed: 49 average time/residue: 0.1649 time to fit residues: 9.9107 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 : 0.389 ------------------------------------------------------------------------------- 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 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 672 ILE Chi-restraints excluded: chain C residue 673 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 38 random chunks: chunk 23 optimal weight: 0.2980 chunk 32 optimal weight: 0.9990 chunk 9 optimal weight: 3.9990 chunk 27 optimal weight: 4.9990 chunk 4 optimal weight: 0.2980 chunk 8 optimal weight: 0.6980 chunk 30 optimal weight: 0.9980 chunk 12 optimal weight: 0.2980 chunk 31 optimal weight: 0.9990 chunk 3 optimal weight: 0.7980 chunk 5 optimal weight: 1.9990 overall best weight: 0.4780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7321 moved from start: 0.2909 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 3278 Z= 0.197 Angle : 0.774 9.668 4475 Z= 0.364 Chirality : 0.050 0.394 539 Planarity : 0.006 0.063 560 Dihedral : 8.980 58.141 693 Min Nonbonded Distance : 2.383 Molprobity Statistics. All-atom Clashscore : 9.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.36 % Favored : 94.64 % Rotamer: Outliers : 3.53 % Allowed : 16.47 % Favored : 80.00 % 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: 0.28 (0.44), residues: 392 helix: None (None), residues: 0 sheet: 0.86 (0.41), residues: 164 loop : -0.30 (0.44), residues: 228 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP C 627 HIS 0.008 0.002 HIS L 91 PHE 0.007 0.001 PHE H 27 TYR 0.011 0.001 TYR H 95 ARG 0.003 0.000 ARG C 554 ********************** 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: 12 poor density : 39 time to evaluate : 0.364 Fit side-chains REVERT: C 524 GLU cc_start: 0.7787 (pp20) cc_final: 0.7543 (pp20) REVERT: C 575 ASN cc_start: 0.8008 (m-40) cc_final: 0.7647 (m-40) REVERT: C 672 ILE cc_start: 0.8565 (OUTLIER) cc_final: 0.8312 (mp) outliers start: 12 outliers final: 9 residues processed: 49 average time/residue: 0.1802 time to fit residues: 10.7760 Evaluate side-chains 47 residues out of total 340 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 37 time to evaluate : 0.392 ------------------------------------------------------------------------------- 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 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 Chi-restraints excluded: chain C residue 673 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 38 random chunks: chunk 26 optimal weight: 2.9990 chunk 1 optimal weight: 2.9990 chunk 21 optimal weight: 3.9990 chunk 34 optimal weight: 2.9990 chunk 20 optimal weight: 0.9980 chunk 25 optimal weight: 0.8980 chunk 24 optimal weight: 0.9990 chunk 23 optimal weight: 5.9990 chunk 14 optimal weight: 0.8980 chunk 37 optimal weight: 2.9990 chunk 0 optimal weight: 4.9990 overall best weight: 1.3584 ------------------------------------------------------------------------------- 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 = 0.4157 r_free = 0.4157 target = 0.137580 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3744 r_free = 0.3744 target = 0.108398 restraints weight = 6103.673| |-----------------------------------------------------------------------------| r_work (start): 0.3747 rms_B_bonded: 3.04 r_work: 0.3610 rms_B_bonded: 3.42 restraints_weight: 0.5000 r_work (final): 0.3610 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7716 moved from start: 0.3314 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.054 3278 Z= 0.364 Angle : 0.847 9.777 4475 Z= 0.408 Chirality : 0.053 0.420 539 Planarity : 0.006 0.064 560 Dihedral : 9.153 57.008 693 Min Nonbonded Distance : 2.333 Molprobity Statistics. All-atom Clashscore : 13.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.89 % Favored : 93.11 % Rotamer: Outliers : 2.94 % Allowed : 17.35 % Favored : 79.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.85 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.01 (0.44), residues: 392 helix: None (None), residues: 0 sheet: 0.63 (0.41), residues: 159 loop : -0.42 (0.44), residues: 233 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.003 TRP H 47 HIS 0.013 0.003 HIS L 91 PHE 0.016 0.002 PHE H 27 TYR 0.016 0.002 TYR H 95 ARG 0.003 0.001 ARG H 67 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1269.45 seconds wall clock time: 23 minutes 42.67 seconds (1422.67 seconds total)