Starting phenix.real_space_refine on Fri Apr 5 14:07:13 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8bw0_16279/04_2024/8bw0_16279.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8bw0_16279/04_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/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8bw0_16279/04_2024/8bw0_16279.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8bw0_16279/04_2024/8bw0_16279.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8bw0_16279/04_2024/8bw0_16279.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8bw0_16279/04_2024/8bw0_16279.pdb" } 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 Residue "L TYR 49": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ASP 515": "OD1" <-> "OD2" Residue "C ASP 565": "OD1" <-> "OD2" Time to flip residues: 0.01s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5288/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: 2.48, per 1000 atoms: 0.77 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 - 3.50 Amino acid : False - 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: 1.55 Conformation dependent library (CDL) restraints added in 572.9 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: 0.36 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: 1.66 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: 100.47 - 107.17: 138 107.17 - 113.87: 1872 113.87 - 120.57: 1126 120.57 - 127.27: 1297 127.27 - 133.97: 42 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 2.440 nonbonded pdb=" O4 NAG A 1 " pdb=" O7 NAG A 1 " model vdw 2.190 2.440 nonbonded pdb=" OG SER H 52 " pdb=" O GLY H 55 " model vdw 2.201 2.440 nonbonded pdb=" OG SER L 26 " pdb=" OE1 GLU L 27 " model vdw 2.241 2.440 nonbonded pdb=" O ALA C 527 " pdb=" OH TYR C 532 " model vdw 2.262 2.440 ... (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 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: 0.710 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: 3.640 Check model and map are aligned: 0.040 Set scattering table: 0.040 Process input model: 13.950 Find NCS groups from input model: 0.090 Set up NCS constraints: 0.010 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:2.900 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 21.380 ------------------------------------------------------------------------------- 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 fitting. rotamer outliers: 0 poor density : 57 time to evaluate : 0.406 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: 0.2158 time to fit residues: 14.3508 Evaluate side-chains 44 residues out of total 340 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 44 time to evaluate : 0.349 ------------------------------------------------------------------------------- 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: 0.4980 chunk 15 optimal weight: 1.9990 chunk 9 optimal weight: 2.9990 chunk 19 optimal weight: 1.9990 chunk 29 optimal weight: 0.7980 chunk 11 optimal weight: 0.3980 chunk 18 optimal weight: 0.9980 chunk 22 optimal weight: 3.9990 chunk 34 optimal weight: 2.9990 chunk 10 optimal weight: 0.7980 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 620 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 666 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7227 moved from start: 0.1175 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= 0.226 Angle : 0.744 11.097 4475 Z= 0.340 Chirality : 0.053 0.409 539 Planarity : 0.006 0.084 560 Dihedral : 16.802 83.839 693 Min Nonbonded Distance : 2.168 Molprobity Statistics. All-atom Clashscore : 12.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.36 % Favored : 94.64 % Rotamer: Outliers : 1.47 % Allowed : 6.47 % Favored : 92.06 % 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: 1.15 (0.42), residues: 163 loop : -0.18 (0.44), residues: 229 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP H 47 HIS 0.009 0.002 HIS L 91 PHE 0.010 0.002 PHE L 83 TYR 0.012 0.001 TYR H 100 ARG 0.003 0.000 ARG L 24 *********************** 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 fitting. rotamer outliers: 5 poor density : 43 time to evaluate : 0.375 Fit side-chains REVERT: L 39 LYS cc_start: 0.7622 (mttm) cc_final: 0.7261 (mmmt) REVERT: C 524 GLU cc_start: 0.7996 (pp20) cc_final: 0.7429 (pp20) REVERT: C 525 PRO cc_start: 0.8992 (Cg_endo) cc_final: 0.8655 (Cg_exo) outliers start: 5 outliers final: 5 residues processed: 46 average time/residue: 0.2233 time to fit residues: 12.0291 Evaluate side-chains 46 residues out of total 340 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 41 time to evaluate : 0.386 ------------------------------------------------------------------------------- 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: 0.5980 chunk 23 optimal weight: 3.9990 chunk 9 optimal weight: 0.9990 chunk 34 optimal weight: 0.6980 chunk 37 optimal weight: 0.6980 chunk 30 optimal weight: 1.9990 chunk 11 optimal weight: 3.9990 chunk 27 optimal weight: 1.9990 chunk 25 optimal weight: 0.8980 chunk 17 optimal weight: 5.9990 chunk 3 optimal weight: 0.5980 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 620 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7269 moved from start: 0.1638 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 3278 Z= 0.223 Angle : 0.743 11.226 4475 Z= 0.343 Chirality : 0.051 0.404 539 Planarity : 0.006 0.069 560 Dihedral : 13.408 74.085 693 Min Nonbonded Distance : 2.178 Molprobity Statistics. All-atom Clashscore : 11.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.36 % Favored : 94.64 % Rotamer: Outliers : 1.76 % Allowed : 11.47 % Favored : 86.76 % 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: 0.51 (0.45), residues: 392 helix: None (None), residues: 0 sheet: 1.10 (0.42), residues: 163 loop : -0.20 (0.44), residues: 229 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 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 0.003 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 50 residues out of total 340 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 44 time to evaluate : 0.358 Fit side-chains REVERT: C 524 GLU cc_start: 0.8034 (pp20) cc_final: 0.7751 (pp20) outliers start: 6 outliers final: 5 residues processed: 47 average time/residue: 0.1776 time to fit residues: 10.1485 Evaluate side-chains 44 residues out of total 340 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 39 time to evaluate : 0.360 ------------------------------------------------------------------------------- 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 16 optimal weight: 1.9990 chunk 23 optimal weight: 3.9990 chunk 34 optimal weight: 0.5980 chunk 36 optimal weight: 0.9980 chunk 18 optimal weight: 1.9990 chunk 32 optimal weight: 0.5980 chunk 9 optimal weight: 2.9990 chunk 30 optimal weight: 0.5980 chunk 20 optimal weight: 0.9990 chunk 0 optimal weight: 6.9990 chunk 27 optimal weight: 3.9990 overall best weight: 0.7582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 551 ASN ** C 620 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 659 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7305 moved from start: 0.2069 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= 0.237 Angle : 0.725 9.891 4475 Z= 0.344 Chirality : 0.051 0.404 539 Planarity : 0.006 0.066 560 Dihedral : 11.495 64.468 693 Min Nonbonded Distance : 2.174 Molprobity Statistics. All-atom Clashscore : 12.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.87 % Favored : 94.13 % Rotamer: Outliers : 2.06 % Allowed : 14.12 % Favored : 83.82 % 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: 0.42 (0.45), residues: 392 helix: None (None), residues: 0 sheet: 1.00 (0.42), residues: 164 loop : -0.23 (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 0.011 0.002 PHE H 27 TYR 0.013 0.001 TYR H 95 ARG 0.003 0.000 ARG C 554 *********************** 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 48 residues out of total 340 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 41 time to evaluate : 0.378 Fit side-chains REVERT: C 524 GLU cc_start: 0.8017 (pp20) cc_final: 0.7697 (pp20) outliers start: 7 outliers final: 6 residues processed: 47 average time/residue: 0.1960 time to fit residues: 11.0137 Evaluate side-chains 44 residues out of total 340 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 38 time to evaluate : 0.344 ------------------------------------------------------------------------------- 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 15 optimal weight: 0.6980 chunk 31 optimal weight: 0.0040 chunk 25 optimal weight: 0.9980 chunk 0 optimal weight: 5.9990 chunk 18 optimal weight: 0.5980 chunk 32 optimal weight: 0.8980 chunk 9 optimal weight: 3.9990 chunk 12 optimal weight: 4.9990 chunk 33 optimal weight: 1.9990 chunk 7 optimal weight: 1.9990 chunk 21 optimal weight: 4.9990 overall best weight: 0.6392 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 620 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7306 moved from start: 0.2227 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= 0.216 Angle : 0.708 9.832 4475 Z= 0.336 Chirality : 0.050 0.397 539 Planarity : 0.005 0.062 560 Dihedral : 10.745 57.751 693 Min Nonbonded Distance : 2.174 Molprobity Statistics. All-atom Clashscore : 12.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.61 % Favored : 94.39 % Rotamer: Outliers : 2.06 % Allowed : 14.71 % Favored : 83.24 % 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: 0.95 (0.42), residues: 164 loop : -0.26 (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 0.009 0.001 PHE H 27 TYR 0.013 0.001 TYR H 95 ARG 0.006 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 47 residues out of total 340 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 40 time to evaluate : 0.382 Fit side-chains REVERT: C 524 GLU cc_start: 0.8010 (pp20) cc_final: 0.7660 (pp20) REVERT: C 575 ASN cc_start: 0.8004 (m-40) cc_final: 0.7741 (m-40) outliers start: 7 outliers final: 6 residues processed: 46 average time/residue: 0.1723 time to fit residues: 9.6906 Evaluate side-chains 43 residues out of total 340 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 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 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=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 38 random chunks: chunk 9 optimal weight: 4.9990 chunk 36 optimal weight: 0.9990 chunk 30 optimal weight: 0.8980 chunk 17 optimal weight: 5.9990 chunk 3 optimal weight: 0.5980 chunk 12 optimal weight: 0.0870 chunk 19 optimal weight: 0.2980 chunk 35 optimal weight: 0.9980 chunk 4 optimal weight: 0.7980 chunk 20 optimal weight: 0.8980 chunk 26 optimal weight: 6.9990 overall best weight: 0.5358 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 620 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7303 moved from start: 0.2311 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 3278 Z= 0.206 Angle : 0.723 9.569 4475 Z= 0.345 Chirality : 0.050 0.397 539 Planarity : 0.005 0.062 560 Dihedral : 10.268 57.467 693 Min Nonbonded Distance : 2.187 Molprobity Statistics. All-atom Clashscore : 12.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.10 % Favored : 94.90 % Rotamer: Outliers : 2.94 % Allowed : 15.00 % 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: 0.34 (0.44), residues: 392 helix: None (None), residues: 0 sheet: 0.92 (0.42), residues: 164 loop : -0.26 (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 0.008 0.001 PHE H 27 TYR 0.013 0.001 TYR H 95 ARG 0.004 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 52 residues out of total 340 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 42 time to evaluate : 0.336 Fit side-chains REVERT: C 672 ILE cc_start: 0.8618 (OUTLIER) cc_final: 0.8340 (mp) outliers start: 10 outliers final: 6 residues processed: 51 average time/residue: 0.1537 time to fit residues: 9.5916 Evaluate side-chains 46 residues out of total 340 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 39 time to evaluate : 0.323 ------------------------------------------------------------------------------- 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 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 20 optimal weight: 0.7980 chunk 30 optimal weight: 3.9990 chunk 36 optimal weight: 0.9990 chunk 22 optimal weight: 0.6980 chunk 16 optimal weight: 1.9990 chunk 14 optimal weight: 1.9990 chunk 21 optimal weight: 0.4980 chunk 11 optimal weight: 0.4980 chunk 7 optimal weight: 3.9990 chunk 23 optimal weight: 4.9990 chunk 24 optimal weight: 0.9980 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 551 ASN ** C 620 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7324 moved from start: 0.2545 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 3278 Z= 0.241 Angle : 0.747 9.556 4475 Z= 0.355 Chirality : 0.050 0.401 539 Planarity : 0.005 0.062 560 Dihedral : 9.967 57.363 693 Min Nonbonded Distance : 2.188 Molprobity Statistics. All-atom Clashscore : 15.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.12 % Favored : 93.88 % Rotamer: Outliers : 3.82 % Allowed : 15.59 % 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: 0.33 (0.44), residues: 392 helix: None (None), residues: 0 sheet: 0.87 (0.41), residues: 164 loop : -0.23 (0.44), residues: 228 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.002 TRP C 534 HIS 0.009 0.002 HIS L 91 PHE 0.010 0.001 PHE H 27 TYR 0.014 0.001 TYR H 95 ARG 0.003 0.000 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 54 residues out of total 340 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 41 time to evaluate : 0.364 Fit side-chains REVERT: C 525 PRO cc_start: 0.9166 (Cg_endo) cc_final: 0.8830 (Cg_exo) REVERT: C 672 ILE cc_start: 0.8616 (OUTLIER) cc_final: 0.8339 (mp) outliers start: 13 outliers final: 8 residues processed: 52 average time/residue: 0.1576 time to fit residues: 10.0648 Evaluate side-chains 47 residues out of total 340 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 38 time to evaluate : 0.378 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 12 VAL Chi-restraints excluded: chain H residue 35 SER Chi-restraints excluded: chain H residue 53 SER Chi-restraints excluded: chain H residue 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 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: 0.6980 chunk 28 optimal weight: 0.0770 chunk 33 optimal weight: 2.9990 chunk 35 optimal weight: 0.0570 chunk 32 optimal weight: 0.7980 chunk 34 optimal weight: 0.6980 chunk 20 optimal weight: 0.7980 chunk 14 optimal weight: 1.9990 chunk 26 optimal weight: 2.9990 chunk 10 optimal weight: 0.6980 overall best weight: 0.4456 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 620 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 630 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7302 moved from start: 0.2626 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 3278 Z= 0.210 Angle : 0.763 9.602 4475 Z= 0.366 Chirality : 0.050 0.394 539 Planarity : 0.005 0.062 560 Dihedral : 9.581 58.369 693 Min Nonbonded Distance : 2.190 Molprobity Statistics. All-atom Clashscore : 13.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.87 % Favored : 94.13 % Rotamer: Outliers : 2.94 % Allowed : 15.88 % 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: 0.36 (0.44), residues: 392 helix: None (None), residues: 0 sheet: 1.02 (0.43), residues: 155 loop : -0.28 (0.42), residues: 237 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP C 534 HIS 0.007 0.001 HIS L 91 PHE 0.007 0.001 PHE H 27 TYR 0.012 0.001 TYR H 95 ARG 0.004 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 fitting. rotamer outliers: 10 poor density : 39 time to evaluate : 0.401 Fit side-chains REVERT: C 672 ILE cc_start: 0.8572 (OUTLIER) cc_final: 0.8321 (mp) outliers start: 10 outliers final: 8 residues processed: 48 average time/residue: 0.1743 time to fit residues: 10.2437 Evaluate side-chains 45 residues out of total 340 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 36 time to evaluate : 0.437 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 12 VAL Chi-restraints excluded: chain H residue 35 SER Chi-restraints excluded: chain H residue 53 SER Chi-restraints excluded: chain H residue 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 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 30 optimal weight: 2.9990 chunk 32 optimal weight: 1.9990 chunk 34 optimal weight: 0.7980 chunk 22 optimal weight: 0.9980 chunk 36 optimal weight: 0.9980 chunk 17 optimal weight: 5.9990 chunk 25 optimal weight: 0.1980 chunk 37 optimal weight: 0.6980 chunk 3 optimal weight: 2.9990 chunk 23 optimal weight: 5.9990 chunk 18 optimal weight: 0.5980 overall best weight: 0.6580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 620 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7327 moved from start: 0.2780 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 3278 Z= 0.226 Angle : 0.769 9.579 4475 Z= 0.364 Chirality : 0.050 0.400 539 Planarity : 0.006 0.062 560 Dihedral : 9.249 57.625 693 Min Nonbonded Distance : 2.203 Molprobity Statistics. All-atom Clashscore : 15.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.12 % Favored : 93.88 % Rotamer: Outliers : 2.65 % Allowed : 16.47 % Favored : 80.88 % 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: 0.30 (0.44), residues: 392 helix: None (None), residues: 0 sheet: 0.93 (0.42), residues: 155 loop : -0.27 (0.43), residues: 237 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.002 TRP C 627 HIS 0.009 0.002 HIS L 91 PHE 0.010 0.001 PHE H 27 TYR 0.014 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 47 residues out of total 340 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 38 time to evaluate : 0.377 Fit side-chains REVERT: C 672 ILE cc_start: 0.8577 (OUTLIER) cc_final: 0.8322 (mp) outliers start: 9 outliers final: 8 residues processed: 46 average time/residue: 0.1553 time to fit residues: 8.9071 Evaluate side-chains 47 residues out of total 340 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 38 time to evaluate : 0.375 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 12 VAL Chi-restraints excluded: chain H residue 35 SER Chi-restraints excluded: chain H residue 53 SER Chi-restraints excluded: chain H residue 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 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: 1.9990 chunk 32 optimal weight: 0.9990 chunk 9 optimal weight: 0.6980 chunk 27 optimal weight: 3.9990 chunk 4 optimal weight: 0.7980 chunk 8 optimal weight: 2.9990 chunk 30 optimal weight: 0.7980 chunk 12 optimal weight: 6.9990 chunk 31 optimal weight: 0.7980 chunk 3 optimal weight: 0.7980 chunk 5 optimal weight: 0.8980 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 620 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7349 moved from start: 0.2977 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 3278 Z= 0.244 Angle : 0.784 9.674 4475 Z= 0.374 Chirality : 0.051 0.399 539 Planarity : 0.006 0.062 560 Dihedral : 8.957 58.246 693 Min Nonbonded Distance : 2.195 Molprobity Statistics. All-atom Clashscore : 15.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.38 % Favored : 93.62 % Rotamer: Outliers : 2.65 % Allowed : 16.18 % 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: 0.16 (0.43), residues: 392 helix: None (None), residues: 0 sheet: 0.88 (0.42), residues: 155 loop : -0.42 (0.42), residues: 237 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 0.011 0.002 PHE H 27 TYR 0.014 0.001 TYR H 95 ARG 0.003 0.000 ARG L 24 ********************** 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 48 residues out of total 340 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 39 time to evaluate : 0.357 Fit side-chains REVERT: C 672 ILE cc_start: 0.8576 (OUTLIER) cc_final: 0.8321 (mp) outliers start: 9 outliers final: 8 residues processed: 47 average time/residue: 0.1787 time to fit residues: 10.2516 Evaluate side-chains 47 residues out of total 340 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 38 time to evaluate : 0.289 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 12 VAL Chi-restraints excluded: chain H residue 35 SER Chi-restraints excluded: chain H residue 53 SER Chi-restraints excluded: chain H residue 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 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: 0.9980 chunk 1 optimal weight: 3.9990 chunk 21 optimal weight: 10.0000 chunk 34 optimal weight: 0.9980 chunk 20 optimal weight: 0.8980 chunk 25 optimal weight: 4.9990 chunk 24 optimal weight: 5.9990 chunk 23 optimal weight: 6.9990 chunk 14 optimal weight: 0.9980 chunk 37 optimal weight: 0.8980 chunk 0 optimal weight: 4.9990 overall best weight: 0.9580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 620 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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 = 0.4171 r_free = 0.4171 target = 0.138922 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3761 r_free = 0.3761 target = 0.109870 restraints weight = 6136.456| |-----------------------------------------------------------------------------| r_work (start): 0.3764 rms_B_bonded: 3.09 r_work: 0.3623 rms_B_bonded: 3.52 restraints_weight: 0.5000 r_work (final): 0.3623 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7688 moved from start: 0.3203 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.046 3278 Z= 0.275 Angle : 0.803 9.797 4475 Z= 0.382 Chirality : 0.051 0.403 539 Planarity : 0.006 0.064 560 Dihedral : 8.893 58.362 693 Min Nonbonded Distance : 2.205 Molprobity Statistics. All-atom Clashscore : 16.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.38 % Favored : 93.62 % Rotamer: Outliers : 2.35 % Allowed : 17.06 % 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: 0.05 (0.43), residues: 392 helix: None (None), residues: 0 sheet: 0.79 (0.42), residues: 155 loop : -0.48 (0.42), residues: 237 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.002 TRP C 627 HIS 0.012 0.002 HIS L 91 PHE 0.013 0.002 PHE H 27 TYR 0.015 0.002 TYR H 95 ARG 0.003 0.000 ARG H 67 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1265.93 seconds wall clock time: 23 minutes 32.14 seconds (1412.14 seconds total)