Sun 23 Dec 22:22:56 GMT 2018 ############### You are running ARP/wARP 8.0 ############### Working directory /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir Job ID is set to 2pnk-3.2-parrot-hancs X-ray data file /users/emra500/scratch/Dataset/hancsChltofom/2pnk-3.2-parrot-hancs.mtz Sequence file /users/emra500/scratch/Dataset/hancsChltofom/2pnk-3.2-parrot-hancs.fasta Tracing mode WARPNTRACEPHASES Creating directory /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/2pnk-3.2-parrot-hancs Accepted label: fp=FP Accepted label: sigfp=SIGFP Accepted label: phibest=hltofom.Phi_fom.phi Accepted label: fom=hltofom.Phi_fom.fom mtz labels taken: FP SIGFP hltofom.Phi_fom.phi hltofom.Phi_fom.fom Parameter file /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/2pnk-3.2-parrot-hancs/arp_warp_classic.par Job launched in /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/2pnk-3.2-parrot-hancs ############### You are running ARP/wARP 8.0 ############### ============================================================ Please cite at least one of the publications below for the ARP/wARP application you are using: Lamzin VS, Wilson KS. (1993) Automated refinement of protein models. Acta Crystallogr D Biol Crystallogr. 49, 129-147 Morris RJ, Perrakis A. Lamzin VS. (2003) ARP/wARP and automatic interpretation of protein electron density maps. In Methods Enzymol. (Carter, C.W. & Sweet, R.M. eds.) 374, 229-244 Langer GG, Hazledine S, Wiegels T, Carolan C, Lamzin VS. (2013) Visual automated macromolecular model building. Acta Crystallogr D Biol Crystallogr. 69, 635-641 Use of Refmac is an essential part of model building with ARP/wARP. Please acknowledge the use of Refmac by citing the following publication: Murshudov GN, Skubak P, Lebedev AA, Pannu NS, Steiner RA, Nicholls RA, Winn MD, Long F, Vagin AA. (2011) REFMAC5 for the refinement of macromolecular crystal structures. Acta Crystallogr D Biol Crystallogr. 67, 355-367 ============================================================ Sun 23 Dec 22:23:05 GMT 2018 You are running ARP/wARP version 8.0 Entering warp_tracing.sh from COMMAND_LINE_SUBMISSION The working directory: /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/2pnk-3.2-parrot-hancs ARP/wARP software version: 8.0 The parameter file: /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/2pnk-3.2-parrot-hancs/arp_warp_classic.par ARP/wARP will run in subdirectory: temp_tracing Checking the estimated solvent content Computed solvent content is outside allowed range. Target number of residues/nucleotides is changed to 4893 and 0 Target number of residues in the AU: 4893 Target solvent content: 0.6253 Target number of residues exceeds 1700, conditional restraints are disabled Checking the provided sequence file Detected sequence length: 428 Maximum limit of NCS related copies: 60 Number of NCS-related molecules: 12 Adjusted target number of residues: 5136 Adjusted target solvent content: 0.61 Input MTZ file: 2pnk-3.2-parrot-hancs.mtz.cad Column labels for model refinement: FP SIGFP Column labels to obtain initial map: FP hltofom.Phi_fom.phi hltofom.Phi_fom.fom Space group number: 5 Cell parameters: 273.720 158.560 181.240 90.000 116.029 90.000 Input sequence file: 2pnk-3.2-parrot-hancs.fasta_lf Building free atoms model in initial map for 41088 target number of atoms Had to go as low as 0.95 sigma, to complete atoms search. ARP/wARP will be iterated with REFMAC5 50 refinement / model update cycles will be run in total. Atoms will be removed below 1.0 sigma in 2mFoDFc map and added above 3.2 sigma in mFoDFc map. Refmac Refinement Parameters 3 REFMAC cycle(s) with 1.0 1.0 fractional shifts damping in each cycle. Weight for restraints is set to AUTO Solvent mask correction will be used Anisotropic scaling with no bulk solvent correction Model Building Parameters Main chain tracing will take place every 5 refinement / model update cycles. Side chain docking will be performed from autobuilding cycle number 1 NCS extension will be performed at every building cycle. NCS restraints will be applied at each refinement cycle. Loops will be built when appropriate and at the last cycle Resolution range: 162.857 3.200 Wilson plot Bfac: 64.11 107474 reflections ( 93.72 % complete ) and 0 restraints for refining 45320 atoms. Observations/parameters ratio is 0.59 ------------------------------------------------------ Starting model: R = 0.2927 (Rfree = 0.000). ------------------------------------------------------ Cycle 0: After refmac, R = 0.2174 (Rfree = 0.000) for 45320 atoms. Found 381 (406 requested) and removed 258 (203 requested) atoms. ------------------------------------------------------ Building Cycle 1 Atomic shape factors 3.16 2.72 Search for helices and strands: 0 residues in 0 chains, 46534 seeds are put forward NCS extension: 0 residues added, 46534 seeds are put forward Round 1: 3223 peptides, 493 chains. Longest chain 29 peptides. Score 0.474 Round 2: 3654 peptides, 421 chains. Longest chain 40 peptides. Score 0.614 Round 3: 3791 peptides, 389 chains. Longest chain 47 peptides. Score 0.659 Round 4: 3881 peptides, 378 chains. Longest chain 51 peptides. Score 0.680 Round 5: 3902 peptides, 366 chains. Longest chain 44 peptides. Score 0.691 Taking the results from Round 5 Chains 390, Residues 3536, Estimated correctness of the model 63.2 % 54 chains (1050 residues) have been docked in sequence ------------------------------------------------------ 107474 reflections ( 93.72 % complete ) and 18179 restraints for refining 39146 atoms. Observations/parameters ratio is 0.69 ------------------------------------------------------ Cycle 1: After refmac, R = 0.2193 (Rfree = 0.000) for 39146 atoms. Found 328 (351 requested) and removed 293 (175 requested) atoms. Cycle 2: After refmac, R = 0.1951 (Rfree = 0.000) for 39181 atoms. Found 137 (351 requested) and removed 196 (175 requested) atoms. Failed to save intermediate PDB Cycle 3: After refmac, R = 0.1870 (Rfree = 0.000) for 39122 atoms. Found 78 (351 requested) and removed 187 (175 requested) atoms. Failed to save intermediate PDB Cycle 4: After refmac, R = 0.1832 (Rfree = 0.000) for 39013 atoms. Found 50 (350 requested) and removed 185 (175 requested) atoms. Cycle 5: After refmac, R = 0.1789 (Rfree = 0.000) for 38878 atoms. Found 62 (348 requested) and removed 183 (174 requested) atoms. ------------------------------------------------------ Building Cycle 2 Atomic shape factors 3.17 2.73 Search for helices and strands: 0 residues in 0 chains, 39922 seeds are put forward NCS extension: 9 residues added (15 deleted due to clashes), 39931 seeds are put forward Round 1: 3729 peptides, 406 chains. Longest chain 46 peptides. Score 0.638 Round 2: 3938 peptides, 366 chains. Longest chain 50 peptides. Score 0.696 Round 3: 3931 peptides, 361 chains. Longest chain 51 peptides. Score 0.698 Round 4: 3915 peptides, 360 chains. Longest chain 45 peptides. Score 0.697 Round 5: 3872 peptides, 373 chains. Longest chain 42 peptides. Score 0.682 Taking the results from Round 3 Chains 387, Residues 3570, Estimated correctness of the model 64.8 % 60 chains (1184 residues) have been docked in sequence ------------------------------------------------------ 107474 reflections ( 93.72 % complete ) and 19024 restraints for refining 37512 atoms. Observations/parameters ratio is 0.72 ------------------------------------------------------ Cycle 6: After refmac, R = 0.2183 (Rfree = 0.000) for 37512 atoms. Found 336 (336 requested) and removed 288 (168 requested) atoms. Cycle 7: After refmac, R = 0.1966 (Rfree = 0.000) for 37560 atoms. Found 96 (337 requested) and removed 183 (168 requested) atoms. Failed to save intermediate PDB Cycle 8: After refmac, R = 0.1885 (Rfree = 0.000) for 37473 atoms. Found 65 (336 requested) and removed 169 (168 requested) atoms. Cycle 9: After refmac, R = 0.1861 (Rfree = 0.000) for 37369 atoms. Found 43 (335 requested) and removed 168 (167 requested) atoms. Cycle 10: After refmac, R = 0.1831 (Rfree = 0.000) for 37244 atoms. Found 53 (334 requested) and removed 169 (167 requested) atoms. ------------------------------------------------------ Building Cycle 3 Atomic shape factors 3.16 2.72 Search for helices and strands: 0 residues in 0 chains, 38263 seeds are put forward NCS extension: 24 residues added (20 deleted due to clashes), 38287 seeds are put forward Round 1: 3627 peptides, 385 chains. Longest chain 47 peptides. Score 0.637 Round 2: 3823 peptides, 355 chains. Longest chain 42 peptides. Score 0.687 Round 3: 3824 peptides, 366 chains. Longest chain 67 peptides. Score 0.680 Round 4: 3791 peptides, 366 chains. Longest chain 42 peptides. Score 0.675 Round 5: 3808 peptides, 360 chains. Longest chain 42 peptides. Score 0.682 Taking the results from Round 2 Chains 374, Residues 3468, Estimated correctness of the model 62.4 % 56 chains (1179 residues) have been docked in sequence ------------------------------------------------------ Failed to save intermediate PDB 107474 reflections ( 93.72 % complete ) and 18616 restraints for refining 37512 atoms. Observations/parameters ratio is 0.72 ------------------------------------------------------ Cycle 11: After refmac, R = 0.2098 (Rfree = 0.000) for 37512 atoms. Found 260 (336 requested) and removed 274 (168 requested) atoms. Cycle 12: After refmac, R = 0.1899 (Rfree = 0.000) for 37498 atoms. Found 77 (336 requested) and removed 174 (168 requested) atoms. Cycle 13: After refmac, R = 0.1832 (Rfree = 0.000) for 37401 atoms. Found 50 (335 requested) and removed 168 (167 requested) atoms. Cycle 14: After refmac, R = 0.1809 (Rfree = 0.000) for 37283 atoms. Found 49 (334 requested) and removed 172 (167 requested) atoms. Failed to save intermediate PDB Cycle 15: After refmac, R = 0.1782 (Rfree = 0.000) for 37160 atoms. Found 55 (333 requested) and removed 169 (166 requested) atoms. ------------------------------------------------------ Building Cycle 4 Atomic shape factors 3.17 2.73 Search for helices and strands: 0 residues in 0 chains, 38190 seeds are put forward NCS extension: 4 residues added (0 deleted due to clashes), 38194 seeds are put forward Round 1: 3589 peptides, 413 chains. Longest chain 44 peptides. Score 0.610 Round 2: 3796 peptides, 359 chains. Longest chain 55 peptides. Score 0.681 Round 3: 3860 peptides, 367 chains. Longest chain 55 peptides. Score 0.684 Round 4: 3864 peptides, 366 chains. Longest chain 59 peptides. Score 0.686 Round 5: 3756 peptides, 365 chains. Longest chain 42 peptides. Score 0.671 Taking the results from Round 4 Chains 396, Residues 3498, Estimated correctness of the model 62.2 % 53 chains (1015 residues) have been docked in sequence ------------------------------------------------------ Failed to save intermediate PDB 107474 reflections ( 93.72 % complete ) and 18094 restraints for refining 37512 atoms. Observations/parameters ratio is 0.72 ------------------------------------------------------ Cycle 16: After refmac, R = 0.2157 (Rfree = 0.000) for 37512 atoms. Found 310 (336 requested) and removed 286 (168 requested) atoms. Cycle 17: After refmac, R = 0.1948 (Rfree = 0.000) for 37536 atoms. Found 78 (336 requested) and removed 173 (168 requested) atoms. Failed to save intermediate PDB Cycle 18: After refmac, R = 0.1880 (Rfree = 0.000) for 37441 atoms. Found 41 (336 requested) and removed 169 (168 requested) atoms. Cycle 19: After refmac, R = 0.1861 (Rfree = 0.000) for 37313 atoms. Found 57 (334 requested) and removed 169 (167 requested) atoms. Cycle 20: After refmac, R = 0.1844 (Rfree = 0.000) for 37201 atoms. Found 49 (333 requested) and removed 168 (166 requested) atoms. ------------------------------------------------------ Building Cycle 5 Atomic shape factors 3.18 2.74 Search for helices and strands: 0 residues in 0 chains, 38233 seeds are put forward NCS extension: 25 residues added (6 deleted due to clashes), 38258 seeds are put forward Round 1: 3459 peptides, 422 chains. Longest chain 37 peptides. Score 0.580 Round 2: 3703 peptides, 378 chains. Longest chain 55 peptides. Score 0.654 Round 3: 3699 peptides, 369 chains. Longest chain 33 peptides. Score 0.660 Round 4: 3721 peptides, 367 chains. Longest chain 51 peptides. Score 0.664 Round 5: 3672 peptides, 377 chains. Longest chain 40 peptides. Score 0.650 Taking the results from Round 4 Chains 402, Residues 3354, Estimated correctness of the model 57.2 % 53 chains (954 residues) have been docked in sequence ------------------------------------------------------ 107474 reflections ( 93.72 % complete ) and 17234 restraints for refining 37512 atoms. Observations/parameters ratio is 0.72 ------------------------------------------------------ Cycle 21: After refmac, R = 0.2169 (Rfree = 0.000) for 37512 atoms. Found 320 (336 requested) and removed 264 (168 requested) atoms. Failed to save intermediate PDB Cycle 22: After refmac, R = 0.1956 (Rfree = 0.000) for 37568 atoms. Found 95 (337 requested) and removed 176 (168 requested) atoms. Cycle 23: After refmac, R = 0.1899 (Rfree = 0.000) for 37487 atoms. Found 53 (336 requested) and removed 169 (168 requested) atoms. Failed to save intermediate PDB Cycle 24: After refmac, R = 0.1865 (Rfree = 0.000) for 37371 atoms. Found 40 (335 requested) and removed 167 (167 requested) atoms. Cycle 25: After refmac, R = 0.1819 (Rfree = 0.000) for 37244 atoms. Found 44 (334 requested) and removed 168 (167 requested) atoms. ------------------------------------------------------ Building Cycle 6 Atomic shape factors 3.17 2.73 Search for helices and strands: 0 residues in 0 chains, 38234 seeds are put forward NCS extension: 22 residues added (30 deleted due to clashes), 38256 seeds are put forward Round 1: 3371 peptides, 413 chains. Longest chain 40 peptides. Score 0.572 Round 2: 3568 peptides, 374 chains. Longest chain 39 peptides. Score 0.636 Round 3: 3613 peptides, 384 chains. Longest chain 44 peptides. Score 0.635 Round 4: 3622 peptides, 386 chains. Longest chain 40 peptides. Score 0.635 Round 5: 3708 peptides, 375 chains. Longest chain 45 peptides. Score 0.657 Taking the results from Round 5 Chains 395, Residues 3333, Estimated correctness of the model 55.5 % 43 chains (750 residues) have been docked in sequence ------------------------------------------------------ Failed to save intermediate PDB 107474 reflections ( 93.72 % complete ) and 16248 restraints for refining 37512 atoms. Observations/parameters ratio is 0.72 ------------------------------------------------------ Cycle 26: After refmac, R = 0.2108 (Rfree = 0.000) for 37512 atoms. Found 296 (336 requested) and removed 234 (168 requested) atoms. Cycle 27: After refmac, R = 0.1927 (Rfree = 0.000) for 37574 atoms. Found 92 (337 requested) and removed 172 (168 requested) atoms. Cycle 28: After refmac, R = 0.1890 (Rfree = 0.000) for 37494 atoms. Found 68 (336 requested) and removed 170 (168 requested) atoms. Failed to save intermediate PDB Cycle 29: After refmac, R = 0.1841 (Rfree = 0.000) for 37392 atoms. Found 51 (335 requested) and removed 168 (167 requested) atoms. Cycle 30: After refmac, R = 0.1800 (Rfree = 0.000) for 37275 atoms. Found 44 (334 requested) and removed 168 (167 requested) atoms. ------------------------------------------------------ Building Cycle 7 Atomic shape factors 3.18 2.74 Search for helices and strands: 0 residues in 0 chains, 38245 seeds are put forward NCS extension: 17 residues added (5 deleted due to clashes), 38262 seeds are put forward Round 1: 3382 peptides, 426 chains. Longest chain 45 peptides. Score 0.563 Round 2: 3564 peptides, 388 chains. Longest chain 54 peptides. Score 0.624 Round 3: 3555 peptides, 379 chains. Longest chain 46 peptides. Score 0.630 Round 4: 3546 peptides, 388 chains. Longest chain 47 peptides. Score 0.622 Round 5: 3587 peptides, 378 chains. Longest chain 49 peptides. Score 0.636 Taking the results from Round 5 Chains 389, Residues 3209, Estimated correctness of the model 50.4 % 39 chains (665 residues) have been docked in sequence ------------------------------------------------------ Failed to save intermediate PDB 107474 reflections ( 93.72 % complete ) and 15312 restraints for refining 37512 atoms. Observations/parameters ratio is 0.72 ------------------------------------------------------ Cycle 31: After refmac, R = 0.2069 (Rfree = 0.000) for 37512 atoms. Found 316 (336 requested) and removed 240 (168 requested) atoms. Cycle 32: After refmac, R = 0.1900 (Rfree = 0.000) for 37588 atoms. Found 107 (337 requested) and removed 171 (168 requested) atoms. Cycle 33: After refmac, R = 0.1864 (Rfree = 0.000) for 37524 atoms. Found 65 (336 requested) and removed 169 (168 requested) atoms. Failed to save intermediate PDB Cycle 34: After refmac, R = 0.1830 (Rfree = 0.000) for 37420 atoms. Found 57 (335 requested) and removed 169 (167 requested) atoms. Cycle 35: After refmac, R = 0.1790 (Rfree = 0.000) for 37308 atoms. Found 52 (334 requested) and removed 169 (167 requested) atoms. ------------------------------------------------------ Building Cycle 8 Atomic shape factors 3.18 2.74 Search for helices and strands: 0 residues in 0 chains, 38382 seeds are put forward NCS extension: 16 residues added (15 deleted due to clashes), 38398 seeds are put forward Round 1: 3166 peptides, 442 chains. Longest chain 28 peptides. Score 0.508 Round 2: 3490 peptides, 401 chains. Longest chain 34 peptides. Score 0.602 Round 3: 3470 peptides, 397 chains. Longest chain 37 peptides. Score 0.602 Round 4: 3519 peptides, 395 chains. Longest chain 54 peptides. Score 0.612 Round 5: 3475 peptides, 397 chains. Longest chain 54 peptides. Score 0.603 Taking the results from Round 4 Chains 421, Residues 3124, Estimated correctness of the model 44.3 % 35 chains (576 residues) have been docked in sequence ------------------------------------------------------ 107474 reflections ( 93.72 % complete ) and 14550 restraints for refining 37512 atoms. Observations/parameters ratio is 0.72 ------------------------------------------------------ Cycle 36: After refmac, R = 0.2023 (Rfree = 0.000) for 37512 atoms. Found 244 (336 requested) and removed 236 (168 requested) atoms. Failed to save intermediate PDB Cycle 37: After refmac, R = 0.1868 (Rfree = 0.000) for 37520 atoms. Found 67 (336 requested) and removed 171 (168 requested) atoms. Failed to save intermediate PDB Cycle 38: After refmac, R = 0.1846 (Rfree = 0.000) for 37416 atoms. Found 74 (335 requested) and removed 167 (167 requested) atoms. Cycle 39: After refmac, R = 0.1832 (Rfree = 0.000) for 37323 atoms. Found 66 (334 requested) and removed 170 (167 requested) atoms. Cycle 40: After refmac, R = 0.1816 (Rfree = 0.000) for 37219 atoms. Found 73 (334 requested) and removed 168 (167 requested) atoms. ------------------------------------------------------ Building Cycle 9 Atomic shape factors 3.19 2.75 Search for helices and strands: 0 residues in 0 chains, 38165 seeds are put forward NCS extension: 0 residues added, 38165 seeds are put forward Round 1: 3046 peptides, 464 chains. Longest chain 23 peptides. Score 0.463 Round 2: 3343 peptides, 409 chains. Longest chain 52 peptides. Score 0.570 Round 3: 3406 peptides, 409 chains. Longest chain 48 peptides. Score 0.581 Round 4: 3366 peptides, 403 chains. Longest chain 48 peptides. Score 0.579 Round 5: 3358 peptides, 385 chains. Longest chain 44 peptides. Score 0.592 Taking the results from Round 5 Chains 401, Residues 2973, Estimated correctness of the model 38.9 % 30 chains (536 residues) have been docked in sequence ------------------------------------------------------ 107474 reflections ( 93.72 % complete ) and 13866 restraints for refining 37512 atoms. Observations/parameters ratio is 0.72 ------------------------------------------------------ Cycle 41: After refmac, R = 0.2061 (Rfree = 0.000) for 37512 atoms. Found 286 (336 requested) and removed 223 (168 requested) atoms. Failed to save intermediate PDB Cycle 42: After refmac, R = 0.1897 (Rfree = 0.000) for 37575 atoms. Found 97 (337 requested) and removed 173 (168 requested) atoms. Cycle 43: After refmac, R = 0.1856 (Rfree = 0.000) for 37499 atoms. Found 71 (336 requested) and removed 171 (168 requested) atoms. Cycle 44: After refmac, R = 0.1843 (Rfree = 0.000) for 37399 atoms. Found 87 (335 requested) and removed 168 (167 requested) atoms. Failed to save intermediate PDB Cycle 45: After refmac, R = 0.1810 (Rfree = 0.000) for 37318 atoms. Found 88 (334 requested) and removed 173 (167 requested) atoms. ------------------------------------------------------ Building Cycle 10 Atomic shape factors 3.18 2.74 Search for helices and strands: 0 residues in 0 chains, 38449 seeds are put forward NCS extension: 21 residues added (5 deleted due to clashes), 38470 seeds are put forward Round 1: 2855 peptides, 430 chains. Longest chain 27 peptides. Score 0.454 Round 2: 3206 peptides, 395 chains. Longest chain 36 peptides. Score 0.556 Round 3: 3209 peptides, 395 chains. Longest chain 36 peptides. Score 0.557 Round 4: 3191 peptides, 383 chains. Longest chain 37 peptides. Score 0.564 Round 5: 3173 peptides, 389 chains. Longest chain 38 peptides. Score 0.555 Taking the results from Round 4 Last building cycle: Chain fragments will be rearranged Chains 403, Residues 2808, Estimated correctness of the model 31.0 % 30 chains (507 residues) have been docked in sequence Sequence coverage is 18 % Consider running further cycles of model building using 2pnk-3_warpNtrace.pdb as input Building loops using Loopy2018 Built loop between residues 175 G and 187 G Built loop between residues 269 G and 276 G 402 chains (2821 residues) following loop building 28 chains (524 residues) in sequence following loop building ------------------------------------------------------ ---> Final restrained refinement block. No atom update. Failed to save intermediate PDB 107474 reflections ( 93.72 % complete ) and 13074 restraints for refining 37512 atoms. Observations/parameters ratio is 0.72 ------------------------------------------------------ Cycle 46: After refmac, R = 0.2006 (Rfree = 0.000) for 37512 atoms. Found 0 (336 requested) and removed 69 (168 requested) atoms. Failed to save intermediate PDB Cycle 47: After refmac, R = 0.1925 (Rfree = 0.000) for 37443 atoms. Found 0 (336 requested) and removed 49 (168 requested) atoms. Failed to save intermediate PDB Cycle 48: After refmac, R = 0.1909 (Rfree = 0.000) for 37394 atoms. Found 0 (335 requested) and removed 89 (167 requested) atoms. Failed to save intermediate PDB Cycle 49: After refmac, R = 0.1849 (Rfree = 0.000) for 37305 atoms. Found 0 (334 requested) and removed 74 (167 requested) atoms. Writing output files ... TimeTaking 422.47