Sun 23 Dec 22:23:14 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 2ii1-3.8-parrot-hancs X-ray data file /users/emra500/scratch/Dataset/hancsChltofom/2ii1-3.8-parrot-hancs.mtz Sequence file /users/emra500/scratch/Dataset/hancsChltofom/2ii1-3.8-parrot-hancs.fasta Tracing mode WARPNTRACEPHASES Creating directory /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/2ii1-3.8-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/2ii1-3.8-parrot-hancs/arp_warp_classic.par Job launched in /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/2ii1-3.8-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 22:23:22 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/2ii1-3.8-parrot-hancs ARP/wARP software version: 8.0 The parameter file: /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/2ii1-3.8-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 748 and 0 Target number of residues in the AU: 748 Target solvent content: 0.6354 Checking the provided sequence file Detected sequence length: 301 Maximum limit of NCS related copies: 60 Number of NCS-related molecules: 4 Adjusted target number of residues: 1204 Adjusted target solvent content: 0.41 Input MTZ file: 2ii1-3.8-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: 1 Cell parameters: 43.759 69.605 94.984 73.954 88.905 86.625 Input sequence file: 2ii1-3.8-parrot-hancs.fasta_lf Building free atoms model in initial map for 9632 target number of atoms Had to go as low as 0.65 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. Conditional restraints will be used 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: 91.283 3.800 Wilson plot Bfac: 69.22 9674 reflections ( 91.17 % complete ) and 0 restraints for refining 10680 atoms. Observations/parameters ratio is 0.23 ------------------------------------------------------ Starting model: R = 0.3249 (Rfree = 0.000). ------------------------------------------------------ Cycle 0: After refmac, R = 0.2995 (Rfree = 0.000) for 10680 atoms. Found 55 (58 requested) and removed 183 (29 requested) atoms. ------------------------------------------------------ Building Cycle 1 Atomic shape factors 3.46 3.91 Search for helices and strands: 0 residues in 0 chains, 10657 seeds are put forward NCS extension: 0 residues added, 10657 seeds are put forward Round 1: 291 peptides, 66 chains. Longest chain 7 peptides. Score 0.217 Round 2: 382 peptides, 82 chains. Longest chain 9 peptides. Score 0.260 Round 3: 378 peptides, 76 chains. Longest chain 9 peptides. Score 0.294 Round 4: 388 peptides, 77 chains. Longest chain 11 peptides. Score 0.303 Round 5: 420 peptides, 79 chains. Longest chain 11 peptides. Score 0.340 Taking the results from Round 5 Chains 79, Residues 341, Estimated correctness of the model 0.0 % 12 chains (46 residues) have been docked in sequence ------------------------------------------------------ 9674 reflections ( 91.17 % complete ) and 21165 restraints for refining 8712 atoms. 19778 conditional restraints added. Observations/parameters ratio is 0.28 ------------------------------------------------------ Cycle 1: After refmac, R = 0.2423 (Rfree = 0.000) for 8712 atoms. Found 35 (47 requested) and removed 60 (23 requested) atoms. Cycle 2: After refmac, R = 0.2377 (Rfree = 0.000) for 8588 atoms. Found 47 (47 requested) and removed 53 (23 requested) atoms. Cycle 3: After refmac, R = 0.2237 (Rfree = 0.000) for 8515 atoms. Found 47 (47 requested) and removed 49 (23 requested) atoms. Cycle 4: After refmac, R = 0.2164 (Rfree = 0.000) for 8471 atoms. Found 42 (46 requested) and removed 63 (23 requested) atoms. Cycle 5: After refmac, R = 0.2040 (Rfree = 0.000) for 8430 atoms. Found 36 (46 requested) and removed 60 (23 requested) atoms. ------------------------------------------------------ Building Cycle 2 Atomic shape factors 3.41 3.85 Search for helices and strands: 0 residues in 0 chains, 8612 seeds are put forward NCS extension: 11 residues added (2 deleted due to clashes), 8623 seeds are put forward Round 1: 357 peptides, 80 chains. Longest chain 8 peptides. Score 0.232 Round 2: 409 peptides, 82 chains. Longest chain 11 peptides. Score 0.303 Round 3: 431 peptides, 83 chains. Longest chain 11 peptides. Score 0.331 Round 4: 424 peptides, 81 chains. Longest chain 11 peptides. Score 0.333 Round 5: 429 peptides, 75 chains. Longest chain 11 peptides. Score 0.380 Taking the results from Round 5 Chains 75, Residues 354, Estimated correctness of the model 0.0 % 10 chains (53 residues) have been docked in sequence ------------------------------------------------------ 9674 reflections ( 91.17 % complete ) and 19387 restraints for refining 8203 atoms. 17925 conditional restraints added. Observations/parameters ratio is 0.29 ------------------------------------------------------ Cycle 6: After refmac, R = 0.2135 (Rfree = 0.000) for 8203 atoms. Found 37 (45 requested) and removed 75 (22 requested) atoms. Cycle 7: After refmac, R = 0.1907 (Rfree = 0.000) for 8123 atoms. Found 29 (44 requested) and removed 42 (22 requested) atoms. Failed to save intermediate PDB Cycle 8: After refmac, R = 0.1788 (Rfree = 0.000) for 8083 atoms. Found 24 (44 requested) and removed 40 (22 requested) atoms. Cycle 9: After refmac, R = 0.1373 (Rfree = 0.000) for 8048 atoms. Found 10 (44 requested) and removed 28 (22 requested) atoms. Cycle 10: After refmac, R = 0.1292 (Rfree = 0.000) for 8025 atoms. Found 5 (44 requested) and removed 23 (22 requested) atoms. ------------------------------------------------------ Building Cycle 3 Atomic shape factors 3.41 3.85 Search for helices and strands: 0 residues in 0 chains, 8198 seeds are put forward NCS extension: 12 residues added (1 deleted due to clashes), 8210 seeds are put forward Round 1: 382 peptides, 86 chains. Longest chain 8 peptides. Score 0.232 Round 2: 416 peptides, 83 chains. Longest chain 13 peptides. Score 0.308 Round 3: 418 peptides, 75 chains. Longest chain 12 peptides. Score 0.363 Round 4: 423 peptides, 76 chains. Longest chain 16 peptides. Score 0.365 Round 5: 414 peptides, 73 chains. Longest chain 18 peptides. Score 0.370 Taking the results from Round 5 Chains 74, Residues 341, Estimated correctness of the model 0.0 % 7 chains (33 residues) have been docked in sequence ------------------------------------------------------ 9674 reflections ( 91.17 % complete ) and 19913 restraints for refining 8348 atoms. 18548 conditional restraints added. Observations/parameters ratio is 0.29 ------------------------------------------------------ Cycle 11: After refmac, R = 0.1737 (Rfree = 0.000) for 8348 atoms. Found 28 (45 requested) and removed 58 (22 requested) atoms. Cycle 12: After refmac, R = 0.1732 (Rfree = 0.000) for 8278 atoms. Found 39 (45 requested) and removed 46 (22 requested) atoms. Cycle 13: After refmac, R = 0.1712 (Rfree = 0.000) for 8255 atoms. Found 25 (45 requested) and removed 48 (22 requested) atoms. Cycle 14: After refmac, R = 0.1664 (Rfree = 0.000) for 8219 atoms. Found 35 (45 requested) and removed 37 (22 requested) atoms. Cycle 15: After refmac, R = 0.1621 (Rfree = 0.000) for 8206 atoms. Found 28 (45 requested) and removed 28 (22 requested) atoms. ------------------------------------------------------ Building Cycle 4 Atomic shape factors 3.40 3.84 Search for helices and strands: 0 residues in 0 chains, 8401 seeds are put forward NCS extension: 16 residues added (0 deleted due to clashes), 8417 seeds are put forward Round 1: 395 peptides, 83 chains. Longest chain 11 peptides. Score 0.274 Round 2: 408 peptides, 80 chains. Longest chain 15 peptides. Score 0.315 Round 3: 428 peptides, 81 chains. Longest chain 11 peptides. Score 0.340 Round 4: 441 peptides, 78 chains. Longest chain 15 peptides. Score 0.379 Round 5: 423 peptides, 78 chains. Longest chain 18 peptides. Score 0.352 Taking the results from Round 4 Chains 78, Residues 363, Estimated correctness of the model 0.0 % 7 chains (30 residues) have been docked in sequence ------------------------------------------------------ 9674 reflections ( 91.17 % complete ) and 20356 restraints for refining 8536 atoms. 18916 conditional restraints added. Observations/parameters ratio is 0.28 ------------------------------------------------------ Cycle 16: After refmac, R = 0.1751 (Rfree = 0.000) for 8536 atoms. Found 44 (46 requested) and removed 62 (23 requested) atoms. Cycle 17: After refmac, R = 0.1702 (Rfree = 0.000) for 8474 atoms. Found 46 (46 requested) and removed 43 (23 requested) atoms. Cycle 18: After refmac, R = 0.1269 (Rfree = 0.000) for 8454 atoms. Found 16 (46 requested) and removed 33 (23 requested) atoms. Cycle 19: After refmac, R = 0.1380 (Rfree = 0.000) for 8419 atoms. Found 23 (46 requested) and removed 28 (23 requested) atoms. Cycle 20: After refmac, R = 0.1214 (Rfree = 0.000) for 8410 atoms. Found 7 (46 requested) and removed 31 (23 requested) atoms. ------------------------------------------------------ Building Cycle 5 Atomic shape factors 3.42 3.86 Search for helices and strands: 0 residues in 0 chains, 8561 seeds are put forward NCS extension: 14 residues added (1 deleted due to clashes), 8575 seeds are put forward Round 1: 377 peptides, 82 chains. Longest chain 8 peptides. Score 0.251 Round 2: 422 peptides, 78 chains. Longest chain 11 peptides. Score 0.350 Round 3: 409 peptides, 73 chains. Longest chain 14 peptides. Score 0.363 Round 4: 411 peptides, 74 chains. Longest chain 12 peptides. Score 0.359 Round 5: 433 peptides, 77 chains. Longest chain 13 peptides. Score 0.373 Taking the results from Round 5 Chains 77, Residues 356, Estimated correctness of the model 0.0 % 4 chains (14 residues) have been docked in sequence ------------------------------------------------------ 9674 reflections ( 91.17 % complete ) and 21179 restraints for refining 8710 atoms. 19808 conditional restraints added. Observations/parameters ratio is 0.28 ------------------------------------------------------ Cycle 21: After refmac, R = 0.1731 (Rfree = 0.000) for 8710 atoms. Found 36 (47 requested) and removed 66 (23 requested) atoms. Cycle 22: After refmac, R = 0.1720 (Rfree = 0.000) for 8652 atoms. Found 47 (47 requested) and removed 43 (23 requested) atoms. Cycle 23: After refmac, R = 0.1693 (Rfree = 0.000) for 8630 atoms. Found 37 (47 requested) and removed 36 (23 requested) atoms. Cycle 24: After refmac, R = 0.1356 (Rfree = 0.000) for 8611 atoms. Found 11 (47 requested) and removed 29 (23 requested) atoms. Cycle 25: After refmac, R = 0.1519 (Rfree = 0.000) for 8579 atoms. Found 20 (47 requested) and removed 33 (23 requested) atoms. ------------------------------------------------------ Building Cycle 6 Atomic shape factors 3.41 3.85 Search for helices and strands: 0 residues in 0 chains, 8714 seeds are put forward NCS extension: 18 residues added (3 deleted due to clashes), 8732 seeds are put forward Round 1: 391 peptides, 84 chains. Longest chain 9 peptides. Score 0.261 Round 2: 423 peptides, 81 chains. Longest chain 11 peptides. Score 0.332 Round 3: 405 peptides, 71 chains. Longest chain 14 peptides. Score 0.370 Round 4: 408 peptides, 74 chains. Longest chain 12 peptides. Score 0.355 Round 5: 409 peptides, 73 chains. Longest chain 12 peptides. Score 0.363 Taking the results from Round 3 Chains 71, Residues 334, Estimated correctness of the model 0.0 % 5 chains (17 residues) have been docked in sequence ------------------------------------------------------ 9674 reflections ( 91.17 % complete ) and 21119 restraints for refining 8711 atoms. 19825 conditional restraints added. Observations/parameters ratio is 0.28 ------------------------------------------------------ Cycle 26: After refmac, R = 0.1658 (Rfree = 0.000) for 8711 atoms. Found 44 (47 requested) and removed 43 (23 requested) atoms. Cycle 27: After refmac, R = 0.1652 (Rfree = 0.000) for 8683 atoms. Found 47 (47 requested) and removed 39 (23 requested) atoms. Cycle 28: After refmac, R = 0.1603 (Rfree = 0.000) for 8682 atoms. Found 46 (47 requested) and removed 43 (23 requested) atoms. Cycle 29: After refmac, R = 0.1229 (Rfree = 0.000) for 8677 atoms. Found 17 (47 requested) and removed 32 (23 requested) atoms. Cycle 30: After refmac, R = 0.1363 (Rfree = 0.000) for 8647 atoms. Found 16 (47 requested) and removed 31 (23 requested) atoms. ------------------------------------------------------ Building Cycle 7 Atomic shape factors 3.44 3.88 Search for helices and strands: 0 residues in 0 chains, 8782 seeds are put forward NCS extension: 18 residues added (1 deleted due to clashes), 8800 seeds are put forward Round 1: 327 peptides, 73 chains. Longest chain 7 peptides. Score 0.230 Round 2: 376 peptides, 76 chains. Longest chain 10 peptides. Score 0.291 Round 3: 375 peptides, 72 chains. Longest chain 11 peptides. Score 0.317 Round 4: 396 peptides, 75 chains. Longest chain 11 peptides. Score 0.330 Round 5: 395 peptides, 71 chains. Longest chain 12 peptides. Score 0.355 Taking the results from Round 5 Chains 71, Residues 324, Estimated correctness of the model 0.0 % 5 chains (24 residues) have been docked in sequence ------------------------------------------------------ 9674 reflections ( 91.17 % complete ) and 21201 restraints for refining 8712 atoms. 19922 conditional restraints added. Observations/parameters ratio is 0.28 ------------------------------------------------------ Cycle 31: After refmac, R = 0.1575 (Rfree = 0.000) for 8712 atoms. Found 26 (47 requested) and removed 36 (23 requested) atoms. Cycle 32: After refmac, R = 0.1618 (Rfree = 0.000) for 8685 atoms. Found 47 (47 requested) and removed 34 (23 requested) atoms. Cycle 33: After refmac, R = 0.1228 (Rfree = 0.000) for 8682 atoms. Found 7 (47 requested) and removed 33 (23 requested) atoms. Cycle 34: After refmac, R = 0.1356 (Rfree = 0.000) for 8641 atoms. Found 30 (47 requested) and removed 29 (23 requested) atoms. Cycle 35: After refmac, R = 0.1200 (Rfree = 0.000) for 8636 atoms. Found 5 (47 requested) and removed 29 (23 requested) atoms. ------------------------------------------------------ Building Cycle 8 Atomic shape factors 3.44 3.88 Search for helices and strands: 0 residues in 0 chains, 8747 seeds are put forward NCS extension: 14 residues added (3 deleted due to clashes), 8761 seeds are put forward Round 1: 333 peptides, 74 chains. Longest chain 10 peptides. Score 0.233 Round 2: 360 peptides, 70 chains. Longest chain 15 peptides. Score 0.306 Round 3: 366 peptides, 72 chains. Longest chain 13 peptides. Score 0.302 Round 4: 370 peptides, 70 chains. Longest chain 14 peptides. Score 0.322 Round 5: 352 peptides, 69 chains. Longest chain 13 peptides. Score 0.300 Taking the results from Round 4 Chains 70, Residues 300, Estimated correctness of the model 0.0 % 5 chains (18 residues) have been docked in sequence ------------------------------------------------------ 9674 reflections ( 91.17 % complete ) and 21215 restraints for refining 8710 atoms. 20049 conditional restraints added. Observations/parameters ratio is 0.28 ------------------------------------------------------ Cycle 36: After refmac, R = 0.1744 (Rfree = 0.000) for 8710 atoms. Found 47 (47 requested) and removed 61 (23 requested) atoms. Cycle 37: After refmac, R = 0.1756 (Rfree = 0.000) for 8672 atoms. Found 47 (47 requested) and removed 34 (23 requested) atoms. Cycle 38: After refmac, R = 0.1751 (Rfree = 0.000) for 8667 atoms. Found 47 (47 requested) and removed 44 (23 requested) atoms. Cycle 39: After refmac, R = 0.1646 (Rfree = 0.000) for 8646 atoms. Found 47 (47 requested) and removed 39 (23 requested) atoms. Cycle 40: After refmac, R = 0.1310 (Rfree = 0.000) for 8633 atoms. Found 12 (47 requested) and removed 31 (23 requested) atoms. ------------------------------------------------------ Building Cycle 9 Atomic shape factors 3.42 3.86 Search for helices and strands: 0 residues in 0 chains, 8782 seeds are put forward NCS extension: 18 residues added (1 deleted due to clashes), 8800 seeds are put forward Round 1: 276 peptides, 62 chains. Longest chain 10 peptides. Score 0.220 Round 2: 328 peptides, 70 chains. Longest chain 11 peptides. Score 0.253 Round 3: 351 peptides, 71 chains. Longest chain 10 peptides. Score 0.284 Round 4: 355 peptides, 66 chains. Longest chain 14 peptides. Score 0.326 Round 5: 341 peptides, 65 chains. Longest chain 11 peptides. Score 0.310 Taking the results from Round 4 Chains 66, Residues 289, Estimated correctness of the model 0.0 % 9 chains (35 residues) have been docked in sequence ------------------------------------------------------ 9674 reflections ( 91.17 % complete ) and 20972 restraints for refining 8659 atoms. 19818 conditional restraints added. Observations/parameters ratio is 0.28 ------------------------------------------------------ Cycle 41: After refmac, R = 0.1700 (Rfree = 0.000) for 8659 atoms. Found 47 (47 requested) and removed 50 (23 requested) atoms. Cycle 42: After refmac, R = 0.1704 (Rfree = 0.000) for 8620 atoms. Found 47 (47 requested) and removed 44 (23 requested) atoms. Failed to save intermediate PDB Cycle 43: After refmac, R = 0.1659 (Rfree = 0.000) for 8600 atoms. Found 47 (47 requested) and removed 34 (23 requested) atoms. Cycle 44: After refmac, R = 0.1616 (Rfree = 0.000) for 8592 atoms. Found 47 (47 requested) and removed 38 (23 requested) atoms. Cycle 45: After refmac, R = 0.1707 (Rfree = 0.000) for 8589 atoms. Found 47 (47 requested) and removed 34 (23 requested) atoms. ------------------------------------------------------ Building Cycle 10 Atomic shape factors 3.41 3.85 Search for helices and strands: 0 residues in 0 chains, 8761 seeds are put forward NCS extension: 21 residues added (1 deleted due to clashes), 8782 seeds are put forward Round 1: 239 peptides, 56 chains. Longest chain 9 peptides. Score 0.196 Round 2: 265 peptides, 53 chains. Longest chain 10 peptides. Score 0.268 Round 3: 287 peptides, 57 chains. Longest chain 10 peptides. Score 0.277 Round 4: 287 peptides, 57 chains. Longest chain 9 peptides. Score 0.277 Round 5: 300 peptides, 57 chains. Longest chain 10 peptides. Score 0.299 Taking the results from Round 5 Last building cycle: Chain fragments will be rearranged Chains 57, Residues 243, Estimated correctness of the model 0.0 % 6 chains (28 residues) have been docked in sequence Sequence coverage is 11 % Consider running further cycles of model building using 2ii1-3_warpNtrace.pdb as input Building loops using Loopy2018 57 chains (243 residues) following loop building 6 chains (28 residues) in sequence following loop building ------------------------------------------------------ ---> Final restrained refinement block. No atom update. 9674 reflections ( 91.17 % complete ) and 21134 restraints for refining 8640 atoms. 20155 conditional restraints added. Observations/parameters ratio is 0.28 ------------------------------------------------------ Cycle 46: After refmac, R = 0.1595 (Rfree = 0.000) for 8640 atoms. Found 0 (47 requested) and removed 23 (23 requested) atoms. Cycle 47: After refmac, R = 0.1616 (Rfree = 0.000) for 8598 atoms. Found 0 (47 requested) and removed 23 (23 requested) atoms. Cycle 48: After refmac, R = 0.1186 (Rfree = 0.000) for 8564 atoms. Found 0 (47 requested) and removed 23 (23 requested) atoms. Cycle 49: After refmac, R = 0.1093 (Rfree = 0.000) for 8529 atoms. TimeTaking 102.82