null Sun 23 Dec 22:23:05 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 2ich-3.8-parrot-hancs X-ray data file /users/emra500/scratch/Dataset/hancsChltofom/2ich-3.8-parrot-hancs.mtz Sequence file /users/emra500/scratch/Dataset/hancsChltofom/2ich-3.8-parrot-hancs.fasta Tracing mode WARPNTRACEPHASES Creating directory /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/2ich-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/2ich-3.8-parrot-hancs/arp_warp_classic.par Job launched in /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/2ich-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 22:23:15 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/2ich-3.8-parrot-hancs ARP/wARP software version: 8.0 The parameter file: /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/2ich-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 509 and 0 Target number of residues in the AU: 509 Target solvent content: 0.6258 Checking the provided sequence file Detected sequence length: 335 Maximum limit of NCS related copies: 60 Number of NCS-related molecules: 2 Adjusted target number of residues: 670 Adjusted target solvent content: 0.51 Input MTZ file: 2ich-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: 19 Cell parameters: 63.275 95.573 121.745 90.000 90.000 90.000 Input sequence file: 2ich-3.8-parrot-hancs.fasta_lf Building free atoms model in initial map for 5360 target number of atoms Had to go as low as 0.70 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: 29.160 3.800 Wilson plot Bfac: 64.14 7662 reflections ( 99.64 % complete ) and 0 restraints for refining 5941 atoms. Observations/parameters ratio is 0.32 ------------------------------------------------------ Starting model: R = 0.3094 (Rfree = 0.000). ------------------------------------------------------ Cycle 0: After refmac, R = 0.3188 (Rfree = 0.000) for 5941 atoms. Found 32 (32 requested) and removed 51 (16 requested) atoms. ------------------------------------------------------ Building Cycle 1 Atomic shape factors 3.42 3.37 Search for helices and strands: 0 residues in 0 chains, 5992 seeds are put forward NCS extension: 0 residues added, 5992 seeds are put forward Round 1: 282 peptides, 57 chains. Longest chain 11 peptides. Score 0.303 Round 2: 372 peptides, 60 chains. Longest chain 13 peptides. Score 0.471 Round 3: 390 peptides, 53 chains. Longest chain 21 peptides. Score 0.561 Round 4: 384 peptides, 52 chains. Longest chain 18 peptides. Score 0.558 Round 5: 408 peptides, 58 chains. Longest chain 28 peptides. Score 0.554 Taking the results from Round 3 Chains 59, Residues 337, Estimated correctness of the model 0.0 % 10 chains (79 residues) have been docked in sequence ------------------------------------------------------ 7662 reflections ( 99.64 % complete ) and 10058 restraints for refining 4848 atoms. 8502 conditional restraints added. Observations/parameters ratio is 0.40 ------------------------------------------------------ Cycle 1: After refmac, R = 0.2724 (Rfree = 0.000) for 4848 atoms. Found 24 (26 requested) and removed 57 (13 requested) atoms. Cycle 2: After refmac, R = 0.2570 (Rfree = 0.000) for 4722 atoms. Found 23 (26 requested) and removed 53 (13 requested) atoms. Cycle 3: After refmac, R = 0.2507 (Rfree = 0.000) for 4659 atoms. Found 25 (25 requested) and removed 44 (12 requested) atoms. Cycle 4: After refmac, R = 0.2102 (Rfree = 0.000) for 4609 atoms. Found 11 (25 requested) and removed 35 (12 requested) atoms. Cycle 5: After refmac, R = 0.2177 (Rfree = 0.000) for 4568 atoms. Found 17 (25 requested) and removed 26 (12 requested) atoms. ------------------------------------------------------ Building Cycle 2 Atomic shape factors 3.43 3.38 Search for helices and strands: 0 residues in 0 chains, 4672 seeds are put forward NCS extension: 21 residues added (1 deleted due to clashes), 4693 seeds are put forward Round 1: 346 peptides, 59 chains. Longest chain 13 peptides. Score 0.427 Round 2: 394 peptides, 54 chains. Longest chain 22 peptides. Score 0.560 Round 3: 398 peptides, 53 chains. Longest chain 19 peptides. Score 0.575 Round 4: 393 peptides, 47 chains. Longest chain 26 peptides. Score 0.611 Round 5: 398 peptides, 53 chains. Longest chain 19 peptides. Score 0.575 Taking the results from Round 4 Chains 50, Residues 346, Estimated correctness of the model 3.9 % 5 chains (50 residues) have been docked in sequence ------------------------------------------------------ 7662 reflections ( 99.64 % complete ) and 10320 restraints for refining 4848 atoms. 8789 conditional restraints added. Observations/parameters ratio is 0.40 ------------------------------------------------------ Cycle 6: After refmac, R = 0.2636 (Rfree = 0.000) for 4848 atoms. Found 26 (26 requested) and removed 62 (13 requested) atoms. Cycle 7: After refmac, R = 0.2447 (Rfree = 0.000) for 4773 atoms. Found 26 (26 requested) and removed 43 (13 requested) atoms. Cycle 8: After refmac, R = 0.2327 (Rfree = 0.000) for 4733 atoms. Found 26 (26 requested) and removed 49 (13 requested) atoms. Cycle 9: After refmac, R = 0.2299 (Rfree = 0.000) for 4696 atoms. Found 25 (25 requested) and removed 35 (12 requested) atoms. Cycle 10: After refmac, R = 0.2362 (Rfree = 0.000) for 4678 atoms. Found 25 (25 requested) and removed 34 (12 requested) atoms. ------------------------------------------------------ Building Cycle 3 Atomic shape factors 3.45 3.40 Search for helices and strands: 0 residues in 0 chains, 4765 seeds are put forward NCS extension: 20 residues added (0 deleted due to clashes), 4785 seeds are put forward Round 1: 321 peptides, 52 chains. Longest chain 13 peptides. Score 0.438 Round 2: 351 peptides, 50 chains. Longest chain 19 peptides. Score 0.515 Round 3: 361 peptides, 45 chains. Longest chain 20 peptides. Score 0.573 Round 4: 348 peptides, 48 chains. Longest chain 21 peptides. Score 0.526 Round 5: 364 peptides, 46 chains. Longest chain 16 peptides. Score 0.570 Taking the results from Round 3 Chains 47, Residues 316, Estimated correctness of the model 0.0 % 5 chains (34 residues) have been docked in sequence ------------------------------------------------------ 7662 reflections ( 99.64 % complete ) and 10818 restraints for refining 4848 atoms. 9489 conditional restraints added. Observations/parameters ratio is 0.40 ------------------------------------------------------ Cycle 11: After refmac, R = 0.2615 (Rfree = 0.000) for 4848 atoms. Found 26 (26 requested) and removed 50 (13 requested) atoms. Cycle 12: After refmac, R = 0.2562 (Rfree = 0.000) for 4791 atoms. Found 26 (26 requested) and removed 59 (13 requested) atoms. Cycle 13: After refmac, R = 0.2012 (Rfree = 0.000) for 4737 atoms. Found 12 (26 requested) and removed 36 (13 requested) atoms. Cycle 14: After refmac, R = 0.1951 (Rfree = 0.000) for 4695 atoms. Found 10 (25 requested) and removed 24 (12 requested) atoms. Cycle 15: After refmac, R = 0.1909 (Rfree = 0.000) for 4675 atoms. Found 5 (25 requested) and removed 27 (12 requested) atoms. ------------------------------------------------------ Building Cycle 4 Atomic shape factors 3.42 3.37 Search for helices and strands: 0 residues in 0 chains, 4765 seeds are put forward NCS extension: 33 residues added (1 deleted due to clashes), 4798 seeds are put forward Round 1: 324 peptides, 55 chains. Longest chain 16 peptides. Score 0.417 Round 2: 359 peptides, 52 chains. Longest chain 15 peptides. Score 0.513 Round 3: 353 peptides, 50 chains. Longest chain 17 peptides. Score 0.518 Round 4: 353 peptides, 50 chains. Longest chain 17 peptides. Score 0.518 Round 5: 352 peptides, 48 chains. Longest chain 18 peptides. Score 0.533 Taking the results from Round 5 Chains 52, Residues 304, Estimated correctness of the model 0.0 % 6 chains (52 residues) have been docked in sequence ------------------------------------------------------ 7662 reflections ( 99.64 % complete ) and 10753 restraints for refining 4848 atoms. 9400 conditional restraints added. Observations/parameters ratio is 0.40 ------------------------------------------------------ Cycle 16: After refmac, R = 0.2589 (Rfree = 0.000) for 4848 atoms. Found 24 (26 requested) and removed 42 (13 requested) atoms. Cycle 17: After refmac, R = 0.2325 (Rfree = 0.000) for 4793 atoms. Found 26 (26 requested) and removed 47 (13 requested) atoms. Cycle 18: After refmac, R = 0.2226 (Rfree = 0.000) for 4748 atoms. Found 26 (26 requested) and removed 39 (13 requested) atoms. Cycle 19: After refmac, R = 0.2050 (Rfree = 0.000) for 4724 atoms. Found 24 (26 requested) and removed 28 (13 requested) atoms. Cycle 20: After refmac, R = 0.1978 (Rfree = 0.000) for 4713 atoms. Found 25 (25 requested) and removed 36 (12 requested) atoms. ------------------------------------------------------ Building Cycle 5 Atomic shape factors 3.38 3.34 Search for helices and strands: 0 residues in 0 chains, 4812 seeds are put forward NCS extension: 14 residues added (2 deleted due to clashes), 4826 seeds are put forward Round 1: 333 peptides, 60 chains. Longest chain 13 peptides. Score 0.390 Round 2: 358 peptides, 54 chains. Longest chain 19 peptides. Score 0.494 Round 3: 374 peptides, 55 chains. Longest chain 16 peptides. Score 0.516 Round 4: 369 peptides, 55 chains. Longest chain 15 peptides. Score 0.507 Round 5: 372 peptides, 57 chains. Longest chain 14 peptides. Score 0.496 Taking the results from Round 3 Chains 56, Residues 319, Estimated correctness of the model 0.0 % 3 chains (18 residues) have been docked in sequence ------------------------------------------------------ 7662 reflections ( 99.64 % complete ) and 10846 restraints for refining 4848 atoms. 9566 conditional restraints added. Observations/parameters ratio is 0.40 ------------------------------------------------------ Cycle 21: After refmac, R = 0.2284 (Rfree = 0.000) for 4848 atoms. Found 21 (26 requested) and removed 33 (13 requested) atoms. Cycle 22: After refmac, R = 0.2089 (Rfree = 0.000) for 4808 atoms. Found 21 (26 requested) and removed 31 (13 requested) atoms. Cycle 23: After refmac, R = 0.1937 (Rfree = 0.000) for 4790 atoms. Found 10 (26 requested) and removed 30 (13 requested) atoms. Cycle 24: After refmac, R = 0.1830 (Rfree = 0.000) for 4765 atoms. Found 9 (26 requested) and removed 27 (13 requested) atoms. Cycle 25: After refmac, R = 0.1760 (Rfree = 0.000) for 4743 atoms. Found 6 (26 requested) and removed 28 (13 requested) atoms. ------------------------------------------------------ Building Cycle 6 Atomic shape factors 3.40 3.36 Search for helices and strands: 0 residues in 0 chains, 4822 seeds are put forward NCS extension: 16 residues added (1 deleted due to clashes), 4838 seeds are put forward Round 1: 290 peptides, 50 chains. Longest chain 13 peptides. Score 0.390 Round 2: 313 peptides, 48 chains. Longest chain 16 peptides. Score 0.457 Round 3: 309 peptides, 45 chains. Longest chain 15 peptides. Score 0.476 Round 4: 324 peptides, 40 chains. Longest chain 35 peptides. Score 0.548 Round 5: 338 peptides, 48 chains. Longest chain 16 peptides. Score 0.507 Taking the results from Round 4 Chains 45, Residues 284, Estimated correctness of the model 0.0 % 7 chains (63 residues) have been docked in sequence ------------------------------------------------------ 7662 reflections ( 99.64 % complete ) and 10492 restraints for refining 4847 atoms. 9160 conditional restraints added. Observations/parameters ratio is 0.40 ------------------------------------------------------ Cycle 26: After refmac, R = 0.2388 (Rfree = 0.000) for 4847 atoms. Found 26 (26 requested) and removed 36 (13 requested) atoms. Cycle 27: After refmac, R = 0.2276 (Rfree = 0.000) for 4821 atoms. Found 26 (26 requested) and removed 25 (13 requested) atoms. Cycle 28: After refmac, R = 0.2258 (Rfree = 0.000) for 4805 atoms. Found 26 (26 requested) and removed 36 (13 requested) atoms. Cycle 29: After refmac, R = 0.2208 (Rfree = 0.000) for 4787 atoms. Found 26 (26 requested) and removed 39 (13 requested) atoms. Cycle 30: After refmac, R = 0.2051 (Rfree = 0.000) for 4766 atoms. Found 26 (26 requested) and removed 31 (13 requested) atoms. ------------------------------------------------------ Building Cycle 7 Atomic shape factors 3.36 3.32 Search for helices and strands: 0 residues in 0 chains, 4850 seeds are put forward NCS extension: 14 residues added (4 deleted due to clashes), 4864 seeds are put forward Round 1: 253 peptides, 47 chains. Longest chain 11 peptides. Score 0.334 Round 2: 292 peptides, 49 chains. Longest chain 15 peptides. Score 0.404 Round 3: 307 peptides, 40 chains. Longest chain 19 peptides. Score 0.516 Round 4: 304 peptides, 40 chains. Longest chain 22 peptides. Score 0.510 Round 5: 298 peptides, 39 chains. Longest chain 22 peptides. Score 0.508 Taking the results from Round 3 Chains 42, Residues 267, Estimated correctness of the model 0.0 % 1 chains (10 residues) have been docked in sequence ------------------------------------------------------ 7662 reflections ( 99.64 % complete ) and 11138 restraints for refining 4846 atoms. 10064 conditional restraints added. Observations/parameters ratio is 0.40 ------------------------------------------------------ Cycle 31: After refmac, R = 0.2411 (Rfree = 0.000) for 4846 atoms. Found 26 (26 requested) and removed 32 (13 requested) atoms. Cycle 32: After refmac, R = 0.2326 (Rfree = 0.000) for 4814 atoms. Found 26 (26 requested) and removed 21 (13 requested) atoms. Cycle 33: After refmac, R = 0.1826 (Rfree = 0.000) for 4797 atoms. Found 17 (26 requested) and removed 34 (13 requested) atoms. Cycle 34: After refmac, R = 0.1737 (Rfree = 0.000) for 4773 atoms. Found 13 (26 requested) and removed 23 (13 requested) atoms. Cycle 35: After refmac, R = 0.2246 (Rfree = 0.000) for 4753 atoms. Found 26 (26 requested) and removed 32 (13 requested) atoms. ------------------------------------------------------ Building Cycle 8 Atomic shape factors 3.43 3.38 Search for helices and strands: 0 residues in 0 chains, 4850 seeds are put forward NCS extension: 30 residues added (1 deleted due to clashes), 4880 seeds are put forward Round 1: 272 peptides, 50 chains. Longest chain 14 peptides. Score 0.349 Round 2: 298 peptides, 49 chains. Longest chain 14 peptides. Score 0.417 Round 3: 309 peptides, 48 chains. Longest chain 16 peptides. Score 0.449 Round 4: 316 peptides, 52 chains. Longest chain 14 peptides. Score 0.427 Round 5: 313 peptides, 49 chains. Longest chain 16 peptides. Score 0.448 Taking the results from Round 3 Chains 50, Residues 261, Estimated correctness of the model 0.0 % 8 chains (36 residues) have been docked in sequence ------------------------------------------------------ 7662 reflections ( 99.64 % complete ) and 10914 restraints for refining 4847 atoms. 9834 conditional restraints added. Observations/parameters ratio is 0.40 ------------------------------------------------------ Cycle 36: After refmac, R = 0.2449 (Rfree = 0.000) for 4847 atoms. Found 26 (26 requested) and removed 39 (13 requested) atoms. Cycle 37: After refmac, R = 0.2120 (Rfree = 0.000) for 4811 atoms. Found 26 (26 requested) and removed 33 (13 requested) atoms. Cycle 38: After refmac, R = 0.2010 (Rfree = 0.000) for 4786 atoms. Found 26 (26 requested) and removed 23 (13 requested) atoms. Cycle 39: After refmac, R = 0.1916 (Rfree = 0.000) for 4777 atoms. Found 26 (26 requested) and removed 22 (13 requested) atoms. Cycle 40: After refmac, R = 0.1869 (Rfree = 0.000) for 4773 atoms. Found 26 (26 requested) and removed 18 (13 requested) atoms. ------------------------------------------------------ Building Cycle 9 Atomic shape factors 3.36 3.32 Search for helices and strands: 0 residues in 0 chains, 4854 seeds are put forward NCS extension: 13 residues added (0 deleted due to clashes), 4867 seeds are put forward Round 1: 245 peptides, 46 chains. Longest chain 10 peptides. Score 0.326 Round 2: 285 peptides, 48 chains. Longest chain 13 peptides. Score 0.398 Round 3: 290 peptides, 45 chains. Longest chain 18 peptides. Score 0.437 Round 4: 298 peptides, 46 chains. Longest chain 19 peptides. Score 0.444 Round 5: 320 peptides, 50 chains. Longest chain 14 peptides. Score 0.454 Taking the results from Round 5 Chains 50, Residues 270, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 7662 reflections ( 99.64 % complete ) and 11253 restraints for refining 4848 atoms. 10223 conditional restraints added. Observations/parameters ratio is 0.40 ------------------------------------------------------ Cycle 41: After refmac, R = 0.2074 (Rfree = 0.000) for 4848 atoms. Found 25 (26 requested) and removed 33 (13 requested) atoms. Cycle 42: After refmac, R = 0.1828 (Rfree = 0.000) for 4824 atoms. Found 15 (26 requested) and removed 28 (13 requested) atoms. Cycle 43: After refmac, R = 0.1762 (Rfree = 0.000) for 4806 atoms. Found 11 (26 requested) and removed 21 (13 requested) atoms. Cycle 44: After refmac, R = 0.1739 (Rfree = 0.000) for 4790 atoms. Found 17 (26 requested) and removed 22 (13 requested) atoms. Cycle 45: After refmac, R = 0.1717 (Rfree = 0.000) for 4781 atoms. Found 9 (26 requested) and removed 22 (13 requested) atoms. ------------------------------------------------------ Building Cycle 10 Atomic shape factors 3.42 3.37 Search for helices and strands: 0 residues in 0 chains, 4892 seeds are put forward NCS extension: 18 residues added (0 deleted due to clashes), 4910 seeds are put forward Round 1: 254 peptides, 52 chains. Longest chain 11 peptides. Score 0.286 Round 2: 292 peptides, 47 chains. Longest chain 18 peptides. Score 0.422 Round 3: 283 peptides, 48 chains. Longest chain 14 peptides. Score 0.393 Round 4: 258 peptides, 44 chains. Longest chain 17 peptides. Score 0.376 Round 5: 287 peptides, 45 chains. Longest chain 16 peptides. Score 0.431 Taking the results from Round 5 Last building cycle: Chain fragments will be rearranged Chains 45, Residues 242, Estimated correctness of the model 0.0 % 3 chains (13 residues) have been docked in sequence Sequence coverage is 5 % Consider running further cycles of model building using 2ich-3_warpNtrace.pdb as input Building loops using Loopy2018 45 chains (242 residues) following loop building 3 chains (13 residues) in sequence following loop building ------------------------------------------------------ ---> Final restrained refinement block. No atom update. 7662 reflections ( 99.64 % complete ) and 11229 restraints for refining 4847 atoms. 10272 conditional restraints added. Observations/parameters ratio is 0.40 ------------------------------------------------------ Cycle 46: After refmac, R = 0.2109 (Rfree = 0.000) for 4847 atoms. Found 0 (26 requested) and removed 13 (13 requested) atoms. Cycle 47: After refmac, R = 0.1924 (Rfree = 0.000) for 4817 atoms. Found 0 (26 requested) and removed 13 (13 requested) atoms. Cycle 48: After refmac, R = 0.1868 (Rfree = 0.000) for 4798 atoms. Found 0 (26 requested) and removed 13 (13 requested) atoms. Cycle 49: After refmac, R = 0.1812 (Rfree = 0.000) for 4778 atoms. Found 0 (26 requested) and removed 13 (13 requested) atoms. Writing output files ... Normal termination of warpNtrace Sun 23 Dec 23:31:20 GMT 2018 Job finished. TimeTaking 68.26 Used memory is bytes: 16933344