Sun 23 Dec 22:22:52 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-3.6-parrot-hancs X-ray data file /users/emra500/scratch/Dataset/hancsChltofom/2ich-3.6-parrot-hancs.mtz Sequence file /users/emra500/scratch/Dataset/hancsChltofom/2ich-3.6-parrot-hancs.fasta Tracing mode WARPNTRACEPHASES Creating directory /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/2ich-3.6-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-3.6-parrot-hancs/arp_warp_classic.par Job launched in /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/2ich-3.6-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 22:23:01 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-3.6-parrot-hancs ARP/wARP software version: 8.0 The parameter file: /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/2ich-3.6-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 522 and 0 Target number of residues in the AU: 522 Target solvent content: 0.6163 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-3.6-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-3.6-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 3.600 Wilson plot Bfac: 59.53 8970 reflections ( 99.62 % complete ) and 0 restraints for refining 5922 atoms. Observations/parameters ratio is 0.38 ------------------------------------------------------ Starting model: R = 0.3053 (Rfree = 0.000). ------------------------------------------------------ Cycle 0: After refmac, R = 0.3039 (Rfree = 0.000) for 5922 atoms. Found 37 (37 requested) and removed 51 (18 requested) atoms. ------------------------------------------------------ Building Cycle 1 Atomic shape factors 3.26 3.22 Search for helices and strands: 0 residues in 0 chains, 5979 seeds are put forward NCS extension: 0 residues added, 5979 seeds are put forward Round 1: 298 peptides, 55 chains. Longest chain 10 peptides. Score 0.360 Round 2: 388 peptides, 50 chains. Longest chain 23 peptides. Score 0.581 Round 3: 413 peptides, 55 chains. Longest chain 18 peptides. Score 0.585 Round 4: 426 peptides, 51 chains. Longest chain 28 peptides. Score 0.634 Round 5: 429 peptides, 50 chains. Longest chain 43 peptides. Score 0.645 Taking the results from Round 5 Chains 58, Residues 379, Estimated correctness of the model 31.4 % 8 chains (98 residues) have been docked in sequence ------------------------------------------------------ 8970 reflections ( 99.62 % complete ) and 9648 restraints for refining 4858 atoms. 7817 conditional restraints added. Observations/parameters ratio is 0.46 ------------------------------------------------------ Cycle 1: After refmac, R = 0.2481 (Rfree = 0.000) for 4858 atoms. Found 30 (31 requested) and removed 66 (15 requested) atoms. Cycle 2: After refmac, R = 0.2296 (Rfree = 0.000) for 4765 atoms. Found 18 (30 requested) and removed 47 (15 requested) atoms. Cycle 3: After refmac, R = 0.2185 (Rfree = 0.000) for 4718 atoms. Found 17 (30 requested) and removed 28 (15 requested) atoms. Cycle 4: After refmac, R = 0.2097 (Rfree = 0.000) for 4691 atoms. Found 10 (30 requested) and removed 32 (15 requested) atoms. Cycle 5: After refmac, R = 0.2046 (Rfree = 0.000) for 4663 atoms. Found 16 (29 requested) and removed 25 (14 requested) atoms. ------------------------------------------------------ Building Cycle 2 Atomic shape factors 3.28 3.24 Search for helices and strands: 0 residues in 0 chains, 4708 seeds are put forward NCS extension: 46 residues added (5 deleted due to clashes), 4754 seeds are put forward Round 1: 388 peptides, 58 chains. Longest chain 23 peptides. Score 0.518 Round 2: 424 peptides, 54 chains. Longest chain 37 peptides. Score 0.610 Round 3: 434 peptides, 48 chains. Longest chain 29 peptides. Score 0.665 Round 4: 442 peptides, 56 chains. Longest chain 23 peptides. Score 0.624 Round 5: 443 peptides, 50 chains. Longest chain 31 peptides. Score 0.665 Taking the results from Round 5 Chains 53, Residues 393, Estimated correctness of the model 38.3 % 8 chains (87 residues) have been docked in sequence ------------------------------------------------------ 8970 reflections ( 99.62 % complete ) and 9661 restraints for refining 4858 atoms. 7799 conditional restraints added. Observations/parameters ratio is 0.46 ------------------------------------------------------ Cycle 6: After refmac, R = 0.2534 (Rfree = 0.000) for 4858 atoms. Found 28 (31 requested) and removed 33 (15 requested) atoms. Cycle 7: After refmac, R = 0.2256 (Rfree = 0.000) for 4817 atoms. Found 10 (31 requested) and removed 33 (15 requested) atoms. Cycle 8: After refmac, R = 0.2140 (Rfree = 0.000) for 4786 atoms. Found 8 (30 requested) and removed 22 (15 requested) atoms. Cycle 9: After refmac, R = 0.2086 (Rfree = 0.000) for 4767 atoms. Found 1 (30 requested) and removed 30 (15 requested) atoms. Cycle 10: After refmac, R = 0.2054 (Rfree = 0.000) for 4737 atoms. Found 6 (30 requested) and removed 16 (15 requested) atoms. ------------------------------------------------------ Building Cycle 3 Atomic shape factors 3.31 3.27 Search for helices and strands: 0 residues in 0 chains, 4833 seeds are put forward NCS extension: 16 residues added (3 deleted due to clashes), 4849 seeds are put forward Round 1: 381 peptides, 55 chains. Longest chain 26 peptides. Score 0.529 Round 2: 412 peptides, 51 chains. Longest chain 21 peptides. Score 0.612 Round 3: 448 peptides, 54 chains. Longest chain 23 peptides. Score 0.646 Round 4: 437 peptides, 51 chains. Longest chain 29 peptides. Score 0.650 Round 5: 427 peptides, 50 chains. Longest chain 28 peptides. Score 0.642 Taking the results from Round 4 Chains 55, Residues 386, Estimated correctness of the model 33.2 % 5 chains (72 residues) have been docked in sequence ------------------------------------------------------ 8970 reflections ( 99.62 % complete ) and 9936 restraints for refining 4859 atoms. 8160 conditional restraints added. Observations/parameters ratio is 0.46 ------------------------------------------------------ Cycle 11: After refmac, R = 0.2460 (Rfree = 0.000) for 4859 atoms. Found 31 (31 requested) and removed 44 (15 requested) atoms. Cycle 12: After refmac, R = 0.2270 (Rfree = 0.000) for 4824 atoms. Found 11 (31 requested) and removed 35 (15 requested) atoms. Cycle 13: After refmac, R = 0.2263 (Rfree = 0.000) for 4784 atoms. Found 16 (30 requested) and removed 27 (15 requested) atoms. Cycle 14: After refmac, R = 0.2855 (Rfree = 0.000) for 4764 atoms. Found 30 (30 requested) and removed 48 (15 requested) atoms. Cycle 15: After refmac, R = 0.2237 (Rfree = 0.000) for 4725 atoms. Found 11 (30 requested) and removed 27 (15 requested) atoms. ------------------------------------------------------ Building Cycle 4 Atomic shape factors 3.27 3.23 Search for helices and strands: 0 residues in 0 chains, 4820 seeds are put forward NCS extension: 22 residues added (6 deleted due to clashes), 4842 seeds are put forward Round 1: 356 peptides, 52 chains. Longest chain 16 peptides. Score 0.507 Round 2: 402 peptides, 47 chains. Longest chain 36 peptides. Score 0.625 Round 3: 403 peptides, 54 chains. Longest chain 29 peptides. Score 0.576 Round 4: 402 peptides, 47 chains. Longest chain 24 peptides. Score 0.625 Round 5: 412 peptides, 47 chains. Longest chain 29 peptides. Score 0.640 Taking the results from Round 5 Chains 55, Residues 365, Estimated correctness of the model 29.6 % 10 chains (93 residues) have been docked in sequence ------------------------------------------------------ 8970 reflections ( 99.62 % complete ) and 9745 restraints for refining 4859 atoms. 7965 conditional restraints added. Observations/parameters ratio is 0.46 ------------------------------------------------------ Cycle 16: After refmac, R = 0.2446 (Rfree = 0.000) for 4859 atoms. Found 28 (31 requested) and removed 47 (15 requested) atoms. Cycle 17: After refmac, R = 0.2232 (Rfree = 0.000) for 4815 atoms. Found 18 (31 requested) and removed 23 (15 requested) atoms. Cycle 18: After refmac, R = 0.2166 (Rfree = 0.000) for 4790 atoms. Found 12 (30 requested) and removed 24 (15 requested) atoms. Cycle 19: After refmac, R = 0.2039 (Rfree = 0.000) for 4776 atoms. Found 7 (30 requested) and removed 21 (15 requested) atoms. Cycle 20: After refmac, R = 0.1968 (Rfree = 0.000) for 4758 atoms. Found 9 (30 requested) and removed 19 (15 requested) atoms. ------------------------------------------------------ Building Cycle 5 Atomic shape factors 3.28 3.24 Search for helices and strands: 0 residues in 0 chains, 4872 seeds are put forward NCS extension: 15 residues added (1 deleted due to clashes), 4887 seeds are put forward Round 1: 368 peptides, 59 chains. Longest chain 23 peptides. Score 0.471 Round 2: 415 peptides, 54 chains. Longest chain 19 peptides. Score 0.596 Round 3: 416 peptides, 48 chains. Longest chain 36 peptides. Score 0.639 Round 4: 423 peptides, 48 chains. Longest chain 26 peptides. Score 0.650 Round 5: 405 peptides, 54 chains. Longest chain 26 peptides. Score 0.579 Taking the results from Round 4 Chains 58, Residues 375, Estimated correctness of the model 33.2 % 7 chains (71 residues) have been docked in sequence ------------------------------------------------------ 8970 reflections ( 99.62 % complete ) and 9956 restraints for refining 4859 atoms. 8249 conditional restraints added. Observations/parameters ratio is 0.46 ------------------------------------------------------ Cycle 21: After refmac, R = 0.2327 (Rfree = 0.000) for 4859 atoms. Found 19 (31 requested) and removed 31 (15 requested) atoms. Cycle 22: After refmac, R = 0.2195 (Rfree = 0.000) for 4828 atoms. Found 14 (31 requested) and removed 25 (15 requested) atoms. Cycle 23: After refmac, R = 0.2086 (Rfree = 0.000) for 4810 atoms. Found 9 (30 requested) and removed 21 (15 requested) atoms. Cycle 24: After refmac, R = 0.2027 (Rfree = 0.000) for 4796 atoms. Found 7 (30 requested) and removed 16 (15 requested) atoms. Cycle 25: After refmac, R = 0.1981 (Rfree = 0.000) for 4781 atoms. Found 5 (30 requested) and removed 18 (15 requested) atoms. ------------------------------------------------------ Building Cycle 6 Atomic shape factors 3.33 3.29 Search for helices and strands: 0 residues in 0 chains, 4875 seeds are put forward NCS extension: 15 residues added (0 deleted due to clashes), 4890 seeds are put forward Round 1: 356 peptides, 57 chains. Longest chain 22 peptides. Score 0.465 Round 2: 356 peptides, 51 chains. Longest chain 17 peptides. Score 0.516 Round 3: 378 peptides, 49 chains. Longest chain 23 peptides. Score 0.571 Round 4: 391 peptides, 54 chains. Longest chain 19 peptides. Score 0.555 Round 5: 394 peptides, 51 chains. Longest chain 25 peptides. Score 0.583 Taking the results from Round 5 Chains 53, Residues 343, Estimated correctness of the model 7.9 % 6 chains (33 residues) have been docked in sequence ------------------------------------------------------ 8970 reflections ( 99.62 % complete ) and 10659 restraints for refining 4859 atoms. 9228 conditional restraints added. Observations/parameters ratio is 0.46 ------------------------------------------------------ Cycle 26: After refmac, R = 0.2306 (Rfree = 0.000) for 4859 atoms. Found 23 (31 requested) and removed 29 (15 requested) atoms. Cycle 27: After refmac, R = 0.2161 (Rfree = 0.000) for 4840 atoms. Found 8 (31 requested) and removed 21 (15 requested) atoms. Cycle 28: After refmac, R = 0.2173 (Rfree = 0.000) for 4823 atoms. Found 7 (30 requested) and removed 18 (15 requested) atoms. Cycle 29: After refmac, R = 0.2118 (Rfree = 0.000) for 4811 atoms. Found 9 (30 requested) and removed 18 (15 requested) atoms. Cycle 30: After refmac, R = 0.2109 (Rfree = 0.000) for 4800 atoms. Found 3 (30 requested) and removed 20 (15 requested) atoms. ------------------------------------------------------ Building Cycle 7 Atomic shape factors 3.30 3.26 Search for helices and strands: 0 residues in 0 chains, 4886 seeds are put forward NCS extension: 18 residues added (1 deleted due to clashes), 4904 seeds are put forward Round 1: 319 peptides, 60 chains. Longest chain 15 peptides. Score 0.359 Round 2: 351 peptides, 55 chains. Longest chain 18 peptides. Score 0.472 Round 3: 364 peptides, 52 chains. Longest chain 21 peptides. Score 0.522 Round 4: 369 peptides, 51 chains. Longest chain 22 peptides. Score 0.540 Round 5: 378 peptides, 52 chains. Longest chain 18 peptides. Score 0.548 Taking the results from Round 5 Chains 54, Residues 326, Estimated correctness of the model 0.0 % 4 chains (49 residues) have been docked in sequence ------------------------------------------------------ 8970 reflections ( 99.62 % complete ) and 10355 restraints for refining 4858 atoms. 8904 conditional restraints added. Observations/parameters ratio is 0.46 ------------------------------------------------------ Cycle 31: After refmac, R = 0.2300 (Rfree = 0.000) for 4858 atoms. Found 20 (31 requested) and removed 27 (15 requested) atoms. Cycle 32: After refmac, R = 0.2125 (Rfree = 0.000) for 4836 atoms. Found 13 (31 requested) and removed 24 (15 requested) atoms. Cycle 33: After refmac, R = 0.2036 (Rfree = 0.000) for 4821 atoms. Found 1 (30 requested) and removed 18 (15 requested) atoms. Cycle 34: After refmac, R = 0.2014 (Rfree = 0.000) for 4804 atoms. Found 11 (30 requested) and removed 17 (15 requested) atoms. Cycle 35: After refmac, R = 0.1985 (Rfree = 0.000) for 4797 atoms. Found 6 (30 requested) and removed 16 (15 requested) atoms. ------------------------------------------------------ Building Cycle 8 Atomic shape factors 3.28 3.24 Search for helices and strands: 0 residues in 0 chains, 4889 seeds are put forward NCS extension: 23 residues added (3 deleted due to clashes), 4912 seeds are put forward Round 1: 336 peptides, 61 chains. Longest chain 12 peptides. Score 0.387 Round 2: 386 peptides, 62 chains. Longest chain 16 peptides. Score 0.481 Round 3: 355 peptides, 53 chains. Longest chain 21 peptides. Score 0.497 Round 4: 381 peptides, 53 chains. Longest chain 22 peptides. Score 0.545 Round 5: 363 peptides, 54 chains. Longest chain 24 peptides. Score 0.504 Taking the results from Round 4 Chains 56, Residues 328, Estimated correctness of the model 0.0 % 2 chains (25 residues) have been docked in sequence ------------------------------------------------------ 8970 reflections ( 99.62 % complete ) and 10563 restraints for refining 4859 atoms. 9208 conditional restraints added. Observations/parameters ratio is 0.46 ------------------------------------------------------ Cycle 36: After refmac, R = 0.2252 (Rfree = 0.000) for 4859 atoms. Found 27 (31 requested) and removed 22 (15 requested) atoms. Cycle 37: After refmac, R = 0.2100 (Rfree = 0.000) for 4852 atoms. Found 15 (31 requested) and removed 20 (15 requested) atoms. Cycle 38: After refmac, R = 0.2060 (Rfree = 0.000) for 4841 atoms. Found 10 (31 requested) and removed 22 (15 requested) atoms. Cycle 39: After refmac, R = 0.2009 (Rfree = 0.000) for 4828 atoms. Found 9 (30 requested) and removed 17 (15 requested) atoms. Cycle 40: After refmac, R = 0.1982 (Rfree = 0.000) for 4819 atoms. Found 10 (30 requested) and removed 17 (15 requested) atoms. ------------------------------------------------------ Building Cycle 9 Atomic shape factors 3.30 3.26 Search for helices and strands: 0 residues in 0 chains, 4910 seeds are put forward NCS extension: 23 residues added (1 deleted due to clashes), 4933 seeds are put forward Round 1: 308 peptides, 52 chains. Longest chain 15 peptides. Score 0.410 Round 2: 335 peptides, 51 chains. Longest chain 16 peptides. Score 0.475 Round 3: 335 peptides, 46 chains. Longest chain 26 peptides. Score 0.518 Round 4: 326 peptides, 45 chains. Longest chain 16 peptides. Score 0.509 Round 5: 340 peptides, 49 chains. Longest chain 25 peptides. Score 0.502 Taking the results from Round 3 Chains 48, Residues 289, Estimated correctness of the model 0.0 % 4 chains (32 residues) have been docked in sequence ------------------------------------------------------ 8970 reflections ( 99.62 % complete ) and 10625 restraints for refining 4857 atoms. 9421 conditional restraints added. Observations/parameters ratio is 0.46 ------------------------------------------------------ Cycle 41: After refmac, R = 0.2204 (Rfree = 0.000) for 4857 atoms. Found 27 (31 requested) and removed 31 (15 requested) atoms. Cycle 42: After refmac, R = 0.2022 (Rfree = 0.000) for 4852 atoms. Found 9 (31 requested) and removed 22 (15 requested) atoms. Cycle 43: After refmac, R = 0.1946 (Rfree = 0.000) for 4837 atoms. Found 5 (31 requested) and removed 20 (15 requested) atoms. Cycle 44: After refmac, R = 0.1888 (Rfree = 0.000) for 4821 atoms. Found 6 (30 requested) and removed 18 (15 requested) atoms. Cycle 45: After refmac, R = 0.1871 (Rfree = 0.000) for 4809 atoms. Found 8 (30 requested) and removed 18 (15 requested) atoms. ------------------------------------------------------ Building Cycle 10 Atomic shape factors 3.31 3.27 Search for helices and strands: 0 residues in 0 chains, 4876 seeds are put forward NCS extension: 17 residues added (1 deleted due to clashes), 4893 seeds are put forward Round 1: 272 peptides, 49 chains. Longest chain 12 peptides. Score 0.359 Round 2: 282 peptides, 42 chains. Longest chain 15 peptides. Score 0.448 Round 3: 299 peptides, 43 chains. Longest chain 16 peptides. Score 0.474 Round 4: 313 peptides, 43 chains. Longest chain 17 peptides. Score 0.502 Round 5: 324 peptides, 44 chains. Longest chain 14 peptides. Score 0.514 Taking the results from Round 5 Last building cycle: Chain fragments will be rearranged Chains 44, Residues 280, Estimated correctness of the model 0.0 % 6 chains (45 residues) have been docked in sequence Sequence coverage is 16 % Consider running further cycles of model building using 2ich-3_warpNtrace.pdb as input Building loops using Loopy2018 Built loop between residues 81 A and 90 A 42 chains (285 residues) following loop building 5 chains (53 residues) in sequence following loop building ------------------------------------------------------ ---> Final restrained refinement block. No atom update. 8970 reflections ( 99.62 % complete ) and 10579 restraints for refining 4859 atoms. 9329 conditional restraints added. Observations/parameters ratio is 0.46 ------------------------------------------------------ Cycle 46: After refmac, R = 0.2292 (Rfree = 0.000) for 4859 atoms. Found 0 (31 requested) and removed 15 (15 requested) atoms. Cycle 47: After refmac, R = 0.2181 (Rfree = 0.000) for 4831 atoms. Found 0 (31 requested) and removed 15 (15 requested) atoms. Cycle 48: After refmac, R = 0.2128 (Rfree = 0.000) for 4810 atoms. Found 0 (30 requested) and removed 15 (15 requested) atoms. Cycle 49: After refmac, R = 0.2162 (Rfree = 0.000) for 4793 atoms. TimeTaking 69.43