Mon 24 Dec 00:19:05 GMT 2018 ############### You are running ARP/wARP 8.0 ############### Working directory /mnt/lustre/users/emra500/PipeliensFastaNoRFree/mrncs/ArpWArp/wArpResults/WorkingDir Job ID is set to 1z82-3.2-parrot-mrncs X-ray data file /users/emra500/scratch/Dataset/mrncsChltofom/1z82-3.2-parrot-mrncs.mtz Sequence file /users/emra500/scratch/Dataset/mrncsChltofom/1z82-3.2-parrot-mrncs.fasta Tracing mode WARPNTRACEPHASES Creating directory /mnt/lustre/users/emra500/PipeliensFastaNoRFree/mrncs/ArpWArp/wArpResults/WorkingDir/1z82-3.2-parrot-mrncs 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/mrncs/ArpWArp/wArpResults/WorkingDir/1z82-3.2-parrot-mrncs/arp_warp_classic.par Job launched in /mnt/lustre/users/emra500/PipeliensFastaNoRFree/mrncs/ArpWArp/wArpResults/WorkingDir/1z82-3.2-parrot-mrncs ############### 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 ============================================================ Mon 24 Dec 00:19:10 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/mrncs/ArpWArp/wArpResults/WorkingDir/1z82-3.2-parrot-mrncs ARP/wARP software version: 8.0 The parameter file: /mnt/lustre/users/emra500/PipeliensFastaNoRFree/mrncs/ArpWArp/wArpResults/WorkingDir/1z82-3.2-parrot-mrncs/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 420 and 0 Target number of residues in the AU: 420 Target solvent content: 0.6268 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: 0.40 Input MTZ file: 1z82-3.2-parrot-mrncs.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: 4 Cell parameters: 65.170 67.461 75.617 90.000 113.643 90.000 Input sequence file: 1z82-3.2-parrot-mrncs.fasta_lf Building free atoms model in initial map for 5360 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: 29.850 3.200 Wilson plot Bfac: 64.58 10035 reflections ( 99.62 % complete ) and 0 restraints for refining 5919 atoms. Observations/parameters ratio is 0.42 ------------------------------------------------------ Starting model: R = 0.2979 (Rfree = 0.000). ------------------------------------------------------ Cycle 0: After refmac, R = 0.2080 (Rfree = 0.000) for 5919 atoms. Found 16 (53 requested) and removed 36 (26 requested) atoms. ------------------------------------------------------ Building Cycle 1 Atomic shape factors 3.18 3.64 Search for helices and strands: 0 residues in 0 chains, 6013 seeds are put forward NCS extension: 0 residues added, 6013 seeds are put forward Round 1: 327 peptides, 60 chains. Longest chain 12 peptides. Score 0.410 Round 2: 391 peptides, 53 chains. Longest chain 22 peptides. Score 0.616 Round 3: 427 peptides, 54 chains. Longest chain 29 peptides. Score 0.671 Round 4: 446 peptides, 58 chains. Longest chain 29 peptides. Score 0.672 Round 5: 449 peptides, 52 chains. Longest chain 22 peptides. Score 0.717 Taking the results from Round 5 Chains 57, Residues 397, Estimated correctness of the model 68.7 % 8 chains (91 residues) have been docked in sequence Building loops using Loopy2018 Built loop between residues 199 A and 205 A 56 chains (400 residues) following loop building 7 chains (96 residues) in sequence following loop building ------------------------------------------------------ 10035 reflections ( 99.62 % complete ) and 9842 restraints for refining 4893 atoms. 8015 conditional restraints added. Observations/parameters ratio is 0.51 ------------------------------------------------------ Cycle 1: After refmac, R = 0.2698 (Rfree = 0.000) for 4893 atoms. Found 43 (43 requested) and removed 47 (21 requested) atoms. Cycle 2: After refmac, R = 0.2484 (Rfree = 0.000) for 4834 atoms. Found 24 (42 requested) and removed 30 (21 requested) atoms. Cycle 3: After refmac, R = 0.2431 (Rfree = 0.000) for 4787 atoms. Found 17 (41 requested) and removed 27 (21 requested) atoms. Cycle 4: After refmac, R = 0.2347 (Rfree = 0.000) for 4769 atoms. Found 7 (39 requested) and removed 24 (21 requested) atoms. Cycle 5: After refmac, R = 0.2261 (Rfree = 0.000) for 4742 atoms. Found 11 (39 requested) and removed 23 (21 requested) atoms. ------------------------------------------------------ Building Cycle 2 Atomic shape factors 3.20 3.66 Search for helices and strands: 0 residues in 0 chains, 4908 seeds are put forward NCS extension: 22 residues added (7 deleted due to clashes), 4930 seeds are put forward Round 1: 385 peptides, 56 chains. Longest chain 19 peptides. Score 0.579 Round 2: 425 peptides, 54 chains. Longest chain 34 peptides. Score 0.667 Round 3: 434 peptides, 54 chains. Longest chain 22 peptides. Score 0.682 Round 4: 434 peptides, 46 chains. Longest chain 33 peptides. Score 0.735 Round 5: 425 peptides, 51 chains. Longest chain 32 peptides. Score 0.689 Taking the results from Round 4 Chains 50, Residues 388, Estimated correctness of the model 72.3 % 7 chains (85 residues) have been docked in sequence Building loops using Loopy2018 Built loop between residues 142 A and 152 A 48 chains (394 residues) following loop building 6 chains (94 residues) in sequence following loop building ------------------------------------------------------ 10035 reflections ( 99.62 % complete ) and 9957 restraints for refining 4836 atoms. 8148 conditional restraints added. Observations/parameters ratio is 0.52 ------------------------------------------------------ Cycle 6: After refmac, R = 0.2984 (Rfree = 0.000) for 4836 atoms. Found 39 (39 requested) and removed 55 (21 requested) atoms. Cycle 7: After refmac, R = 0.2708 (Rfree = 0.000) for 4816 atoms. Found 21 (38 requested) and removed 22 (21 requested) atoms. Cycle 8: After refmac, R = 0.2597 (Rfree = 0.000) for 4806 atoms. Found 14 (37 requested) and removed 21 (21 requested) atoms. Cycle 9: After refmac, R = 0.2391 (Rfree = 0.000) for 4793 atoms. Found 6 (36 requested) and removed 23 (21 requested) atoms. Cycle 10: After refmac, R = 0.2337 (Rfree = 0.000) for 4761 atoms. Found 6 (34 requested) and removed 21 (21 requested) atoms. ------------------------------------------------------ Building Cycle 3 Atomic shape factors 3.20 3.66 Search for helices and strands: 0 residues in 0 chains, 4912 seeds are put forward NCS extension: 36 residues added (0 deleted due to clashes), 4948 seeds are put forward Round 1: 376 peptides, 57 chains. Longest chain 21 peptides. Score 0.552 Round 2: 423 peptides, 53 chains. Longest chain 26 peptides. Score 0.671 Round 3: 416 peptides, 55 chains. Longest chain 26 peptides. Score 0.645 Round 4: 419 peptides, 48 chains. Longest chain 22 peptides. Score 0.700 Round 5: 444 peptides, 51 chains. Longest chain 22 peptides. Score 0.717 Taking the results from Round 5 Chains 52, Residues 393, Estimated correctness of the model 68.7 % 3 chains (42 residues) have been docked in sequence Building loops using Loopy2018 52 chains (393 residues) following loop building 3 chains (42 residues) in sequence following loop building ------------------------------------------------------ 10035 reflections ( 99.62 % complete ) and 10494 restraints for refining 4874 atoms. 8810 conditional restraints added. Observations/parameters ratio is 0.51 ------------------------------------------------------ Cycle 11: After refmac, R = 0.2676 (Rfree = 0.000) for 4874 atoms. Found 34 (34 requested) and removed 31 (21 requested) atoms. Cycle 12: After refmac, R = 0.2388 (Rfree = 0.000) for 4873 atoms. Found 15 (34 requested) and removed 27 (21 requested) atoms. Cycle 13: After refmac, R = 0.2248 (Rfree = 0.000) for 4851 atoms. Found 10 (33 requested) and removed 22 (21 requested) atoms. Cycle 14: After refmac, R = 0.2201 (Rfree = 0.000) for 4830 atoms. Found 4 (32 requested) and removed 22 (21 requested) atoms. Cycle 15: After refmac, R = 0.2164 (Rfree = 0.000) for 4806 atoms. Found 7 (31 requested) and removed 21 (21 requested) atoms. ------------------------------------------------------ Building Cycle 4 Atomic shape factors 3.20 3.66 Search for helices and strands: 0 residues in 0 chains, 4963 seeds are put forward NCS extension: 20 residues added (12 deleted due to clashes), 4983 seeds are put forward Round 1: 354 peptides, 54 chains. Longest chain 16 peptides. Score 0.533 Round 2: 389 peptides, 47 chains. Longest chain 27 peptides. Score 0.660 Round 3: 385 peptides, 52 chains. Longest chain 20 peptides. Score 0.613 Round 4: 396 peptides, 48 chains. Longest chain 29 peptides. Score 0.664 Round 5: 393 peptides, 52 chains. Longest chain 28 peptides. Score 0.628 Taking the results from Round 4 Chains 52, Residues 348, Estimated correctness of the model 57.2 % 9 chains (89 residues) have been docked in sequence ------------------------------------------------------ 10035 reflections ( 99.62 % complete ) and 10356 restraints for refining 4893 atoms. 8742 conditional restraints added. Observations/parameters ratio is 0.51 ------------------------------------------------------ Cycle 16: After refmac, R = 0.2302 (Rfree = 0.000) for 4893 atoms. Found 20 (30 requested) and removed 33 (21 requested) atoms. Cycle 17: After refmac, R = 0.2137 (Rfree = 0.000) for 4854 atoms. Found 17 (30 requested) and removed 26 (21 requested) atoms. Cycle 18: After refmac, R = 0.2087 (Rfree = 0.000) for 4832 atoms. Found 12 (30 requested) and removed 27 (21 requested) atoms. Cycle 19: After refmac, R = 0.2090 (Rfree = 0.000) for 4814 atoms. Found 12 (30 requested) and removed 24 (21 requested) atoms. Cycle 20: After refmac, R = 0.2130 (Rfree = 0.000) for 4788 atoms. Found 24 (30 requested) and removed 28 (21 requested) atoms. ------------------------------------------------------ Building Cycle 5 Atomic shape factors 3.17 3.63 Search for helices and strands: 0 residues in 0 chains, 4976 seeds are put forward NCS extension: 31 residues added (9 deleted due to clashes), 5007 seeds are put forward Round 1: 343 peptides, 55 chains. Longest chain 21 peptides. Score 0.499 Round 2: 387 peptides, 50 chains. Longest chain 29 peptides. Score 0.633 Round 3: 388 peptides, 51 chains. Longest chain 22 peptides. Score 0.627 Round 4: 399 peptides, 56 chains. Longest chain 25 peptides. Score 0.606 Round 5: 370 peptides, 48 chains. Longest chain 22 peptides. Score 0.618 Taking the results from Round 2 Chains 51, Residues 337, Estimated correctness of the model 49.7 % 5 chains (50 residues) have been docked in sequence ------------------------------------------------------ 10035 reflections ( 99.62 % complete ) and 10607 restraints for refining 4864 atoms. 9162 conditional restraints added. Observations/parameters ratio is 0.52 ------------------------------------------------------ Cycle 21: After refmac, R = 0.2148 (Rfree = 0.000) for 4864 atoms. Found 18 (30 requested) and removed 30 (21 requested) atoms. Cycle 22: After refmac, R = 0.2079 (Rfree = 0.000) for 4840 atoms. Found 20 (30 requested) and removed 25 (21 requested) atoms. Cycle 23: After refmac, R = 0.1947 (Rfree = 0.000) for 4822 atoms. Found 6 (30 requested) and removed 26 (21 requested) atoms. Cycle 24: After refmac, R = 0.1907 (Rfree = 0.000) for 4801 atoms. Found 3 (30 requested) and removed 23 (21 requested) atoms. Cycle 25: After refmac, R = 0.1966 (Rfree = 0.000) for 4777 atoms. Found 11 (29 requested) and removed 25 (21 requested) atoms. ------------------------------------------------------ Building Cycle 6 Atomic shape factors 3.18 3.64 Search for helices and strands: 0 residues in 0 chains, 4967 seeds are put forward NCS extension: 11 residues added (12 deleted due to clashes), 4978 seeds are put forward Round 1: 321 peptides, 51 chains. Longest chain 18 peptides. Score 0.488 Round 2: 364 peptides, 48 chains. Longest chain 18 peptides. Score 0.607 Round 3: 365 peptides, 48 chains. Longest chain 18 peptides. Score 0.609 Round 4: 363 peptides, 51 chains. Longest chain 15 peptides. Score 0.579 Round 5: 384 peptides, 45 chains. Longest chain 23 peptides. Score 0.667 Taking the results from Round 5 Chains 47, Residues 339, Estimated correctness of the model 57.9 % 1 chains (10 residues) have been docked in sequence ------------------------------------------------------ 10035 reflections ( 99.62 % complete ) and 10869 restraints for refining 4872 atoms. 9520 conditional restraints added. Observations/parameters ratio is 0.51 ------------------------------------------------------ Cycle 26: After refmac, R = 0.2133 (Rfree = 0.000) for 4872 atoms. Found 23 (30 requested) and removed 29 (21 requested) atoms. Cycle 27: After refmac, R = 0.2074 (Rfree = 0.000) for 4854 atoms. Found 9 (30 requested) and removed 24 (21 requested) atoms. Cycle 28: After refmac, R = 0.2044 (Rfree = 0.000) for 4838 atoms. Found 8 (30 requested) and removed 24 (21 requested) atoms. Cycle 29: After refmac, R = 0.2028 (Rfree = 0.000) for 4820 atoms. Found 12 (30 requested) and removed 25 (21 requested) atoms. Cycle 30: After refmac, R = 0.2005 (Rfree = 0.000) for 4801 atoms. Found 15 (30 requested) and removed 22 (21 requested) atoms. ------------------------------------------------------ Building Cycle 7 Atomic shape factors 3.20 3.66 Search for helices and strands: 0 residues in 0 chains, 4960 seeds are put forward NCS extension: 37 residues added (3 deleted due to clashes), 4997 seeds are put forward Round 1: 316 peptides, 49 chains. Longest chain 18 peptides. Score 0.497 Round 2: 342 peptides, 43 chains. Longest chain 22 peptides. Score 0.608 Round 3: 340 peptides, 46 chains. Longest chain 18 peptides. Score 0.577 Round 4: 339 peptides, 45 chains. Longest chain 19 peptides. Score 0.584 Round 5: 353 peptides, 44 chains. Longest chain 24 peptides. Score 0.620 Taking the results from Round 5 Chains 44, Residues 309, Estimated correctness of the model 46.3 % 4 chains (37 residues) have been docked in sequence ------------------------------------------------------ 10035 reflections ( 99.62 % complete ) and 10953 restraints for refining 4893 atoms. 9629 conditional restraints added. Observations/parameters ratio is 0.51 ------------------------------------------------------ Cycle 31: After refmac, R = 0.2511 (Rfree = 0.000) for 4893 atoms. Found 30 (30 requested) and removed 29 (21 requested) atoms. Cycle 32: After refmac, R = 0.2368 (Rfree = 0.000) for 4894 atoms. Found 11 (30 requested) and removed 21 (21 requested) atoms. Cycle 33: After refmac, R = 0.2281 (Rfree = 0.000) for 4883 atoms. Found 11 (30 requested) and removed 21 (21 requested) atoms. Cycle 34: After refmac, R = 0.2180 (Rfree = 0.000) for 4873 atoms. Found 3 (30 requested) and removed 21 (21 requested) atoms. Cycle 35: After refmac, R = 0.2128 (Rfree = 0.000) for 4852 atoms. Found 5 (30 requested) and removed 21 (21 requested) atoms. ------------------------------------------------------ Building Cycle 8 Atomic shape factors 3.20 3.66 Search for helices and strands: 0 residues in 0 chains, 4991 seeds are put forward NCS extension: 20 residues added (10 deleted due to clashes), 5011 seeds are put forward Round 1: 323 peptides, 56 chains. Longest chain 12 peptides. Score 0.442 Round 2: 351 peptides, 48 chains. Longest chain 23 peptides. Score 0.582 Round 3: 338 peptides, 49 chains. Longest chain 23 peptides. Score 0.546 Round 4: 310 peptides, 45 chains. Longest chain 17 peptides. Score 0.523 Round 5: 333 peptides, 48 chains. Longest chain 14 peptides. Score 0.544 Taking the results from Round 2 Chains 50, Residues 303, Estimated correctness of the model 36.1 % 4 chains (40 residues) have been docked in sequence ------------------------------------------------------ 10035 reflections ( 99.62 % complete ) and 10937 restraints for refining 4890 atoms. 9642 conditional restraints added. Observations/parameters ratio is 0.51 ------------------------------------------------------ Cycle 36: After refmac, R = 0.2341 (Rfree = 0.000) for 4890 atoms. Found 28 (30 requested) and removed 28 (21 requested) atoms. Cycle 37: After refmac, R = 0.2153 (Rfree = 0.000) for 4884 atoms. Found 4 (30 requested) and removed 21 (21 requested) atoms. Cycle 38: After refmac, R = 0.2106 (Rfree = 0.000) for 4862 atoms. Found 4 (30 requested) and removed 21 (21 requested) atoms. Cycle 39: After refmac, R = 0.2102 (Rfree = 0.000) for 4842 atoms. Found 9 (30 requested) and removed 21 (21 requested) atoms. Cycle 40: After refmac, R = 0.2048 (Rfree = 0.000) for 4827 atoms. Found 6 (30 requested) and removed 21 (21 requested) atoms. ------------------------------------------------------ Building Cycle 9 Atomic shape factors 3.20 3.66 Search for helices and strands: 0 residues in 0 chains, 4976 seeds are put forward NCS extension: 20 residues added (9 deleted due to clashes), 4996 seeds are put forward Round 1: 310 peptides, 53 chains. Longest chain 15 peptides. Score 0.441 Round 2: 345 peptides, 47 chains. Longest chain 21 peptides. Score 0.579 Round 3: 338 peptides, 47 chains. Longest chain 28 peptides. Score 0.564 Round 4: 321 peptides, 43 chains. Longest chain 31 peptides. Score 0.566 Round 5: 349 peptides, 46 chains. Longest chain 28 peptides. Score 0.595 Taking the results from Round 5 Chains 49, Residues 303, Estimated correctness of the model 39.7 % 5 chains (43 residues) have been docked in sequence ------------------------------------------------------ 10035 reflections ( 99.62 % complete ) and 11026 restraints for refining 4879 atoms. 9722 conditional restraints added. Observations/parameters ratio is 0.51 ------------------------------------------------------ Cycle 41: After refmac, R = 0.2474 (Rfree = 0.000) for 4879 atoms. Found 30 (30 requested) and removed 30 (21 requested) atoms. Cycle 42: After refmac, R = 0.2291 (Rfree = 0.000) for 4876 atoms. Found 14 (30 requested) and removed 21 (21 requested) atoms. Cycle 43: After refmac, R = 0.2203 (Rfree = 0.000) for 4868 atoms. Found 9 (30 requested) and removed 21 (21 requested) atoms. Cycle 44: After refmac, R = 0.2109 (Rfree = 0.000) for 4852 atoms. Found 6 (30 requested) and removed 21 (21 requested) atoms. Cycle 45: After refmac, R = 0.2064 (Rfree = 0.000) for 4834 atoms. Found 4 (30 requested) and removed 22 (21 requested) atoms. ------------------------------------------------------ Building Cycle 10 Atomic shape factors 3.18 3.64 Search for helices and strands: 0 residues in 0 chains, 4978 seeds are put forward NCS extension: 14 residues added (4 deleted due to clashes), 4992 seeds are put forward Round 1: 259 peptides, 43 chains. Longest chain 11 peptides. Score 0.421 Round 2: 306 peptides, 46 chains. Longest chain 22 peptides. Score 0.504 Round 3: 312 peptides, 43 chains. Longest chain 21 peptides. Score 0.547 Round 4: 303 peptides, 47 chains. Longest chain 22 peptides. Score 0.487 Round 5: 319 peptides, 46 chains. Longest chain 25 peptides. Score 0.533 Taking the results from Round 3 Last building cycle: Chain fragments will be rearranged Chains 45, Residues 269, Estimated correctness of the model 26.0 % 5 chains (49 residues) have been docked in sequence Sequence coverage is 18 % Consider running further cycles of model building using 1z82-3_warpNtrace.pdb as input Building loops using Loopy2018 45 chains (269 residues) following loop building 5 chains (49 residues) in sequence following loop building ------------------------------------------------------ ---> Final restrained refinement block. No atom update. 10035 reflections ( 99.62 % complete ) and 11109 restraints for refining 4893 atoms. 9920 conditional restraints added. Observations/parameters ratio is 0.51 ------------------------------------------------------ Cycle 46: After refmac, R = 0.2197 (Rfree = 0.000) for 4893 atoms. Found 0 (30 requested) and removed 6 (21 requested) atoms. Cycle 47: After refmac, R = 0.2071 (Rfree = 0.000) for 4884 atoms. Found 0 (30 requested) and removed 15 (21 requested) atoms. Cycle 48: After refmac, R = 0.2036 (Rfree = 0.000) for 4866 atoms. Found 0 (30 requested) and removed 15 (21 requested) atoms. Cycle 49: After refmac, R = 0.2020 (Rfree = 0.000) for 4846 atoms. TimeTaking 55.22