Mon 24 Dec 00:33:15 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 2anu-4.0-parrot-mrncs X-ray data file /users/emra500/scratch/Dataset/mrncsChltofom/2anu-4.0-parrot-mrncs.mtz Sequence file /users/emra500/scratch/Dataset/mrncsChltofom/2anu-4.0-parrot-mrncs.fasta Tracing mode WARPNTRACEPHASES Creating directory /mnt/lustre/users/emra500/PipeliensFastaNoRFree/mrncs/ArpWArp/wArpResults/WorkingDir/2anu-4.0-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/2anu-4.0-parrot-mrncs/arp_warp_classic.par Job launched in /mnt/lustre/users/emra500/PipeliensFastaNoRFree/mrncs/ArpWArp/wArpResults/WorkingDir/2anu-4.0-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 00:33:20 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/2anu-4.0-parrot-mrncs ARP/wARP software version: 8.0 The parameter file: /mnt/lustre/users/emra500/PipeliensFastaNoRFree/mrncs/ArpWArp/wArpResults/WorkingDir/2anu-4.0-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 1242 and 0 Target number of residues in the AU: 1242 Target solvent content: 0.6319 Checking the provided sequence file Detected sequence length: 255 Maximum limit of NCS related copies: 60 Number of NCS-related molecules: 6 Adjusted target number of residues: 1530 Adjusted target solvent content: 0.55 Input MTZ file: 2anu-4.0-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: 146 Cell parameters: 111.273 111.273 383.188 90.000 90.000 120.000 Input sequence file: 2anu-4.0-parrot-mrncs.fasta_lf Building free atoms model in initial map for 12240 target number of atoms Had to go as low as 0.85 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: 127.729 4.001 Wilson plot Bfac: 67.56 *** WARNING *** *** WARNING *** This resolution is too low for ARP/wARP protein chain tracing *** WARNING *** 14900 reflections ( 99.71 % complete ) and 0 restraints for refining 13478 atoms. Observations/parameters ratio is 0.28 ------------------------------------------------------ Starting model: R = 0.2969 (Rfree = 0.000). ------------------------------------------------------ Cycle 0: After refmac, R = 0.2844 (Rfree = 0.000) for 13478 atoms. Found 63 (63 requested) and removed 212 (31 requested) atoms. ------------------------------------------------------ Building Cycle 1 Atomic shape factors 3.55 3.32 Search for helices and strands: 0 residues in 0 chains, 13533 seeds are put forward NCS extension: 0 residues added, 13533 seeds are put forward Round 1: 516 peptides, 102 chains. Longest chain 11 peptides. Score 0.286 Round 2: 725 peptides, 118 chains. Longest chain 19 peptides. Score 0.418 Round 3: 792 peptides, 115 chains. Longest chain 24 peptides. Score 0.485 Round 4: 814 peptides, 113 chains. Longest chain 24 peptides. Score 0.509 Round 5: 874 peptides, 108 chains. Longest chain 28 peptides. Score 0.570 Taking the results from Round 5 Chains 111, Residues 766, Estimated correctness of the model 0.0 % 4 chains (59 residues) have been docked in sequence ------------------------------------------------------ 14900 reflections ( 99.71 % complete ) and 24111 restraints for refining 10848 atoms. 20917 conditional restraints added. Observations/parameters ratio is 0.34 ------------------------------------------------------ Cycle 1: After refmac, R = 0.2603 (Rfree = 0.000) for 10848 atoms. Found 51 (51 requested) and removed 204 (25 requested) atoms. Cycle 2: After refmac, R = 0.2166 (Rfree = 0.000) for 10569 atoms. Found 40 (50 requested) and removed 76 (25 requested) atoms. Cycle 3: After refmac, R = 0.2149 (Rfree = 0.000) for 10471 atoms. Found 32 (50 requested) and removed 65 (25 requested) atoms. Cycle 4: After refmac, R = 0.2115 (Rfree = 0.000) for 10412 atoms. Found 46 (49 requested) and removed 74 (24 requested) atoms. Failed to save intermediate PDB Cycle 5: After refmac, R = 0.2150 (Rfree = 0.000) for 10350 atoms. Found 49 (49 requested) and removed 59 (24 requested) atoms. ------------------------------------------------------ Building Cycle 2 Atomic shape factors 3.53 3.30 Search for helices and strands: 0 residues in 0 chains, 10726 seeds are put forward NCS extension: 18 residues added (8 deleted due to clashes), 10744 seeds are put forward Round 1: 760 peptides, 124 chains. Longest chain 14 peptides. Score 0.425 Round 2: 824 peptides, 112 chains. Longest chain 20 peptides. Score 0.520 Round 3: 824 peptides, 101 chains. Longest chain 22 peptides. Score 0.557 Round 4: 833 peptides, 108 chains. Longest chain 23 peptides. Score 0.540 Round 5: 843 peptides, 100 chains. Longest chain 30 peptides. Score 0.574 Taking the results from Round 5 Chains 102, Residues 743, Estimated correctness of the model 0.0 % 1 chains (10 residues) have been docked in sequence ------------------------------------------------------ 14900 reflections ( 99.71 % complete ) and 25420 restraints for refining 10931 atoms. 22513 conditional restraints added. Observations/parameters ratio is 0.34 ------------------------------------------------------ Cycle 6: After refmac, R = 0.2056 (Rfree = 0.000) for 10931 atoms. Found 49 (51 requested) and removed 167 (25 requested) atoms. Cycle 7: After refmac, R = 0.1944 (Rfree = 0.000) for 10742 atoms. Found 22 (51 requested) and removed 48 (25 requested) atoms. Cycle 8: After refmac, R = 0.1897 (Rfree = 0.000) for 10694 atoms. Found 15 (50 requested) and removed 43 (25 requested) atoms. Cycle 9: After refmac, R = 0.1928 (Rfree = 0.000) for 10643 atoms. Found 23 (50 requested) and removed 40 (25 requested) atoms. Cycle 10: After refmac, R = 0.1909 (Rfree = 0.000) for 10612 atoms. Found 32 (50 requested) and removed 38 (25 requested) atoms. ------------------------------------------------------ Building Cycle 3 Atomic shape factors 3.54 3.31 Search for helices and strands: 0 residues in 0 chains, 11019 seeds are put forward NCS extension: 32 residues added (1 deleted due to clashes), 11051 seeds are put forward Round 1: 743 peptides, 127 chains. Longest chain 15 peptides. Score 0.399 Round 2: 825 peptides, 107 chains. Longest chain 24 peptides. Score 0.538 Round 3: 795 peptides, 113 chains. Longest chain 18 peptides. Score 0.494 Round 4: 811 peptides, 101 chains. Longest chain 24 peptides. Score 0.547 Round 5: 818 peptides, 101 chains. Longest chain 26 peptides. Score 0.553 Taking the results from Round 5 Chains 105, Residues 717, Estimated correctness of the model 0.0 % 2 chains (28 residues) have been docked in sequence ------------------------------------------------------ 14900 reflections ( 99.71 % complete ) and 25956 restraints for refining 11052 atoms. 23062 conditional restraints added. Observations/parameters ratio is 0.34 ------------------------------------------------------ Cycle 11: After refmac, R = 0.2099 (Rfree = 0.000) for 11052 atoms. Found 52 (52 requested) and removed 41 (26 requested) atoms. Cycle 12: After refmac, R = 0.2147 (Rfree = 0.000) for 10990 atoms. Found 52 (52 requested) and removed 48 (26 requested) atoms. Cycle 13: After refmac, R = 0.2160 (Rfree = 0.000) for 10954 atoms. Found 52 (52 requested) and removed 44 (26 requested) atoms. Cycle 14: After refmac, R = 0.1798 (Rfree = 0.000) for 10926 atoms. Found 19 (52 requested) and removed 36 (26 requested) atoms. Cycle 15: After refmac, R = 0.1761 (Rfree = 0.000) for 10891 atoms. Found 15 (51 requested) and removed 38 (25 requested) atoms. ------------------------------------------------------ Building Cycle 4 Atomic shape factors 3.57 3.34 Search for helices and strands: 0 residues in 0 chains, 11233 seeds are put forward NCS extension: 12 residues added (6 deleted due to clashes), 11245 seeds are put forward Round 1: 681 peptides, 117 chains. Longest chain 24 peptides. Score 0.383 Round 2: 759 peptides, 113 chains. Longest chain 24 peptides. Score 0.465 Round 3: 782 peptides, 108 chains. Longest chain 26 peptides. Score 0.502 Round 4: 759 peptides, 103 chains. Longest chain 19 peptides. Score 0.501 Round 5: 772 peptides, 100 chains. Longest chain 28 peptides. Score 0.522 Taking the results from Round 5 Chains 100, Residues 672, Estimated correctness of the model 0.0 % 1 chains (27 residues) have been docked in sequence ------------------------------------------------------ 14900 reflections ( 99.71 % complete ) and 26032 restraints for refining 11051 atoms. 23295 conditional restraints added. Observations/parameters ratio is 0.34 ------------------------------------------------------ Cycle 16: After refmac, R = 0.2136 (Rfree = 0.000) for 11051 atoms. Found 52 (52 requested) and removed 83 (26 requested) atoms. Cycle 17: After refmac, R = 0.2129 (Rfree = 0.000) for 10928 atoms. Found 52 (52 requested) and removed 55 (26 requested) atoms. Cycle 18: After refmac, R = 0.2102 (Rfree = 0.000) for 10883 atoms. Found 51 (51 requested) and removed 310 (25 requested) atoms. Cycle 19: After refmac, R = 0.1743 (Rfree = 0.000) for 10574 atoms. Found 21 (50 requested) and removed 52 (25 requested) atoms. Cycle 20: After refmac, R = 0.1670 (Rfree = 0.000) for 10495 atoms. Found 20 (50 requested) and removed 33 (25 requested) atoms. ------------------------------------------------------ Building Cycle 5 Atomic shape factors 3.58 3.35 Search for helices and strands: 0 residues in 0 chains, 10831 seeds are put forward NCS extension: 14 residues added (8 deleted due to clashes), 10845 seeds are put forward Round 1: 625 peptides, 107 chains. Longest chain 15 peptides. Score 0.371 Round 2: 697 peptides, 100 chains. Longest chain 21 peptides. Score 0.462 Round 3: 734 peptides, 104 chains. Longest chain 21 peptides. Score 0.478 Round 4: 728 peptides, 101 chains. Longest chain 28 peptides. Score 0.484 Round 5: 746 peptides, 96 chains. Longest chain 29 peptides. Score 0.516 Taking the results from Round 5 Chains 96, Residues 650, Estimated correctness of the model 0.0 % 2 chains (41 residues) have been docked in sequence ------------------------------------------------------ 14900 reflections ( 99.71 % complete ) and 25962 restraints for refining 11051 atoms. 23281 conditional restraints added. Observations/parameters ratio is 0.34 ------------------------------------------------------ Cycle 21: After refmac, R = 0.2051 (Rfree = 0.000) for 11051 atoms. Found 52 (52 requested) and removed 46 (26 requested) atoms. Cycle 22: After refmac, R = 0.2021 (Rfree = 0.000) for 10990 atoms. Found 52 (52 requested) and removed 43 (26 requested) atoms. Cycle 23: After refmac, R = 0.1976 (Rfree = 0.000) for 10948 atoms. Found 52 (52 requested) and removed 49 (26 requested) atoms. Cycle 24: After refmac, R = 0.1917 (Rfree = 0.000) for 10920 atoms. Found 51 (51 requested) and removed 52 (25 requested) atoms. Cycle 25: After refmac, R = 0.1803 (Rfree = 0.000) for 10894 atoms. Found 50 (51 requested) and removed 57 (25 requested) atoms. ------------------------------------------------------ Building Cycle 6 Atomic shape factors 3.51 3.28 Search for helices and strands: 0 residues in 0 chains, 11229 seeds are put forward NCS extension: 15 residues added (1 deleted due to clashes), 11244 seeds are put forward Round 1: 621 peptides, 110 chains. Longest chain 14 peptides. Score 0.355 Round 2: 658 peptides, 96 chains. Longest chain 16 peptides. Score 0.444 Round 3: 650 peptides, 96 chains. Longest chain 18 peptides. Score 0.437 Round 4: 666 peptides, 99 chains. Longest chain 19 peptides. Score 0.439 Round 5: 663 peptides, 97 chains. Longest chain 22 peptides. Score 0.444 Taking the results from Round 5 Chains 97, Residues 566, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 14900 reflections ( 99.71 % complete ) and 27154 restraints for refining 11053 atoms. 24987 conditional restraints added. Observations/parameters ratio is 0.34 ------------------------------------------------------ Cycle 26: After refmac, R = 0.2175 (Rfree = 0.000) for 11053 atoms. Found 52 (52 requested) and removed 42 (26 requested) atoms. Cycle 27: After refmac, R = 0.1993 (Rfree = 0.000) for 10973 atoms. Found 52 (52 requested) and removed 48 (26 requested) atoms. Cycle 28: After refmac, R = 0.1935 (Rfree = 0.000) for 10931 atoms. Found 52 (52 requested) and removed 42 (26 requested) atoms. Cycle 29: After refmac, R = 0.1923 (Rfree = 0.000) for 10914 atoms. Found 51 (51 requested) and removed 48 (25 requested) atoms. Cycle 30: After refmac, R = 0.1848 (Rfree = 0.000) for 10894 atoms. Found 51 (51 requested) and removed 46 (25 requested) atoms. ------------------------------------------------------ Building Cycle 7 Atomic shape factors 3.48 3.26 Search for helices and strands: 0 residues in 0 chains, 11236 seeds are put forward NCS extension: 30 residues added (1 deleted due to clashes), 11266 seeds are put forward Round 1: 546 peptides, 110 chains. Longest chain 12 peptides. Score 0.282 Round 2: 619 peptides, 105 chains. Longest chain 16 peptides. Score 0.374 Round 3: 641 peptides, 98 chains. Longest chain 17 peptides. Score 0.422 Round 4: 656 peptides, 105 chains. Longest chain 16 peptides. Score 0.407 Round 5: 656 peptides, 99 chains. Longest chain 21 peptides. Score 0.431 Taking the results from Round 5 Chains 101, Residues 557, Estimated correctness of the model 0.0 % 2 chains (25 residues) have been docked in sequence ------------------------------------------------------ 14900 reflections ( 99.71 % complete ) and 26949 restraints for refining 11050 atoms. 24710 conditional restraints added. Observations/parameters ratio is 0.34 ------------------------------------------------------ Cycle 31: After refmac, R = 0.2146 (Rfree = 0.000) for 11050 atoms. Found 52 (52 requested) and removed 34 (26 requested) atoms. Cycle 32: After refmac, R = 0.2091 (Rfree = 0.000) for 10983 atoms. Found 52 (52 requested) and removed 48 (26 requested) atoms. Cycle 33: After refmac, R = 0.1693 (Rfree = 0.000) for 10929 atoms. Found 21 (52 requested) and removed 27 (26 requested) atoms. Cycle 34: After refmac, R = 0.1615 (Rfree = 0.000) for 10873 atoms. Found 16 (51 requested) and removed 29 (25 requested) atoms. Cycle 35: After refmac, R = 0.1831 (Rfree = 0.000) for 10838 atoms. Found 51 (51 requested) and removed 36 (25 requested) atoms. ------------------------------------------------------ Building Cycle 8 Atomic shape factors 3.54 3.31 Search for helices and strands: 0 residues in 0 chains, 11214 seeds are put forward NCS extension: 19 residues added (0 deleted due to clashes), 11233 seeds are put forward Round 1: 538 peptides, 110 chains. Longest chain 11 peptides. Score 0.274 Round 2: 614 peptides, 105 chains. Longest chain 16 peptides. Score 0.369 Round 3: 589 peptides, 96 chains. Longest chain 20 peptides. Score 0.383 Round 4: 588 peptides, 89 chains. Longest chain 18 peptides. Score 0.410 Round 5: 622 peptides, 98 chains. Longest chain 21 peptides. Score 0.405 Taking the results from Round 4 Chains 89, Residues 499, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 14900 reflections ( 99.71 % complete ) and 27514 restraints for refining 11053 atoms. 25607 conditional restraints added. Observations/parameters ratio is 0.34 ------------------------------------------------------ Cycle 36: After refmac, R = 0.2123 (Rfree = 0.000) for 11053 atoms. Found 52 (52 requested) and removed 39 (26 requested) atoms. Cycle 37: After refmac, R = 0.2072 (Rfree = 0.000) for 11002 atoms. Found 52 (52 requested) and removed 48 (26 requested) atoms. Cycle 38: After refmac, R = 0.1637 (Rfree = 0.000) for 10979 atoms. Found 18 (52 requested) and removed 35 (26 requested) atoms. Cycle 39: After refmac, R = 0.1575 (Rfree = 0.000) for 10934 atoms. Found 34 (52 requested) and removed 35 (26 requested) atoms. Cycle 40: After refmac, R = 0.1564 (Rfree = 0.000) for 10920 atoms. Found 26 (51 requested) and removed 31 (25 requested) atoms. ------------------------------------------------------ Building Cycle 9 Atomic shape factors 3.57 3.34 Search for helices and strands: 0 residues in 0 chains, 11235 seeds are put forward NCS extension: 18 residues added (1 deleted due to clashes), 11253 seeds are put forward Round 1: 500 peptides, 99 chains. Longest chain 14 peptides. Score 0.283 Round 2: 575 peptides, 102 chains. Longest chain 15 peptides. Score 0.345 Round 3: 572 peptides, 94 chains. Longest chain 18 peptides. Score 0.375 Round 4: 590 peptides, 93 chains. Longest chain 18 peptides. Score 0.396 Round 5: 576 peptides, 94 chains. Longest chain 15 peptides. Score 0.379 Taking the results from Round 4 Chains 93, Residues 497, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 14900 reflections ( 99.71 % complete ) and 27383 restraints for refining 11052 atoms. 25488 conditional restraints added. Observations/parameters ratio is 0.34 ------------------------------------------------------ Cycle 41: After refmac, R = 0.1963 (Rfree = 0.000) for 11052 atoms. Found 52 (52 requested) and removed 42 (26 requested) atoms. Failed to save intermediate PDB Cycle 42: After refmac, R = 0.2016 (Rfree = 0.000) for 11009 atoms. Found 52 (52 requested) and removed 50 (26 requested) atoms. Cycle 43: After refmac, R = 0.1886 (Rfree = 0.000) for 10972 atoms. Found 52 (52 requested) and removed 42 (26 requested) atoms. Cycle 44: After refmac, R = 0.1869 (Rfree = 0.000) for 10958 atoms. Found 52 (52 requested) and removed 38 (26 requested) atoms. Cycle 45: After refmac, R = 0.1416 (Rfree = 0.000) for 10942 atoms. Found 14 (52 requested) and removed 37 (26 requested) atoms. ------------------------------------------------------ Building Cycle 10 Atomic shape factors 3.54 3.31 Search for helices and strands: 0 residues in 0 chains, 11247 seeds are put forward NCS extension: 22 residues added (0 deleted due to clashes), 11269 seeds are put forward Round 1: 500 peptides, 109 chains. Longest chain 9 peptides. Score 0.238 Round 2: 536 peptides, 98 chains. Longest chain 15 peptides. Score 0.323 Round 3: 569 peptides, 101 chains. Longest chain 15 peptides. Score 0.343 Round 4: 600 peptides, 102 chains. Longest chain 15 peptides. Score 0.368 Round 5: 584 peptides, 97 chains. Longest chain 18 peptides. Score 0.374 Taking the results from Round 5 Last building cycle: Chain fragments will be rearranged Chains 97, Residues 487, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence Sequence coverage is 0 % Consider running further cycles of model building using 2anu-4_warpNtrace.pdb as input ------------------------------------------------------ ---> Final restrained refinement block. No atom update. Failed to save intermediate PDB 14900 reflections ( 99.71 % complete ) and 27462 restraints for refining 11053 atoms. 25611 conditional restraints added. Observations/parameters ratio is 0.34 ------------------------------------------------------ Cycle 46: After refmac, R = 0.1969 (Rfree = 0.000) for 11053 atoms. Found 0 (52 requested) and removed 26 (26 requested) atoms. Cycle 47: After refmac, R = 0.2009 (Rfree = 0.000) for 10943 atoms. Found 0 (52 requested) and removed 26 (26 requested) atoms. Cycle 48: After refmac, R = 0.1920 (Rfree = 0.000) for 10873 atoms. Found 0 (51 requested) and removed 25 (25 requested) atoms. Cycle 49: After refmac, R = 0.2027 (Rfree = 0.000) for 10821 atoms. TimeTaking 135.85