Mon 24 Dec 07:52:13 GMT 2018 ############### You are running ARP/wARP 8.0 ############### Working directory /mnt/lustre/users/emra500/PipeliensFastaNoRFree/noncs/ArpWArp/wArpResults/WorkingDir Job ID is set to 1zkg-3.8-parrot-noncs X-ray data file /users/emra500/scratch/Dataset/noncsChltofom/1zkg-3.8-parrot-noncs.mtz Sequence file /users/emra500/scratch/Dataset/noncsChltofom/1zkg-3.8-parrot-noncs.fasta Tracing mode WARPNTRACEPHASES Creating directory /mnt/lustre/users/emra500/PipeliensFastaNoRFree/noncs/ArpWArp/wArpResults/WorkingDir/1zkg-3.8-parrot-noncs 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/noncs/ArpWArp/wArpResults/WorkingDir/1zkg-3.8-parrot-noncs/arp_warp_classic.par Job launched in /mnt/lustre/users/emra500/PipeliensFastaNoRFree/noncs/ArpWArp/wArpResults/WorkingDir/1zkg-3.8-parrot-noncs ############### 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 07:52:18 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/noncs/ArpWArp/wArpResults/WorkingDir/1zkg-3.8-parrot-noncs ARP/wARP software version: 8.0 The parameter file: /mnt/lustre/users/emra500/PipeliensFastaNoRFree/noncs/ArpWArp/wArpResults/WorkingDir/1zkg-3.8-parrot-noncs/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 299 and 0 Target number of residues in the AU: 299 Target solvent content: 0.6678 Checking the provided sequence file Detected sequence length: 212 Maximum limit of NCS related copies: 60 Number of NCS-related molecules: 2 Adjusted target number of residues: 424 Adjusted target solvent content: 0.53 Input MTZ file: 1zkg-3.8-parrot-noncs.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: 50.537 87.114 59.148 90.000 110.732 90.000 Input sequence file: 1zkg-3.8-parrot-noncs.fasta_lf Building free atoms model in initial map for 3392 target number of atoms Had to go as low as 0.75 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: 29.148 3.801 Wilson plot Bfac: 90.41 4788 reflections ( 99.75 % complete ) and 0 restraints for refining 3754 atoms. Observations/parameters ratio is 0.32 ------------------------------------------------------ Starting model: R = 0.3478 (Rfree = 0.000). ------------------------------------------------------ Cycle 0: After refmac, R = 0.3574 (Rfree = 0.000) for 3754 atoms. Found 20 (20 requested) and removed 22 (10 requested) atoms. ------------------------------------------------------ Building Cycle 1 Atomic shape factors 3.71 3.56 Search for helices and strands: 0 residues in 0 chains, 3863 seeds are put forward NCS extension: 0 residues added, 3863 seeds are put forward Round 1: 149 peptides, 33 chains. Longest chain 8 peptides. Score 0.236 Round 2: 193 peptides, 33 chains. Longest chain 10 peptides. Score 0.395 Round 3: 198 peptides, 30 chains. Longest chain 14 peptides. Score 0.453 Round 4: 176 peptides, 29 chains. Longest chain 14 peptides. Score 0.396 Round 5: 183 peptides, 31 chains. Longest chain 13 peptides. Score 0.390 Taking the results from Round 3 Chains 30, Residues 168, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 4788 reflections ( 99.75 % complete ) and 7582 restraints for refining 3068 atoms. 6940 conditional restraints added. Observations/parameters ratio is 0.39 ------------------------------------------------------ Cycle 1: After refmac, R = 0.2562 (Rfree = 0.000) for 3068 atoms. Found 16 (16 requested) and removed 24 (8 requested) atoms. Cycle 2: After refmac, R = 0.2279 (Rfree = 0.000) for 3020 atoms. Found 16 (16 requested) and removed 27 (8 requested) atoms. Cycle 3: After refmac, R = 0.2149 (Rfree = 0.000) for 2996 atoms. Found 12 (16 requested) and removed 17 (8 requested) atoms. Cycle 4: After refmac, R = 0.2084 (Rfree = 0.000) for 2972 atoms. Found 10 (16 requested) and removed 20 (8 requested) atoms. Cycle 5: After refmac, R = 0.2020 (Rfree = 0.000) for 2956 atoms. Found 9 (16 requested) and removed 15 (8 requested) atoms. ------------------------------------------------------ Building Cycle 2 Atomic shape factors 3.69 3.55 Search for helices and strands: 0 residues in 0 chains, 3129 seeds are put forward NCS extension: 12 residues added (2 deleted due to clashes), 3141 seeds are put forward Round 1: 164 peptides, 34 chains. Longest chain 9 peptides. Score 0.277 Round 2: 192 peptides, 30 chains. Longest chain 15 peptides. Score 0.434 Round 3: 200 peptides, 27 chains. Longest chain 13 peptides. Score 0.500 Round 4: 216 peptides, 29 chains. Longest chain 16 peptides. Score 0.520 Round 5: 207 peptides, 29 chains. Longest chain 16 peptides. Score 0.494 Taking the results from Round 4 Chains 29, Residues 187, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 4788 reflections ( 99.75 % complete ) and 6832 restraints for refining 2998 atoms. 6113 conditional restraints added. Observations/parameters ratio is 0.40 ------------------------------------------------------ Cycle 6: After refmac, R = 0.2286 (Rfree = 0.000) for 2998 atoms. Found 8 (16 requested) and removed 33 (8 requested) atoms. Cycle 7: After refmac, R = 0.1991 (Rfree = 0.000) for 2954 atoms. Found 8 (16 requested) and removed 15 (8 requested) atoms. Cycle 8: After refmac, R = 0.1892 (Rfree = 0.000) for 2940 atoms. Found 16 (16 requested) and removed 16 (8 requested) atoms. Cycle 9: After refmac, R = 0.1599 (Rfree = 0.000) for 2933 atoms. Found 4 (16 requested) and removed 13 (8 requested) atoms. Failed to save intermediate PDB Cycle 10: After refmac, R = 0.1617 (Rfree = 0.000) for 2920 atoms. Found 2 (16 requested) and removed 10 (8 requested) atoms. ------------------------------------------------------ Building Cycle 3 Atomic shape factors 3.67 3.53 Search for helices and strands: 0 residues in 0 chains, 3109 seeds are put forward NCS extension: 17 residues added (0 deleted due to clashes), 3126 seeds are put forward Round 1: 167 peptides, 33 chains. Longest chain 10 peptides. Score 0.304 Round 2: 194 peptides, 31 chains. Longest chain 14 peptides. Score 0.427 Round 3: 184 peptides, 28 chains. Longest chain 13 peptides. Score 0.437 Round 4: 195 peptides, 28 chains. Longest chain 15 peptides. Score 0.472 Round 5: 188 peptides, 28 chains. Longest chain 10 peptides. Score 0.450 Taking the results from Round 4 Chains 29, Residues 167, Estimated correctness of the model 0.0 % 1 chains (9 residues) have been docked in sequence ------------------------------------------------------ 4788 reflections ( 99.75 % complete ) and 7048 restraints for refining 3068 atoms. 6373 conditional restraints added. Observations/parameters ratio is 0.39 ------------------------------------------------------ Cycle 11: After refmac, R = 0.2128 (Rfree = 0.000) for 3068 atoms. Found 14 (16 requested) and removed 26 (8 requested) atoms. Cycle 12: After refmac, R = 0.1984 (Rfree = 0.000) for 3030 atoms. Found 8 (16 requested) and removed 17 (8 requested) atoms. Cycle 13: After refmac, R = 0.1933 (Rfree = 0.000) for 3015 atoms. Found 9 (16 requested) and removed 16 (8 requested) atoms. Cycle 14: After refmac, R = 0.1935 (Rfree = 0.000) for 3001 atoms. Found 11 (16 requested) and removed 18 (8 requested) atoms. Cycle 15: After refmac, R = 0.1915 (Rfree = 0.000) for 2985 atoms. Found 16 (16 requested) and removed 14 (8 requested) atoms. ------------------------------------------------------ Building Cycle 4 Atomic shape factors 3.70 3.55 Search for helices and strands: 0 residues in 0 chains, 3169 seeds are put forward NCS extension: 19 residues added (1 deleted due to clashes), 3188 seeds are put forward Round 1: 172 peptides, 34 chains. Longest chain 8 peptides. Score 0.307 Round 2: 184 peptides, 31 chains. Longest chain 10 peptides. Score 0.394 Round 3: 192 peptides, 31 chains. Longest chain 10 peptides. Score 0.420 Round 4: 182 peptides, 26 chains. Longest chain 11 peptides. Score 0.459 Round 5: 192 peptides, 30 chains. Longest chain 12 peptides. Score 0.434 Taking the results from Round 4 Chains 26, Residues 156, Estimated correctness of the model 0.0 % 1 chains (6 residues) have been docked in sequence ------------------------------------------------------ 4788 reflections ( 99.75 % complete ) and 7137 restraints for refining 3068 atoms. 6523 conditional restraints added. Observations/parameters ratio is 0.39 ------------------------------------------------------ Cycle 16: After refmac, R = 0.2347 (Rfree = 0.000) for 3068 atoms. Found 16 (16 requested) and removed 27 (8 requested) atoms. Cycle 17: After refmac, R = 0.2080 (Rfree = 0.000) for 3031 atoms. Found 16 (16 requested) and removed 18 (8 requested) atoms. Cycle 18: After refmac, R = 0.1620 (Rfree = 0.000) for 3012 atoms. Found 7 (16 requested) and removed 13 (8 requested) atoms. Cycle 19: After refmac, R = 0.1818 (Rfree = 0.000) for 2997 atoms. Found 6 (16 requested) and removed 15 (8 requested) atoms. Cycle 20: After refmac, R = 0.1912 (Rfree = 0.000) for 2983 atoms. Found 15 (16 requested) and removed 8 (8 requested) atoms. ------------------------------------------------------ Building Cycle 5 Atomic shape factors 3.71 3.56 Search for helices and strands: 0 residues in 0 chains, 3164 seeds are put forward NCS extension: 8 residues added (1 deleted due to clashes), 3172 seeds are put forward Round 1: 174 peptides, 35 chains. Longest chain 11 peptides. Score 0.299 Round 2: 191 peptides, 32 chains. Longest chain 13 peptides. Score 0.402 Round 3: 190 peptides, 29 chains. Longest chain 13 peptides. Score 0.442 Round 4: 200 peptides, 32 chains. Longest chain 17 peptides. Score 0.432 Round 5: 201 peptides, 30 chains. Longest chain 16 peptides. Score 0.463 Taking the results from Round 5 Chains 32, Residues 171, Estimated correctness of the model 0.0 % 1 chains (10 residues) have been docked in sequence ------------------------------------------------------ 4788 reflections ( 99.75 % complete ) and 7047 restraints for refining 3068 atoms. 6365 conditional restraints added. Observations/parameters ratio is 0.39 ------------------------------------------------------ Cycle 21: After refmac, R = 0.2321 (Rfree = 0.000) for 3068 atoms. Found 16 (16 requested) and removed 15 (8 requested) atoms. Cycle 22: After refmac, R = 0.1928 (Rfree = 0.000) for 3054 atoms. Found 7 (16 requested) and removed 14 (8 requested) atoms. Cycle 23: After refmac, R = 0.1908 (Rfree = 0.000) for 3039 atoms. Found 15 (16 requested) and removed 14 (8 requested) atoms. Cycle 24: After refmac, R = 0.1840 (Rfree = 0.000) for 3028 atoms. Found 11 (16 requested) and removed 11 (8 requested) atoms. Cycle 25: After refmac, R = 0.1829 (Rfree = 0.000) for 3018 atoms. Found 15 (16 requested) and removed 14 (8 requested) atoms. ------------------------------------------------------ Building Cycle 6 Atomic shape factors 3.67 3.53 Search for helices and strands: 0 residues in 0 chains, 3201 seeds are put forward NCS extension: 3 residues added (0 deleted due to clashes), 3204 seeds are put forward Round 1: 150 peptides, 29 chains. Longest chain 12 peptides. Score 0.304 Round 2: 169 peptides, 28 chains. Longest chain 14 peptides. Score 0.387 Round 3: 169 peptides, 29 chains. Longest chain 14 peptides. Score 0.372 Round 4: 168 peptides, 27 chains. Longest chain 13 peptides. Score 0.399 Round 5: 159 peptides, 27 chains. Longest chain 13 peptides. Score 0.368 Taking the results from Round 4 Chains 27, Residues 141, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 4788 reflections ( 99.75 % complete ) and 7325 restraints for refining 3068 atoms. 6788 conditional restraints added. Observations/parameters ratio is 0.39 ------------------------------------------------------ Cycle 26: After refmac, R = 0.2060 (Rfree = 0.000) for 3068 atoms. Found 16 (16 requested) and removed 14 (8 requested) atoms. Cycle 27: After refmac, R = 0.1973 (Rfree = 0.000) for 3055 atoms. Found 16 (16 requested) and removed 11 (8 requested) atoms. Cycle 28: After refmac, R = 0.2003 (Rfree = 0.000) for 3049 atoms. Found 16 (16 requested) and removed 11 (8 requested) atoms. Cycle 29: After refmac, R = 0.1967 (Rfree = 0.000) for 3046 atoms. Found 16 (16 requested) and removed 11 (8 requested) atoms. Cycle 30: After refmac, R = 0.1480 (Rfree = 0.000) for 3045 atoms. Found 4 (16 requested) and removed 10 (8 requested) atoms. ------------------------------------------------------ Building Cycle 7 Atomic shape factors 3.68 3.54 Search for helices and strands: 0 residues in 0 chains, 3212 seeds are put forward NCS extension: 10 residues added (1 deleted due to clashes), 3222 seeds are put forward Round 1: 137 peptides, 27 chains. Longest chain 8 peptides. Score 0.287 Round 2: 155 peptides, 29 chains. Longest chain 9 peptides. Score 0.322 Round 3: 159 peptides, 25 chains. Longest chain 15 peptides. Score 0.398 Round 4: 160 peptides, 26 chains. Longest chain 16 peptides. Score 0.387 Round 5: 162 peptides, 28 chains. Longest chain 11 peptides. Score 0.363 Taking the results from Round 3 Chains 25, Residues 134, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 4788 reflections ( 99.75 % complete ) and 7179 restraints for refining 3066 atoms. 6668 conditional restraints added. Observations/parameters ratio is 0.39 ------------------------------------------------------ Cycle 31: After refmac, R = 0.2016 (Rfree = 0.000) for 3066 atoms. Found 16 (16 requested) and removed 26 (8 requested) atoms. Cycle 32: After refmac, R = 0.1895 (Rfree = 0.000) for 3041 atoms. Found 15 (16 requested) and removed 21 (8 requested) atoms. Cycle 33: After refmac, R = 0.1860 (Rfree = 0.000) for 3026 atoms. Found 16 (16 requested) and removed 16 (8 requested) atoms. Cycle 34: After refmac, R = 0.1406 (Rfree = 0.000) for 3019 atoms. Found 6 (16 requested) and removed 12 (8 requested) atoms. Cycle 35: After refmac, R = 0.1502 (Rfree = 0.000) for 3011 atoms. Found 5 (16 requested) and removed 10 (8 requested) atoms. ------------------------------------------------------ Building Cycle 8 Atomic shape factors 3.73 3.58 Search for helices and strands: 0 residues in 0 chains, 3167 seeds are put forward NCS extension: 25 residues added (2 deleted due to clashes), 3192 seeds are put forward Round 1: 135 peptides, 29 chains. Longest chain 8 peptides. Score 0.246 Round 2: 152 peptides, 27 chains. Longest chain 13 peptides. Score 0.343 Round 3: 153 peptides, 26 chains. Longest chain 11 peptides. Score 0.362 Round 4: 153 peptides, 27 chains. Longest chain 11 peptides. Score 0.346 Round 5: 150 peptides, 26 chains. Longest chain 18 peptides. Score 0.351 Taking the results from Round 3 Chains 26, Residues 127, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 4788 reflections ( 99.75 % complete ) and 7227 restraints for refining 3058 atoms. 6745 conditional restraints added. Observations/parameters ratio is 0.39 ------------------------------------------------------ Cycle 36: After refmac, R = 0.1795 (Rfree = 0.000) for 3058 atoms. Found 16 (16 requested) and removed 19 (8 requested) atoms. Cycle 37: After refmac, R = 0.1716 (Rfree = 0.000) for 3043 atoms. Found 16 (16 requested) and removed 14 (8 requested) atoms. Cycle 38: After refmac, R = 0.1727 (Rfree = 0.000) for 3035 atoms. Found 16 (16 requested) and removed 16 (8 requested) atoms. Cycle 39: After refmac, R = 0.1757 (Rfree = 0.000) for 3032 atoms. Found 16 (16 requested) and removed 17 (8 requested) atoms. Cycle 40: After refmac, R = 0.1750 (Rfree = 0.000) for 3026 atoms. Found 16 (16 requested) and removed 17 (8 requested) atoms. ------------------------------------------------------ Building Cycle 9 Atomic shape factors 3.67 3.53 Search for helices and strands: 0 residues in 0 chains, 3178 seeds are put forward NCS extension: 11 residues added (1 deleted due to clashes), 3189 seeds are put forward Round 1: 120 peptides, 27 chains. Longest chain 6 peptides. Score 0.219 Round 2: 161 peptides, 32 chains. Longest chain 8 peptides. Score 0.297 Round 3: 157 peptides, 27 chains. Longest chain 10 peptides. Score 0.361 Round 4: 147 peptides, 25 chains. Longest chain 15 peptides. Score 0.356 Round 5: 151 peptides, 27 chains. Longest chain 15 peptides. Score 0.339 Taking the results from Round 3 Chains 27, Residues 130, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 4788 reflections ( 99.75 % complete ) and 7152 restraints for refining 3060 atoms. 6659 conditional restraints added. Observations/parameters ratio is 0.39 ------------------------------------------------------ Cycle 41: After refmac, R = 0.1855 (Rfree = 0.000) for 3060 atoms. Found 12 (16 requested) and removed 20 (8 requested) atoms. Cycle 42: After refmac, R = 0.1766 (Rfree = 0.000) for 3044 atoms. Found 16 (16 requested) and removed 16 (8 requested) atoms. Cycle 43: After refmac, R = 0.1768 (Rfree = 0.000) for 3039 atoms. Found 16 (16 requested) and removed 22 (8 requested) atoms. Cycle 44: After refmac, R = 0.1662 (Rfree = 0.000) for 3027 atoms. Found 11 (16 requested) and removed 13 (8 requested) atoms. Cycle 45: After refmac, R = 0.1647 (Rfree = 0.000) for 3012 atoms. Found 16 (16 requested) and removed 14 (8 requested) atoms. ------------------------------------------------------ Building Cycle 10 Atomic shape factors 3.68 3.54 Search for helices and strands: 0 residues in 0 chains, 3186 seeds are put forward NCS extension: 3 residues added (0 deleted due to clashes), 3189 seeds are put forward Round 1: 101 peptides, 19 chains. Longest chain 13 peptides. Score 0.281 Round 2: 130 peptides, 21 chains. Longest chain 13 peptides. Score 0.359 Round 3: 130 peptides, 20 chains. Longest chain 15 peptides. Score 0.376 Round 4: 136 peptides, 21 chains. Longest chain 15 peptides. Score 0.381 Round 5: 124 peptides, 19 chains. Longest chain 18 peptides. Score 0.370 Taking the results from Round 4 Last building cycle: Chain fragments will be rearranged Chains 21, Residues 115, 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 1zkg-3_warpNtrace.pdb as input ------------------------------------------------------ ---> Final restrained refinement block. No atom update. 4788 reflections ( 99.75 % complete ) and 7251 restraints for refining 3053 atoms. 6812 conditional restraints added. Observations/parameters ratio is 0.39 ------------------------------------------------------ Cycle 46: After refmac, R = 0.1914 (Rfree = 0.000) for 3053 atoms. Found 0 (16 requested) and removed 8 (8 requested) atoms. Cycle 47: After refmac, R = 0.2000 (Rfree = 0.000) for 3035 atoms. Found 0 (16 requested) and removed 8 (8 requested) atoms. Cycle 48: After refmac, R = 0.1872 (Rfree = 0.000) for 3025 atoms. Found 0 (16 requested) and removed 8 (8 requested) atoms. Cycle 49: After refmac, R = 0.1805 (Rfree = 0.000) for 3007 atoms. TimeTaking 35.3