Mon 24 Dec 01:00:08 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 2fur-3.8-parrot-mrncs X-ray data file /users/emra500/scratch/Dataset/mrncsChltofom/2fur-3.8-parrot-mrncs.mtz Sequence file /users/emra500/scratch/Dataset/mrncsChltofom/2fur-3.8-parrot-mrncs.fasta Tracing mode WARPNTRACEPHASES Creating directory /mnt/lustre/users/emra500/PipeliensFastaNoRFree/mrncs/ArpWArp/wArpResults/WorkingDir/2fur-3.8-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/2fur-3.8-parrot-mrncs/arp_warp_classic.par Job launched in /mnt/lustre/users/emra500/PipeliensFastaNoRFree/mrncs/ArpWArp/wArpResults/WorkingDir/2fur-3.8-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 01:00:13 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/2fur-3.8-parrot-mrncs ARP/wARP software version: 8.0 The parameter file: /mnt/lustre/users/emra500/PipeliensFastaNoRFree/mrncs/ArpWArp/wArpResults/WorkingDir/2fur-3.8-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 250 and 0 Target number of residues in the AU: 250 Target solvent content: 0.6674 Checking the provided sequence file Detected sequence length: 209 Maximum limit of NCS related copies: 60 Number of NCS-related molecules: 2 Adjusted target number of residues: 418 Adjusted target solvent content: 0.44 Input MTZ file: 2fur-3.8-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: 19 Cell parameters: 61.040 66.690 99.940 90.000 90.000 90.000 Input sequence file: 2fur-3.8-parrot-mrncs.fasta_lf Building free atoms model in initial map for 3344 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: 55.473 3.800 Wilson plot Bfac: 89.68 4300 reflections ( 99.54 % complete ) and 0 restraints for refining 3703 atoms. Observations/parameters ratio is 0.29 ------------------------------------------------------ Starting model: R = 0.3257 (Rfree = 0.000). ------------------------------------------------------ Cycle 0: After refmac, R = 0.2776 (Rfree = 0.000) for 3703 atoms. Found 13 (20 requested) and removed 28 (10 requested) atoms. ------------------------------------------------------ Building Cycle 1 Atomic shape factors 3.72 4.03 Search for helices and strands: 0 residues in 0 chains, 3751 seeds are put forward NCS extension: 0 residues added, 3751 seeds are put forward Round 1: 146 peptides, 28 chains. Longest chain 12 peptides. Score 0.324 Round 2: 208 peptides, 34 chains. Longest chain 15 peptides. Score 0.467 Round 3: 231 peptides, 34 chains. Longest chain 18 peptides. Score 0.545 Round 4: 227 peptides, 29 chains. Longest chain 15 peptides. Score 0.600 Round 5: 222 peptides, 30 chains. Longest chain 22 peptides. Score 0.572 Taking the results from Round 4 Chains 29, Residues 198, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 4300 reflections ( 99.54 % complete ) and 7007 restraints for refining 3018 atoms. 6244 conditional restraints added. Observations/parameters ratio is 0.36 ------------------------------------------------------ Cycle 1: After refmac, R = 0.2414 (Rfree = 0.000) for 3018 atoms. Found 5 (16 requested) and removed 30 (8 requested) atoms. Cycle 2: After refmac, R = 0.2401 (Rfree = 0.000) for 2944 atoms. Found 7 (16 requested) and removed 24 (8 requested) atoms. Cycle 3: After refmac, R = 0.2226 (Rfree = 0.000) for 2898 atoms. Found 8 (16 requested) and removed 22 (8 requested) atoms. Cycle 4: After refmac, R = 0.2167 (Rfree = 0.000) for 2868 atoms. Found 10 (15 requested) and removed 11 (7 requested) atoms. Cycle 5: After refmac, R = 0.2009 (Rfree = 0.000) for 2855 atoms. Found 6 (15 requested) and removed 15 (7 requested) atoms. ------------------------------------------------------ Building Cycle 2 Atomic shape factors 3.70 4.01 Search for helices and strands: 0 residues in 0 chains, 2948 seeds are put forward NCS extension: 14 residues added (3 deleted due to clashes), 2962 seeds are put forward Round 1: 172 peptides, 33 chains. Longest chain 10 peptides. Score 0.344 Round 2: 200 peptides, 33 chains. Longest chain 11 peptides. Score 0.453 Round 3: 203 peptides, 29 chains. Longest chain 14 peptides. Score 0.525 Round 4: 200 peptides, 31 chains. Longest chain 15 peptides. Score 0.485 Round 5: 225 peptides, 30 chains. Longest chain 18 peptides. Score 0.581 Taking the results from Round 5 Chains 30, Residues 195, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 4300 reflections ( 99.54 % complete ) and 6720 restraints for refining 2922 atoms. 5970 conditional restraints added. Observations/parameters ratio is 0.37 ------------------------------------------------------ Cycle 6: After refmac, R = 0.2064 (Rfree = 0.000) for 2922 atoms. Found 3 (16 requested) and removed 25 (8 requested) atoms. Cycle 7: After refmac, R = 0.1942 (Rfree = 0.000) for 2878 atoms. Found 5 (15 requested) and removed 14 (7 requested) atoms. Cycle 8: After refmac, R = 0.1947 (Rfree = 0.000) for 2865 atoms. Found 2 (15 requested) and removed 10 (7 requested) atoms. Cycle 9: After refmac, R = 0.1904 (Rfree = 0.000) for 2849 atoms. Found 2 (15 requested) and removed 13 (7 requested) atoms. Cycle 10: After refmac, R = 0.1747 (Rfree = 0.000) for 2834 atoms. Found 3 (15 requested) and removed 9 (7 requested) atoms. ------------------------------------------------------ Building Cycle 3 Atomic shape factors 3.67 3.98 Search for helices and strands: 0 residues in 0 chains, 2945 seeds are put forward NCS extension: 28 residues added (0 deleted due to clashes), 2973 seeds are put forward Round 1: 180 peptides, 32 chains. Longest chain 11 peptides. Score 0.394 Round 2: 220 peptides, 33 chains. Longest chain 18 peptides. Score 0.523 Round 3: 227 peptides, 31 chains. Longest chain 15 peptides. Score 0.573 Round 4: 220 peptides, 34 chains. Longest chain 17 peptides. Score 0.509 Round 5: 231 peptides, 33 chains. Longest chain 15 peptides. Score 0.558 Taking the results from Round 3 Chains 34, Residues 196, Estimated correctness of the model 0.0 % 3 chains (27 residues) have been docked in sequence ------------------------------------------------------ 4300 reflections ( 99.54 % complete ) and 6581 restraints for refining 3022 atoms. 5730 conditional restraints added. Observations/parameters ratio is 0.36 ------------------------------------------------------ Cycle 11: After refmac, R = 0.1930 (Rfree = 0.000) for 3022 atoms. Found 7 (16 requested) and removed 21 (8 requested) atoms. Cycle 12: After refmac, R = 0.1772 (Rfree = 0.000) for 2984 atoms. Found 6 (16 requested) and removed 16 (8 requested) atoms. Cycle 13: After refmac, R = 0.1754 (Rfree = 0.000) for 2959 atoms. Found 6 (16 requested) and removed 12 (8 requested) atoms. Cycle 14: After refmac, R = 0.1724 (Rfree = 0.000) for 2941 atoms. Found 5 (16 requested) and removed 10 (8 requested) atoms. Cycle 15: After refmac, R = 0.1649 (Rfree = 0.000) for 2929 atoms. Found 1 (16 requested) and removed 14 (8 requested) atoms. ------------------------------------------------------ Building Cycle 4 Atomic shape factors 3.71 4.02 Search for helices and strands: 0 residues in 0 chains, 3026 seeds are put forward NCS extension: 13 residues added (1 deleted due to clashes), 3039 seeds are put forward Round 1: 172 peptides, 32 chains. Longest chain 9 peptides. Score 0.362 Round 2: 199 peptides, 33 chains. Longest chain 13 peptides. Score 0.450 Round 3: 203 peptides, 31 chains. Longest chain 18 peptides. Score 0.495 Round 4: 218 peptides, 34 chains. Longest chain 23 peptides. Score 0.502 Round 5: 222 peptides, 32 chains. Longest chain 14 peptides. Score 0.544 Taking the results from Round 5 Chains 33, Residues 190, Estimated correctness of the model 0.0 % 2 chains (18 residues) have been docked in sequence ------------------------------------------------------ 4300 reflections ( 99.54 % complete ) and 6752 restraints for refining 3024 atoms. 5958 conditional restraints added. Observations/parameters ratio is 0.36 ------------------------------------------------------ Cycle 16: After refmac, R = 0.1994 (Rfree = 0.000) for 3024 atoms. Found 9 (16 requested) and removed 15 (8 requested) atoms. Cycle 17: After refmac, R = 0.1773 (Rfree = 0.000) for 3009 atoms. Found 2 (16 requested) and removed 13 (8 requested) atoms. Cycle 18: After refmac, R = 0.1810 (Rfree = 0.000) for 2994 atoms. Found 2 (16 requested) and removed 11 (8 requested) atoms. Cycle 19: After refmac, R = 0.1755 (Rfree = 0.000) for 2979 atoms. Found 6 (16 requested) and removed 12 (8 requested) atoms. Cycle 20: After refmac, R = 0.1715 (Rfree = 0.000) for 2967 atoms. Found 3 (16 requested) and removed 11 (8 requested) atoms. ------------------------------------------------------ Building Cycle 5 Atomic shape factors 3.69 4.00 Search for helices and strands: 0 residues in 0 chains, 3050 seeds are put forward NCS extension: 17 residues added (0 deleted due to clashes), 3067 seeds are put forward Round 1: 162 peptides, 29 chains. Longest chain 11 peptides. Score 0.373 Round 2: 178 peptides, 27 chains. Longest chain 14 peptides. Score 0.468 Round 3: 181 peptides, 23 chains. Longest chain 23 peptides. Score 0.541 Round 4: 177 peptides, 25 chains. Longest chain 19 peptides. Score 0.497 Round 5: 193 peptides, 26 chains. Longest chain 18 peptides. Score 0.536 Taking the results from Round 3 Chains 23, Residues 158, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 4300 reflections ( 99.54 % complete ) and 7198 restraints for refining 3024 atoms. 6589 conditional restraints added. Observations/parameters ratio is 0.36 ------------------------------------------------------ Cycle 21: After refmac, R = 0.1814 (Rfree = 0.000) for 3024 atoms. Found 6 (16 requested) and removed 17 (8 requested) atoms. Cycle 22: After refmac, R = 0.1771 (Rfree = 0.000) for 3009 atoms. Found 8 (16 requested) and removed 12 (8 requested) atoms. Failed to save intermediate PDB Cycle 23: After refmac, R = 0.1740 (Rfree = 0.000) for 3001 atoms. Found 1 (16 requested) and removed 9 (8 requested) atoms. Cycle 24: After refmac, R = 0.1776 (Rfree = 0.000) for 2986 atoms. Found 6 (16 requested) and removed 11 (8 requested) atoms. Cycle 25: After refmac, R = 0.1781 (Rfree = 0.000) for 2980 atoms. Found 4 (16 requested) and removed 9 (8 requested) atoms. ------------------------------------------------------ Building Cycle 6 Atomic shape factors 3.70 4.01 Search for helices and strands: 0 residues in 0 chains, 3063 seeds are put forward NCS extension: 27 residues added (3 deleted due to clashes), 3090 seeds are put forward Round 1: 154 peptides, 32 chains. Longest chain 10 peptides. Score 0.286 Round 2: 171 peptides, 27 chains. Longest chain 19 peptides. Score 0.442 Round 3: 166 peptides, 28 chains. Longest chain 16 peptides. Score 0.406 Round 4: 167 peptides, 27 chains. Longest chain 12 peptides. Score 0.427 Round 5: 171 peptides, 29 chains. Longest chain 13 peptides. Score 0.409 Taking the results from Round 2 Chains 27, Residues 144, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 4300 reflections ( 99.54 % complete ) and 7261 restraints for refining 3011 atoms. 6712 conditional restraints added. Observations/parameters ratio is 0.36 ------------------------------------------------------ Cycle 26: After refmac, R = 0.1801 (Rfree = 0.000) for 3011 atoms. Found 8 (16 requested) and removed 15 (8 requested) atoms. Cycle 27: After refmac, R = 0.1700 (Rfree = 0.000) for 2991 atoms. Found 6 (16 requested) and removed 11 (8 requested) atoms. Cycle 28: After refmac, R = 0.1634 (Rfree = 0.000) for 2982 atoms. Found 7 (16 requested) and removed 11 (8 requested) atoms. Cycle 29: After refmac, R = 0.1498 (Rfree = 0.000) for 2978 atoms. Found 4 (16 requested) and removed 10 (8 requested) atoms. Cycle 30: After refmac, R = 0.1607 (Rfree = 0.000) for 2969 atoms. Found 4 (16 requested) and removed 11 (8 requested) atoms. ------------------------------------------------------ Building Cycle 7 Atomic shape factors 3.71 4.02 Search for helices and strands: 0 residues in 0 chains, 3054 seeds are put forward NCS extension: 36 residues added (0 deleted due to clashes), 3090 seeds are put forward Round 1: 142 peptides, 31 chains. Longest chain 7 peptides. Score 0.251 Round 2: 161 peptides, 29 chains. Longest chain 11 peptides. Score 0.369 Round 3: 161 peptides, 29 chains. Longest chain 10 peptides. Score 0.369 Round 4: 164 peptides, 28 chains. Longest chain 9 peptides. Score 0.398 Round 5: 182 peptides, 31 chains. Longest chain 11 peptides. Score 0.418 Taking the results from Round 5 Chains 31, Residues 151, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 4300 reflections ( 99.54 % complete ) and 7262 restraints for refining 3024 atoms. 6689 conditional restraints added. Observations/parameters ratio is 0.36 ------------------------------------------------------ Cycle 31: After refmac, R = 0.1758 (Rfree = 0.000) for 3024 atoms. Found 6 (16 requested) and removed 12 (8 requested) atoms. Cycle 32: After refmac, R = 0.1587 (Rfree = 0.000) for 3005 atoms. Found 4 (16 requested) and removed 12 (8 requested) atoms. Cycle 33: After refmac, R = 0.1518 (Rfree = 0.000) for 2995 atoms. Found 1 (16 requested) and removed 9 (8 requested) atoms. Cycle 34: After refmac, R = 0.1916 (Rfree = 0.000) for 2981 atoms. Found 6 (16 requested) and removed 8 (8 requested) atoms. Cycle 35: After refmac, R = 0.1675 (Rfree = 0.000) for 2971 atoms. Found 4 (16 requested) and removed 13 (8 requested) atoms. ------------------------------------------------------ Building Cycle 8 Atomic shape factors 3.65 3.96 Search for helices and strands: 0 residues in 0 chains, 3048 seeds are put forward NCS extension: 6 residues added (0 deleted due to clashes), 3054 seeds are put forward Round 1: 134 peptides, 30 chains. Longest chain 7 peptides. Score 0.233 Round 2: 155 peptides, 30 chains. Longest chain 9 peptides. Score 0.326 Round 3: 161 peptides, 29 chains. Longest chain 12 peptides. Score 0.369 Round 4: 163 peptides, 29 chains. Longest chain 9 peptides. Score 0.377 Round 5: 163 peptides, 30 chains. Longest chain 10 peptides. Score 0.360 Taking the results from Round 4 Chains 29, Residues 134, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 4300 reflections ( 99.54 % complete ) and 7119 restraints for refining 3024 atoms. 6612 conditional restraints added. Observations/parameters ratio is 0.36 ------------------------------------------------------ Cycle 36: After refmac, R = 0.1677 (Rfree = 0.000) for 3024 atoms. Found 7 (16 requested) and removed 14 (8 requested) atoms. Cycle 37: After refmac, R = 0.2385 (Rfree = 0.000) for 3001 atoms. Found 16 (16 requested) and removed 16 (8 requested) atoms. Cycle 38: After refmac, R = 0.1588 (Rfree = 0.000) for 2982 atoms. Found 9 (16 requested) and removed 13 (8 requested) atoms. Cycle 39: After refmac, R = 0.1480 (Rfree = 0.000) for 2970 atoms. Found 6 (16 requested) and removed 8 (8 requested) atoms. Cycle 40: After refmac, R = 0.2223 (Rfree = 0.000) for 2959 atoms. Found 16 (16 requested) and removed 17 (8 requested) atoms. ------------------------------------------------------ Building Cycle 9 Atomic shape factors 3.65 3.96 Search for helices and strands: 0 residues in 0 chains, 3073 seeds are put forward NCS extension: 0 residues added, 3073 seeds are put forward Round 1: 127 peptides, 28 chains. Longest chain 8 peptides. Score 0.239 Round 2: 138 peptides, 27 chains. Longest chain 9 peptides. Score 0.308 Round 3: 149 peptides, 28 chains. Longest chain 14 peptides. Score 0.337 Round 4: 155 peptides, 29 chains. Longest chain 9 peptides. Score 0.344 Round 5: 157 peptides, 29 chains. Longest chain 15 peptides. Score 0.353 Taking the results from Round 5 Chains 29, Residues 128, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 4300 reflections ( 99.54 % complete ) and 7238 restraints for refining 3024 atoms. 6755 conditional restraints added. Observations/parameters ratio is 0.36 ------------------------------------------------------ Cycle 41: After refmac, R = 0.1676 (Rfree = 0.000) for 3024 atoms. Found 9 (16 requested) and removed 14 (8 requested) atoms. Cycle 42: After refmac, R = 0.1630 (Rfree = 0.000) for 2999 atoms. Found 9 (16 requested) and removed 16 (8 requested) atoms. Cycle 43: After refmac, R = 0.1503 (Rfree = 0.000) for 2987 atoms. Found 9 (16 requested) and removed 10 (8 requested) atoms. Cycle 44: After refmac, R = 0.1474 (Rfree = 0.000) for 2982 atoms. Found 6 (16 requested) and removed 8 (8 requested) atoms. Cycle 45: After refmac, R = 0.1349 (Rfree = 0.000) for 2978 atoms. Found 3 (16 requested) and removed 10 (8 requested) atoms. ------------------------------------------------------ Building Cycle 10 Atomic shape factors 3.66 3.97 Search for helices and strands: 0 residues in 0 chains, 3045 seeds are put forward NCS extension: 12 residues added (3 deleted due to clashes), 3057 seeds are put forward Round 1: 126 peptides, 28 chains. Longest chain 8 peptides. Score 0.234 Round 2: 142 peptides, 26 chains. Longest chain 9 peptides. Score 0.344 Round 3: 135 peptides, 23 chains. Longest chain 15 peptides. Score 0.369 Round 4: 134 peptides, 24 chains. Longest chain 12 peptides. Score 0.346 Round 5: 133 peptides, 23 chains. Longest chain 14 peptides. Score 0.360 Taking the results from Round 3 Last building cycle: Chain fragments will be rearranged Chains 23, Residues 112, 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 2fur-3_warpNtrace.pdb as input ------------------------------------------------------ ---> Final restrained refinement block. No atom update. 4300 reflections ( 99.54 % complete ) and 7135 restraints for refining 2995 atoms. 6710 conditional restraints added. Observations/parameters ratio is 0.36 ------------------------------------------------------ Cycle 46: After refmac, R = 0.1588 (Rfree = 0.000) for 2995 atoms. Found 0 (16 requested) and removed 8 (8 requested) atoms. Cycle 47: After refmac, R = 0.1476 (Rfree = 0.000) for 2981 atoms. Found 0 (16 requested) and removed 8 (8 requested) atoms. Cycle 48: After refmac, R = 0.1341 (Rfree = 0.000) for 2971 atoms. Found 0 (16 requested) and removed 8 (8 requested) atoms. Failed to save intermediate PDB Cycle 49: After refmac, R = 0.1573 (Rfree = 0.000) for 2961 atoms. Found 0 (16 requested) and removed 8 (8 requested) atoms. Writing output files ... TimeTaking 37.58