Sun 23 Dec 22:22:50 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 2oyo-3.2-parrot-hancs X-ray data file /users/emra500/scratch/Dataset/hancsChltofom/2oyo-3.2-parrot-hancs.mtz Sequence file /users/emra500/scratch/Dataset/hancsChltofom/2oyo-3.2-parrot-hancs.fasta Tracing mode WARPNTRACEPHASES Creating directory /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/2oyo-3.2-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/2oyo-3.2-parrot-hancs/arp_warp_classic.par Job launched in /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/2oyo-3.2-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 22:22:59 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/2oyo-3.2-parrot-hancs ARP/wARP software version: 8.0 The parameter file: /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/2oyo-3.2-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 288 and 0 Target number of residues in the AU: 288 Target solvent content: 0.6274 Checking the provided sequence file Detected sequence length: 196 Maximum limit of NCS related copies: 60 Number of NCS-related molecules: 2 Adjusted target number of residues: 392 Adjusted target solvent content: 0.49 Input MTZ file: 2oyo-3.2-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: 155 Cell parameters: 135.664 135.664 118.109 90.000 90.000 120.000 Input sequence file: 2oyo-3.2-parrot-hancs.fasta_lf Building free atoms model in initial map for 3136 target number of atoms Had to go as low as 0.80 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: 83.295 3.200 Wilson plot Bfac: 64.87 7050 reflections ( 99.87 % complete ) and 0 restraints for refining 3454 atoms. Observations/parameters ratio is 0.51 ------------------------------------------------------ Starting model: R = 0.3113 (Rfree = 0.000). ------------------------------------------------------ Cycle 0: After refmac, R = 0.2453 (Rfree = 0.000) for 3454 atoms. Found 25 (30 requested) and removed 23 (15 requested) atoms. ------------------------------------------------------ Building Cycle 1 Atomic shape factors 3.15 3.19 Search for helices and strands: 0 residues in 0 chains, 3551 seeds are put forward NCS extension: 0 residues added, 3551 seeds are put forward Round 1: 198 peptides, 37 chains. Longest chain 11 peptides. Score 0.377 Round 2: 233 peptides, 34 chains. Longest chain 13 peptides. Score 0.543 Round 3: 251 peptides, 36 chains. Longest chain 13 peptides. Score 0.571 Round 4: 247 peptides, 32 chains. Longest chain 13 peptides. Score 0.611 Round 5: 250 peptides, 33 chains. Longest chain 15 peptides. Score 0.607 Taking the results from Round 4 Chains 32, Residues 215, Estimated correctness of the model 44.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 7050 reflections ( 99.87 % complete ) and 6336 restraints for refining 2862 atoms. 5508 conditional restraints added. Observations/parameters ratio is 0.62 ------------------------------------------------------ Cycle 1: After refmac, R = 0.2345 (Rfree = 0.000) for 2862 atoms. Found 14 (25 requested) and removed 16 (12 requested) atoms. Cycle 2: After refmac, R = 0.2173 (Rfree = 0.000) for 2835 atoms. Found 7 (25 requested) and removed 14 (12 requested) atoms. Cycle 3: After refmac, R = 0.2075 (Rfree = 0.000) for 2817 atoms. Found 2 (25 requested) and removed 13 (12 requested) atoms. Cycle 4: After refmac, R = 0.2032 (Rfree = 0.000) for 2799 atoms. Found 5 (25 requested) and removed 13 (12 requested) atoms. Cycle 5: After refmac, R = 0.1991 (Rfree = 0.000) for 2791 atoms. Found 1 (25 requested) and removed 12 (12 requested) atoms. ------------------------------------------------------ Building Cycle 2 Atomic shape factors 3.15 3.19 Search for helices and strands: 0 residues in 0 chains, 2919 seeds are put forward NCS extension: 8 residues added (1 deleted due to clashes), 2927 seeds are put forward Round 1: 243 peptides, 33 chains. Longest chain 23 peptides. Score 0.587 Round 2: 251 peptides, 30 chains. Longest chain 18 peptides. Score 0.645 Round 3: 271 peptides, 33 chains. Longest chain 23 peptides. Score 0.661 Round 4: 265 peptides, 30 chains. Longest chain 18 peptides. Score 0.680 Round 5: 281 peptides, 29 chains. Longest chain 23 peptides. Score 0.725 Taking the results from Round 5 Chains 33, Residues 252, Estimated correctness of the model 70.3 % 5 chains (61 residues) have been docked in sequence Building loops using Loopy2018 Built loop between residues 87 A and 98 A 30 chains (255 residues) following loop building 4 chains (71 residues) in sequence following loop building ------------------------------------------------------ 7050 reflections ( 99.87 % complete ) and 5512 restraints for refining 2863 atoms. 4293 conditional restraints added. Observations/parameters ratio is 0.62 ------------------------------------------------------ Cycle 6: After refmac, R = 0.2446 (Rfree = 0.000) for 2863 atoms. Found 18 (25 requested) and removed 21 (12 requested) atoms. Cycle 7: After refmac, R = 0.2279 (Rfree = 0.000) for 2855 atoms. Found 11 (24 requested) and removed 17 (12 requested) atoms. Cycle 8: After refmac, R = 0.2200 (Rfree = 0.000) for 2843 atoms. Found 5 (24 requested) and removed 12 (12 requested) atoms. Cycle 9: After refmac, R = 0.2141 (Rfree = 0.000) for 2833 atoms. Found 3 (23 requested) and removed 13 (12 requested) atoms. Cycle 10: After refmac, R = 0.2109 (Rfree = 0.000) for 2821 atoms. Found 5 (23 requested) and removed 12 (12 requested) atoms. ------------------------------------------------------ Building Cycle 3 Atomic shape factors 3.16 3.20 Search for helices and strands: 0 residues in 0 chains, 2920 seeds are put forward NCS extension: 41 residues added (1 deleted due to clashes), 2961 seeds are put forward Round 1: 244 peptides, 32 chains. Longest chain 26 peptides. Score 0.602 Round 2: 253 peptides, 27 chains. Longest chain 42 peptides. Score 0.684 Round 3: 244 peptides, 30 chains. Longest chain 37 peptides. Score 0.627 Round 4: 236 peptides, 26 chains. Longest chain 33 peptides. Score 0.654 Round 5: 229 peptides, 29 chains. Longest chain 17 peptides. Score 0.598 Taking the results from Round 2 Chains 31, Residues 226, Estimated correctness of the model 61.7 % 4 chains (48 residues) have been docked in sequence ------------------------------------------------------ 7050 reflections ( 99.87 % complete ) and 5924 restraints for refining 2863 atoms. 4872 conditional restraints added. Observations/parameters ratio is 0.62 ------------------------------------------------------ Cycle 11: After refmac, R = 0.2265 (Rfree = 0.000) for 2863 atoms. Found 13 (22 requested) and removed 19 (12 requested) atoms. Cycle 12: After refmac, R = 0.2105 (Rfree = 0.000) for 2851 atoms. Found 5 (22 requested) and removed 12 (12 requested) atoms. Cycle 13: After refmac, R = 0.2047 (Rfree = 0.000) for 2843 atoms. Found 4 (22 requested) and removed 12 (12 requested) atoms. Cycle 14: After refmac, R = 0.2016 (Rfree = 0.000) for 2835 atoms. Found 2 (22 requested) and removed 12 (12 requested) atoms. Cycle 15: After refmac, R = 0.2037 (Rfree = 0.000) for 2822 atoms. Found 3 (22 requested) and removed 12 (12 requested) atoms. ------------------------------------------------------ Building Cycle 4 Atomic shape factors 3.20 3.24 Search for helices and strands: 0 residues in 0 chains, 2940 seeds are put forward NCS extension: 15 residues added (7 deleted due to clashes), 2955 seeds are put forward Round 1: 227 peptides, 37 chains. Longest chain 19 peptides. Score 0.481 Round 2: 250 peptides, 32 chains. Longest chain 23 peptides. Score 0.619 Round 3: 256 peptides, 35 chains. Longest chain 23 peptides. Score 0.599 Round 4: 258 peptides, 30 chains. Longest chain 26 peptides. Score 0.663 Round 5: 245 peptides, 33 chains. Longest chain 20 peptides. Score 0.592 Taking the results from Round 4 Chains 30, Residues 228, Estimated correctness of the model 56.9 % 1 chains (8 residues) have been docked in sequence ------------------------------------------------------ 7050 reflections ( 99.87 % complete ) and 6376 restraints for refining 2862 atoms. 5470 conditional restraints added. Observations/parameters ratio is 0.62 ------------------------------------------------------ Cycle 16: After refmac, R = 0.2282 (Rfree = 0.000) for 2862 atoms. Found 20 (22 requested) and removed 13 (12 requested) atoms. Cycle 17: After refmac, R = 0.2156 (Rfree = 0.000) for 2863 atoms. Found 8 (22 requested) and removed 12 (12 requested) atoms. Cycle 18: After refmac, R = 0.2062 (Rfree = 0.000) for 2856 atoms. Found 3 (22 requested) and removed 12 (12 requested) atoms. Cycle 19: After refmac, R = 0.2039 (Rfree = 0.000) for 2840 atoms. Found 6 (22 requested) and removed 12 (12 requested) atoms. Cycle 20: After refmac, R = 0.2166 (Rfree = 0.000) for 2831 atoms. Found 2 (22 requested) and removed 12 (12 requested) atoms. ------------------------------------------------------ Building Cycle 5 Atomic shape factors 3.14 3.18 Search for helices and strands: 0 residues in 0 chains, 2970 seeds are put forward NCS extension: 40 residues added (4 deleted due to clashes), 3010 seeds are put forward Round 1: 234 peptides, 38 chains. Longest chain 13 peptides. Score 0.491 Round 2: 260 peptides, 37 chains. Longest chain 18 peptides. Score 0.585 Round 3: 259 peptides, 33 chains. Longest chain 23 peptides. Score 0.631 Round 4: 254 peptides, 33 chains. Longest chain 16 peptides. Score 0.618 Round 5: 260 peptides, 28 chains. Longest chain 36 peptides. Score 0.689 Taking the results from Round 5 Chains 29, Residues 232, Estimated correctness of the model 62.8 % 2 chains (18 residues) have been docked in sequence ------------------------------------------------------ 7050 reflections ( 99.87 % complete ) and 6236 restraints for refining 2863 atoms. 5271 conditional restraints added. Observations/parameters ratio is 0.62 ------------------------------------------------------ Cycle 21: After refmac, R = 0.2337 (Rfree = 0.000) for 2863 atoms. Found 14 (22 requested) and removed 14 (12 requested) atoms. Cycle 22: After refmac, R = 0.2175 (Rfree = 0.000) for 2861 atoms. Found 6 (22 requested) and removed 12 (12 requested) atoms. Cycle 23: After refmac, R = 0.2122 (Rfree = 0.000) for 2852 atoms. Found 5 (22 requested) and removed 16 (12 requested) atoms. Cycle 24: After refmac, R = 0.2022 (Rfree = 0.000) for 2839 atoms. Found 4 (22 requested) and removed 13 (12 requested) atoms. Cycle 25: After refmac, R = 0.2028 (Rfree = 0.000) for 2828 atoms. Found 2 (22 requested) and removed 12 (12 requested) atoms. ------------------------------------------------------ Building Cycle 6 Atomic shape factors 3.18 3.22 Search for helices and strands: 0 residues in 0 chains, 2947 seeds are put forward NCS extension: 34 residues added (9 deleted due to clashes), 2981 seeds are put forward Round 1: 214 peptides, 29 chains. Longest chain 26 peptides. Score 0.553 Round 2: 235 peptides, 28 chains. Longest chain 31 peptides. Score 0.627 Round 3: 231 peptides, 28 chains. Longest chain 24 peptides. Score 0.616 Round 4: 257 peptides, 26 chains. Longest chain 38 peptides. Score 0.704 Round 5: 239 peptides, 29 chains. Longest chain 24 peptides. Score 0.626 Taking the results from Round 4 Chains 28, Residues 231, Estimated correctness of the model 66.0 % 3 chains (30 residues) have been docked in sequence Building loops using Loopy2018 28 chains (231 residues) following loop building 3 chains (30 residues) in sequence following loop building ------------------------------------------------------ 7050 reflections ( 99.87 % complete ) and 6010 restraints for refining 2863 atoms. 5016 conditional restraints added. Observations/parameters ratio is 0.62 ------------------------------------------------------ Cycle 26: After refmac, R = 0.2123 (Rfree = 0.000) for 2863 atoms. Found 9 (22 requested) and removed 14 (12 requested) atoms. Cycle 27: After refmac, R = 0.2045 (Rfree = 0.000) for 2856 atoms. Found 5 (22 requested) and removed 12 (12 requested) atoms. Cycle 28: After refmac, R = 0.1985 (Rfree = 0.000) for 2847 atoms. Found 3 (21 requested) and removed 12 (12 requested) atoms. Cycle 29: After refmac, R = 0.2089 (Rfree = 0.000) for 2837 atoms. Found 13 (21 requested) and removed 13 (12 requested) atoms. Cycle 30: After refmac, R = 0.2119 (Rfree = 0.000) for 2831 atoms. Found 15 (20 requested) and removed 14 (12 requested) atoms. ------------------------------------------------------ Building Cycle 7 Atomic shape factors 3.16 3.20 Search for helices and strands: 0 residues in 0 chains, 2979 seeds are put forward NCS extension: 15 residues added (1 deleted due to clashes), 2994 seeds are put forward Round 1: 221 peptides, 31 chains. Longest chain 19 peptides. Score 0.547 Round 2: 228 peptides, 29 chains. Longest chain 23 peptides. Score 0.595 Round 3: 240 peptides, 30 chains. Longest chain 22 peptides. Score 0.616 Round 4: 237 peptides, 24 chains. Longest chain 29 peptides. Score 0.679 Round 5: 230 peptides, 28 chains. Longest chain 18 peptides. Score 0.613 Taking the results from Round 4 Chains 29, Residues 213, Estimated correctness of the model 60.6 % 4 chains (46 residues) have been docked in sequence ------------------------------------------------------ 7050 reflections ( 99.87 % complete ) and 5828 restraints for refining 2863 atoms. 4830 conditional restraints added. Observations/parameters ratio is 0.62 ------------------------------------------------------ Cycle 31: After refmac, R = 0.2179 (Rfree = 0.000) for 2863 atoms. Found 15 (20 requested) and removed 14 (12 requested) atoms. Cycle 32: After refmac, R = 0.2052 (Rfree = 0.000) for 2862 atoms. Found 9 (20 requested) and removed 14 (12 requested) atoms. Cycle 33: After refmac, R = 0.2287 (Rfree = 0.000) for 2854 atoms. Found 16 (20 requested) and removed 12 (12 requested) atoms. Cycle 34: After refmac, R = 0.2161 (Rfree = 0.000) for 2850 atoms. Found 16 (20 requested) and removed 12 (12 requested) atoms. Cycle 35: After refmac, R = 0.1954 (Rfree = 0.000) for 2851 atoms. Found 10 (20 requested) and removed 12 (12 requested) atoms. ------------------------------------------------------ Building Cycle 8 Atomic shape factors 3.18 3.22 Search for helices and strands: 0 residues in 0 chains, 2979 seeds are put forward NCS extension: 12 residues added (6 deleted due to clashes), 2991 seeds are put forward Round 1: 214 peptides, 33 chains. Longest chain 16 peptides. Score 0.496 Round 2: 229 peptides, 29 chains. Longest chain 23 peptides. Score 0.598 Round 3: 236 peptides, 29 chains. Longest chain 18 peptides. Score 0.617 Round 4: 229 peptides, 26 chains. Longest chain 32 peptides. Score 0.635 Round 5: 222 peptides, 28 chains. Longest chain 27 peptides. Score 0.591 Taking the results from Round 4 Chains 29, Residues 203, Estimated correctness of the model 50.2 % 3 chains (31 residues) have been docked in sequence ------------------------------------------------------ 7050 reflections ( 99.87 % complete ) and 6050 restraints for refining 2863 atoms. 5135 conditional restraints added. Observations/parameters ratio is 0.62 ------------------------------------------------------ Cycle 36: After refmac, R = 0.2170 (Rfree = 0.000) for 2863 atoms. Found 9 (20 requested) and removed 18 (12 requested) atoms. Cycle 37: After refmac, R = 0.2048 (Rfree = 0.000) for 2850 atoms. Found 8 (20 requested) and removed 14 (12 requested) atoms. Cycle 38: After refmac, R = 0.1989 (Rfree = 0.000) for 2838 atoms. Found 7 (20 requested) and removed 14 (12 requested) atoms. Cycle 39: After refmac, R = 0.1839 (Rfree = 0.000) for 2830 atoms. Found 5 (20 requested) and removed 16 (12 requested) atoms. Cycle 40: After refmac, R = 0.1841 (Rfree = 0.000) for 2819 atoms. Found 5 (20 requested) and removed 12 (12 requested) atoms. ------------------------------------------------------ Building Cycle 9 Atomic shape factors 3.15 3.19 Search for helices and strands: 0 residues in 0 chains, 2944 seeds are put forward NCS extension: 11 residues added (1 deleted due to clashes), 2955 seeds are put forward Round 1: 202 peptides, 33 chains. Longest chain 13 peptides. Score 0.455 Round 2: 223 peptides, 30 chains. Longest chain 25 peptides. Score 0.567 Round 3: 222 peptides, 27 chains. Longest chain 20 peptides. Score 0.604 Round 4: 214 peptides, 32 chains. Longest chain 18 peptides. Score 0.511 Round 5: 224 peptides, 29 chains. Longest chain 22 peptides. Score 0.583 Taking the results from Round 3 Chains 27, Residues 195, Estimated correctness of the model 42.1 % 3 chains (25 residues) have been docked in sequence ------------------------------------------------------ 7050 reflections ( 99.87 % complete ) and 6200 restraints for refining 2863 atoms. 5354 conditional restraints added. Observations/parameters ratio is 0.62 ------------------------------------------------------ Cycle 41: After refmac, R = 0.1998 (Rfree = 0.000) for 2863 atoms. Found 10 (20 requested) and removed 15 (12 requested) atoms. Cycle 42: After refmac, R = 0.1866 (Rfree = 0.000) for 2856 atoms. Found 2 (20 requested) and removed 13 (12 requested) atoms. Cycle 43: After refmac, R = 0.1981 (Rfree = 0.000) for 2844 atoms. Found 9 (20 requested) and removed 13 (12 requested) atoms. Cycle 44: After refmac, R = 0.1791 (Rfree = 0.000) for 2839 atoms. Found 3 (20 requested) and removed 12 (12 requested) atoms. Cycle 45: After refmac, R = 0.1789 (Rfree = 0.000) for 2828 atoms. Found 8 (20 requested) and removed 13 (12 requested) atoms. ------------------------------------------------------ Building Cycle 10 Atomic shape factors 3.16 3.20 Search for helices and strands: 0 residues in 0 chains, 2951 seeds are put forward NCS extension: 18 residues added (2 deleted due to clashes), 2969 seeds are put forward Round 1: 192 peptides, 31 chains. Longest chain 17 peptides. Score 0.450 Round 2: 214 peptides, 28 chains. Longest chain 21 peptides. Score 0.567 Round 3: 202 peptides, 27 chains. Longest chain 19 peptides. Score 0.543 Round 4: 202 peptides, 27 chains. Longest chain 16 peptides. Score 0.543 Round 5: 200 peptides, 28 chains. Longest chain 20 peptides. Score 0.523 Taking the results from Round 2 Last building cycle: Chain fragments will be rearranged Chains 29, Residues 186, Estimated correctness of the model 31.9 % 2 chains (13 residues) have been docked in sequence Sequence coverage is 6 % Consider running further cycles of model building using 2oyo-3_warpNtrace.pdb as input Building loops using Loopy2018 29 chains (186 residues) following loop building 2 chains (13 residues) in sequence following loop building ------------------------------------------------------ ---> Final restrained refinement block. No atom update. 7050 reflections ( 99.87 % complete ) and 6264 restraints for refining 2863 atoms. 5510 conditional restraints added. Observations/parameters ratio is 0.62 ------------------------------------------------------ Cycle 46: After refmac, R = 0.2018 (Rfree = 0.000) for 2863 atoms. Found 0 (20 requested) and removed 12 (12 requested) atoms. Cycle 47: After refmac, R = 0.1898 (Rfree = 0.000) for 2849 atoms. Found 0 (20 requested) and removed 12 (12 requested) atoms. Cycle 48: After refmac, R = 0.1806 (Rfree = 0.000) for 2836 atoms. Found 0 (20 requested) and removed 6 (12 requested) atoms. Cycle 49: After refmac, R = 0.1720 (Rfree = 0.000) for 2830 atoms. TimeTaking 58.08