Mon 24 Dec 07:26:56 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 1vlm-3.6-parrot-noncs X-ray data file /users/emra500/scratch/Dataset/noncsChltofom/1vlm-3.6-parrot-noncs.mtz Sequence file /users/emra500/scratch/Dataset/noncsChltofom/1vlm-3.6-parrot-noncs.fasta Tracing mode WARPNTRACEPHASES Creating directory /mnt/lustre/users/emra500/PipeliensFastaNoRFree/noncs/ArpWArp/wArpResults/WorkingDir/1vlm-3.6-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/1vlm-3.6-parrot-noncs/arp_warp_classic.par Job launched in /mnt/lustre/users/emra500/PipeliensFastaNoRFree/noncs/ArpWArp/wArpResults/WorkingDir/1vlm-3.6-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 07:27:01 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/1vlm-3.6-parrot-noncs ARP/wARP software version: 8.0 The parameter file: /mnt/lustre/users/emra500/PipeliensFastaNoRFree/noncs/ArpWArp/wArpResults/WorkingDir/1vlm-3.6-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: 0.6290 Checking the provided sequence file Detected sequence length: 219 Maximum limit of NCS related copies: 60 Number of NCS-related molecules: 2 Adjusted target number of residues: 438 Adjusted target solvent content: 0.46 Input MTZ file: 1vlm-3.6-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: 18 Cell parameters: 65.648 70.734 93.922 90.000 90.000 90.000 Input sequence file: 1vlm-3.6-parrot-noncs.fasta_lf Building free atoms model in initial map for 3504 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: 93.922 3.600 Wilson plot Bfac: 65.87 5411 reflections ( 99.69 % complete ) and 0 restraints for refining 3870 atoms. Observations/parameters ratio is 0.35 ------------------------------------------------------ Starting model: R = 0.3249 (Rfree = 0.000). ------------------------------------------------------ Cycle 0: After refmac, R = 0.3115 (Rfree = 0.000) for 3870 atoms. Found 24 (24 requested) and removed 66 (12 requested) atoms. ------------------------------------------------------ Building Cycle 1 Atomic shape factors 3.38 3.57 Search for helices and strands: 0 residues in 0 chains, 3881 seeds are put forward NCS extension: 0 residues added, 3881 seeds are put forward Round 1: 150 peptides, 32 chains. Longest chain 9 peptides. Score 0.263 Round 2: 203 peptides, 33 chains. Longest chain 13 peptides. Score 0.449 Round 3: 216 peptides, 32 chains. Longest chain 15 peptides. Score 0.507 Round 4: 213 peptides, 29 chains. Longest chain 17 peptides. Score 0.539 Round 5: 235 peptides, 33 chains. Longest chain 19 peptides. Score 0.552 Taking the results from Round 5 Chains 35, Residues 202, Estimated correctness of the model 0.0 % 1 chains (14 residues) have been docked in sequence ------------------------------------------------------ 5411 reflections ( 99.69 % complete ) and 7189 restraints for refining 3175 atoms. 6361 conditional restraints added. Observations/parameters ratio is 0.43 ------------------------------------------------------ Cycle 1: After refmac, R = 0.2594 (Rfree = 0.000) for 3175 atoms. Found 15 (20 requested) and removed 42 (10 requested) atoms. Cycle 2: After refmac, R = 0.2356 (Rfree = 0.000) for 3106 atoms. Found 7 (20 requested) and removed 24 (10 requested) atoms. Cycle 3: After refmac, R = 0.2183 (Rfree = 0.000) for 3072 atoms. Found 5 (19 requested) and removed 23 (9 requested) atoms. Cycle 4: After refmac, R = 0.2229 (Rfree = 0.000) for 3051 atoms. Found 7 (19 requested) and removed 27 (9 requested) atoms. Cycle 5: After refmac, R = 0.2209 (Rfree = 0.000) for 3027 atoms. Found 5 (19 requested) and removed 20 (9 requested) atoms. ------------------------------------------------------ Building Cycle 2 Atomic shape factors 3.38 3.57 Search for helices and strands: 0 residues in 0 chains, 3145 seeds are put forward NCS extension: 15 residues added (2 deleted due to clashes), 3160 seeds are put forward Round 1: 171 peptides, 31 chains. Longest chain 16 peptides. Score 0.364 Round 2: 219 peptides, 33 chains. Longest chain 16 peptides. Score 0.502 Round 3: 227 peptides, 29 chains. Longest chain 27 peptides. Score 0.580 Round 4: 240 peptides, 31 chains. Longest chain 20 peptides. Score 0.592 Round 5: 218 peptides, 31 chains. Longest chain 13 peptides. Score 0.527 Taking the results from Round 4 Chains 31, Residues 209, Estimated correctness of the model 11.5 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 5411 reflections ( 99.69 % complete ) and 7221 restraints for refining 3134 atoms. 6416 conditional restraints added. Observations/parameters ratio is 0.43 ------------------------------------------------------ Cycle 6: After refmac, R = 0.2471 (Rfree = 0.000) for 3134 atoms. Found 15 (20 requested) and removed 32 (10 requested) atoms. Cycle 7: After refmac, R = 0.2155 (Rfree = 0.000) for 3103 atoms. Found 11 (19 requested) and removed 29 (9 requested) atoms. Cycle 8: After refmac, R = 0.2103 (Rfree = 0.000) for 3078 atoms. Found 13 (19 requested) and removed 24 (9 requested) atoms. Cycle 9: After refmac, R = 0.1906 (Rfree = 0.000) for 3059 atoms. Found 15 (19 requested) and removed 21 (9 requested) atoms. Cycle 10: After refmac, R = 0.1956 (Rfree = 0.000) for 3045 atoms. Found 9 (19 requested) and removed 16 (9 requested) atoms. ------------------------------------------------------ Building Cycle 3 Atomic shape factors 3.34 3.52 Search for helices and strands: 0 residues in 0 chains, 3143 seeds are put forward NCS extension: 20 residues added (1 deleted due to clashes), 3163 seeds are put forward Round 1: 190 peptides, 35 chains. Longest chain 12 peptides. Score 0.371 Round 2: 217 peptides, 34 chains. Longest chain 17 peptides. Score 0.482 Round 3: 228 peptides, 33 chains. Longest chain 13 peptides. Score 0.530 Round 4: 228 peptides, 30 chains. Longest chain 22 peptides. Score 0.570 Round 5: 227 peptides, 33 chains. Longest chain 18 peptides. Score 0.527 Taking the results from Round 4 Chains 30, Residues 198, Estimated correctness of the model 2.6 % 1 chains (7 residues) have been docked in sequence ------------------------------------------------------ 5411 reflections ( 99.69 % complete ) and 7354 restraints for refining 3177 atoms. 6569 conditional restraints added. Observations/parameters ratio is 0.43 ------------------------------------------------------ Cycle 11: After refmac, R = 0.2258 (Rfree = 0.000) for 3177 atoms. Found 20 (20 requested) and removed 17 (10 requested) atoms. Cycle 12: After refmac, R = 0.2075 (Rfree = 0.000) for 3173 atoms. Found 8 (20 requested) and removed 15 (10 requested) atoms. Cycle 13: After refmac, R = 0.1992 (Rfree = 0.000) for 3165 atoms. Found 6 (20 requested) and removed 12 (10 requested) atoms. Cycle 14: After refmac, R = 0.1964 (Rfree = 0.000) for 3158 atoms. Found 3 (20 requested) and removed 10 (10 requested) atoms. Cycle 15: After refmac, R = 0.1868 (Rfree = 0.000) for 3148 atoms. Found 6 (20 requested) and removed 14 (10 requested) atoms. ------------------------------------------------------ Building Cycle 4 Atomic shape factors 3.34 3.52 Search for helices and strands: 0 residues in 0 chains, 3245 seeds are put forward NCS extension: 33 residues added (0 deleted due to clashes), 3278 seeds are put forward Round 1: 188 peptides, 34 chains. Longest chain 12 peptides. Score 0.380 Round 2: 206 peptides, 32 chains. Longest chain 13 peptides. Score 0.474 Round 3: 210 peptides, 33 chains. Longest chain 13 peptides. Score 0.473 Round 4: 202 peptides, 31 chains. Longest chain 13 peptides. Score 0.475 Round 5: 223 peptides, 32 chains. Longest chain 18 peptides. Score 0.529 Taking the results from Round 5 Chains 32, Residues 191, Estimated correctness of the model 0.0 % 1 chains (8 residues) have been docked in sequence ------------------------------------------------------ 5411 reflections ( 99.69 % complete ) and 7274 restraints for refining 3177 atoms. 6514 conditional restraints added. Observations/parameters ratio is 0.43 ------------------------------------------------------ Cycle 16: After refmac, R = 0.2303 (Rfree = 0.000) for 3177 atoms. Found 16 (20 requested) and removed 14 (10 requested) atoms. Cycle 17: After refmac, R = 0.2240 (Rfree = 0.000) for 3162 atoms. Found 7 (20 requested) and removed 14 (10 requested) atoms. Cycle 18: After refmac, R = 0.2089 (Rfree = 0.000) for 3148 atoms. Found 5 (20 requested) and removed 11 (10 requested) atoms. Cycle 19: After refmac, R = 0.2153 (Rfree = 0.000) for 3139 atoms. Found 1 (20 requested) and removed 10 (10 requested) atoms. Cycle 20: After refmac, R = 0.2037 (Rfree = 0.000) for 3128 atoms. Found 3 (20 requested) and removed 10 (10 requested) atoms. ------------------------------------------------------ Building Cycle 5 Atomic shape factors 3.38 3.57 Search for helices and strands: 0 residues in 0 chains, 3219 seeds are put forward NCS extension: 0 residues added, 3219 seeds are put forward Round 1: 182 peptides, 36 chains. Longest chain 9 peptides. Score 0.325 Round 2: 204 peptides, 31 chains. Longest chain 14 peptides. Score 0.482 Round 3: 219 peptides, 36 chains. Longest chain 14 peptides. Score 0.459 Round 4: 212 peptides, 32 chains. Longest chain 14 peptides. Score 0.494 Round 5: 216 peptides, 30 chains. Longest chain 16 peptides. Score 0.534 Taking the results from Round 5 Chains 30, Residues 186, Estimated correctness of the model 0.0 % 1 chains (15 residues) have been docked in sequence ------------------------------------------------------ 5411 reflections ( 99.69 % complete ) and 7368 restraints for refining 3175 atoms. 6586 conditional restraints added. Observations/parameters ratio is 0.43 ------------------------------------------------------ Cycle 21: After refmac, R = 0.2227 (Rfree = 0.000) for 3175 atoms. Found 16 (20 requested) and removed 15 (10 requested) atoms. Cycle 22: After refmac, R = 0.2093 (Rfree = 0.000) for 3162 atoms. Found 12 (20 requested) and removed 15 (10 requested) atoms. Cycle 23: After refmac, R = 0.2101 (Rfree = 0.000) for 3152 atoms. Found 20 (20 requested) and removed 18 (10 requested) atoms. Cycle 24: After refmac, R = 0.1998 (Rfree = 0.000) for 3144 atoms. Found 10 (20 requested) and removed 32 (10 requested) atoms. Cycle 25: After refmac, R = 0.1887 (Rfree = 0.000) for 3111 atoms. Found 8 (20 requested) and removed 15 (10 requested) atoms. ------------------------------------------------------ Building Cycle 6 Atomic shape factors 3.38 3.57 Search for helices and strands: 0 residues in 0 chains, 3212 seeds are put forward NCS extension: 17 residues added (4 deleted due to clashes), 3229 seeds are put forward Round 1: 162 peptides, 33 chains. Longest chain 12 peptides. Score 0.295 Round 2: 188 peptides, 34 chains. Longest chain 8 peptides. Score 0.380 Round 3: 191 peptides, 32 chains. Longest chain 12 peptides. Score 0.422 Round 4: 196 peptides, 33 chains. Longest chain 11 peptides. Score 0.425 Round 5: 185 peptides, 31 chains. Longest chain 16 peptides. Score 0.416 Taking the results from Round 4 Chains 33, Residues 163, Estimated correctness of the model 0.0 % 2 chains (14 residues) have been docked in sequence ------------------------------------------------------ 5411 reflections ( 99.69 % complete ) and 7436 restraints for refining 3177 atoms. 6764 conditional restraints added. Observations/parameters ratio is 0.43 ------------------------------------------------------ Cycle 26: After refmac, R = 0.2187 (Rfree = 0.000) for 3177 atoms. Found 20 (20 requested) and removed 26 (10 requested) atoms. Cycle 27: After refmac, R = 0.2003 (Rfree = 0.000) for 3160 atoms. Found 10 (20 requested) and removed 23 (10 requested) atoms. Cycle 28: After refmac, R = 0.1935 (Rfree = 0.000) for 3144 atoms. Found 13 (20 requested) and removed 14 (10 requested) atoms. Cycle 29: After refmac, R = 0.1816 (Rfree = 0.000) for 3140 atoms. Found 9 (20 requested) and removed 12 (10 requested) atoms. Cycle 30: After refmac, R = 0.1754 (Rfree = 0.000) for 3135 atoms. Found 10 (20 requested) and removed 13 (10 requested) atoms. ------------------------------------------------------ Building Cycle 7 Atomic shape factors 3.34 3.52 Search for helices and strands: 0 residues in 0 chains, 3237 seeds are put forward NCS extension: 13 residues added (1 deleted due to clashes), 3250 seeds are put forward Round 1: 173 peptides, 34 chains. Longest chain 8 peptides. Score 0.323 Round 2: 181 peptides, 32 chains. Longest chain 11 peptides. Score 0.386 Round 3: 202 peptides, 33 chains. Longest chain 13 peptides. Score 0.446 Round 4: 218 peptides, 37 chains. Longest chain 13 peptides. Score 0.441 Round 5: 204 peptides, 35 chains. Longest chain 13 peptides. Score 0.422 Taking the results from Round 3 Chains 33, Residues 169, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 5411 reflections ( 99.69 % complete ) and 7446 restraints for refining 3177 atoms. 6803 conditional restraints added. Observations/parameters ratio is 0.43 ------------------------------------------------------ Cycle 31: After refmac, R = 0.2012 (Rfree = 0.000) for 3177 atoms. Found 17 (20 requested) and removed 15 (10 requested) atoms. Cycle 32: After refmac, R = 0.1890 (Rfree = 0.000) for 3171 atoms. Found 9 (20 requested) and removed 26 (10 requested) atoms. Cycle 33: After refmac, R = 0.1875 (Rfree = 0.000) for 3149 atoms. Found 10 (20 requested) and removed 15 (10 requested) atoms. Cycle 34: After refmac, R = 0.1853 (Rfree = 0.000) for 3141 atoms. Found 8 (20 requested) and removed 24 (10 requested) atoms. Cycle 35: After refmac, R = 0.1883 (Rfree = 0.000) for 3122 atoms. Found 7 (20 requested) and removed 14 (10 requested) atoms. ------------------------------------------------------ Building Cycle 8 Atomic shape factors 3.34 3.52 Search for helices and strands: 0 residues in 0 chains, 3223 seeds are put forward NCS extension: 16 residues added (2 deleted due to clashes), 3239 seeds are put forward Round 1: 139 peptides, 29 chains. Longest chain 9 peptides. Score 0.269 Round 2: 174 peptides, 29 chains. Longest chain 11 peptides. Score 0.408 Round 3: 180 peptides, 28 chains. Longest chain 13 peptides. Score 0.445 Round 4: 190 peptides, 28 chains. Longest chain 12 peptides. Score 0.479 Round 5: 193 peptides, 32 chains. Longest chain 13 peptides. Score 0.429 Taking the results from Round 4 Chains 28, Residues 162, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 5411 reflections ( 99.69 % complete ) and 7500 restraints for refining 3177 atoms. 6880 conditional restraints added. Observations/parameters ratio is 0.43 ------------------------------------------------------ Cycle 36: After refmac, R = 0.2075 (Rfree = 0.000) for 3177 atoms. Found 11 (20 requested) and removed 14 (10 requested) atoms. Cycle 37: After refmac, R = 0.1925 (Rfree = 0.000) for 3166 atoms. Found 6 (20 requested) and removed 12 (10 requested) atoms. Cycle 38: After refmac, R = 0.1894 (Rfree = 0.000) for 3157 atoms. Found 3 (20 requested) and removed 10 (10 requested) atoms. Cycle 39: After refmac, R = 0.1869 (Rfree = 0.000) for 3149 atoms. Found 3 (20 requested) and removed 10 (10 requested) atoms. Cycle 40: After refmac, R = 0.1846 (Rfree = 0.000) for 3141 atoms. Found 1 (20 requested) and removed 11 (10 requested) atoms. ------------------------------------------------------ Building Cycle 9 Atomic shape factors 3.35 3.53 Search for helices and strands: 0 residues in 0 chains, 3218 seeds are put forward NCS extension: 15 residues added (0 deleted due to clashes), 3233 seeds are put forward Round 1: 146 peptides, 28 chains. Longest chain 10 peptides. Score 0.316 Round 2: 170 peptides, 26 chains. Longest chain 14 peptides. Score 0.441 Round 3: 175 peptides, 27 chains. Longest chain 20 peptides. Score 0.443 Round 4: 187 peptides, 27 chains. Longest chain 18 peptides. Score 0.484 Round 5: 175 peptides, 26 chains. Longest chain 20 peptides. Score 0.458 Taking the results from Round 4 Chains 27, Residues 160, Estimated correctness of the model 0.0 % 1 chains (11 residues) have been docked in sequence ------------------------------------------------------ 5411 reflections ( 99.69 % complete ) and 7349 restraints for refining 3177 atoms. 6687 conditional restraints added. Observations/parameters ratio is 0.43 ------------------------------------------------------ Cycle 41: After refmac, R = 0.2181 (Rfree = 0.000) for 3177 atoms. Found 15 (20 requested) and removed 19 (10 requested) atoms. Cycle 42: After refmac, R = 0.2008 (Rfree = 0.000) for 3168 atoms. Found 12 (20 requested) and removed 17 (10 requested) atoms. Cycle 43: After refmac, R = 0.1899 (Rfree = 0.000) for 3159 atoms. Found 11 (20 requested) and removed 17 (10 requested) atoms. Cycle 44: After refmac, R = 0.1924 (Rfree = 0.000) for 3149 atoms. Found 9 (20 requested) and removed 15 (10 requested) atoms. Cycle 45: After refmac, R = 0.1743 (Rfree = 0.000) for 3140 atoms. Found 8 (20 requested) and removed 11 (10 requested) atoms. ------------------------------------------------------ Building Cycle 10 Atomic shape factors 3.34 3.52 Search for helices and strands: 0 residues in 0 chains, 3230 seeds are put forward NCS extension: 14 residues added (0 deleted due to clashes), 3244 seeds are put forward Round 1: 155 peptides, 31 chains. Longest chain 10 peptides. Score 0.301 Round 2: 169 peptides, 26 chains. Longest chain 14 peptides. Score 0.437 Round 3: 158 peptides, 27 chains. Longest chain 9 peptides. Score 0.380 Round 4: 165 peptides, 29 chains. Longest chain 9 peptides. Score 0.374 Round 5: 173 peptides, 25 chains. Longest chain 16 peptides. Score 0.467 Taking the results from Round 5 Last building cycle: Chain fragments will be rearranged Chains 25, Residues 148, 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 1vlm-3_warpNtrace.pdb as input ------------------------------------------------------ ---> Final restrained refinement block. No atom update. 5411 reflections ( 99.69 % complete ) and 7563 restraints for refining 3177 atoms. 6996 conditional restraints added. Observations/parameters ratio is 0.43 ------------------------------------------------------ Cycle 46: After refmac, R = 0.2117 (Rfree = 0.000) for 3177 atoms. Found 0 (20 requested) and removed 10 (10 requested) atoms. Cycle 47: After refmac, R = 0.2069 (Rfree = 0.000) for 3159 atoms. Found 0 (20 requested) and removed 10 (10 requested) atoms. Cycle 48: After refmac, R = 0.1876 (Rfree = 0.000) for 3141 atoms. Found 0 (20 requested) and removed 10 (10 requested) atoms. Cycle 49: After refmac, R = 0.1800 (Rfree = 0.000) for 3126 atoms. TimeTaking 36.12