null Mon 24 Dec 08:03:13 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 1vlm-3.2-parrot-noncs X-ray data file /users/emra500/scratch/Dataset/noncsChltofom/1vlm-3.2-parrot-noncs.mtz Sequence file /users/emra500/scratch/Dataset/noncsChltofom/1vlm-3.2-parrot-noncs.fasta Tracing mode WARPNTRACEPHASES Creating directory /mnt/lustre/users/emra500/PipeliensFastaNoRFree/noncs/ArpWArp/wArpResults/WorkingDir/1vlm-3.2-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-3.2-parrot-noncs/arp_warp_classic.par Job launched in /mnt/lustre/users/emra500/PipeliensFastaNoRFree/noncs/ArpWArp/wArpResults/WorkingDir/1vlm-3.2-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 08:03:19 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-3.2-parrot-noncs ARP/wARP software version: 8.0 The parameter file: /mnt/lustre/users/emra500/PipeliensFastaNoRFree/noncs/ArpWArp/wArpResults/WorkingDir/1vlm-3.2-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 316 and 0 Target number of residues in the AU: 316 Target solvent content: 0.6079 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-3.2-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-3.2-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 3.200 Wilson plot Bfac: 55.83 7616 reflections ( 99.75 % complete ) and 0 restraints for refining 3865 atoms. Observations/parameters ratio is 0.49 ------------------------------------------------------ Starting model: R = 0.3132 (Rfree = 0.000). ------------------------------------------------------ Cycle 0: After refmac, R = 0.2710 (Rfree = 0.000) for 3865 atoms. Found 34 (34 requested) and removed 70 (17 requested) atoms. ------------------------------------------------------ Building Cycle 1 Atomic shape factors 3.04 3.21 Search for helices and strands: 0 residues in 0 chains, 3893 seeds are put forward NCS extension: 0 residues added, 3893 seeds are put forward Round 1: 186 peptides, 35 chains. Longest chain 10 peptides. Score 0.356 Round 2: 241 peptides, 35 chains. Longest chain 29 peptides. Score 0.543 Round 3: 266 peptides, 33 chains. Longest chain 21 peptides. Score 0.636 Round 4: 255 peptides, 33 chains. Longest chain 18 peptides. Score 0.608 Round 5: 265 peptides, 31 chains. Longest chain 24 peptides. Score 0.656 Taking the results from Round 5 Chains 32, Residues 234, Estimated correctness of the model 55.3 % 1 chains (17 residues) have been docked in sequence ------------------------------------------------------ 7616 reflections ( 99.75 % complete ) and 6926 restraints for refining 3196 atoms. 5961 conditional restraints added. Observations/parameters ratio is 0.60 ------------------------------------------------------ Cycle 1: After refmac, R = 0.2630 (Rfree = 0.000) for 3196 atoms. Found 28 (28 requested) and removed 38 (14 requested) atoms. Cycle 2: After refmac, R = 0.2545 (Rfree = 0.000) for 3149 atoms. Found 28 (28 requested) and removed 27 (14 requested) atoms. Cycle 3: After refmac, R = 0.2508 (Rfree = 0.000) for 3139 atoms. Found 24 (28 requested) and removed 26 (14 requested) atoms. Cycle 4: After refmac, R = 0.2494 (Rfree = 0.000) for 3128 atoms. Found 19 (28 requested) and removed 22 (14 requested) atoms. Cycle 5: After refmac, R = 0.2466 (Rfree = 0.000) for 3116 atoms. Found 23 (28 requested) and removed 19 (14 requested) atoms. ------------------------------------------------------ Building Cycle 2 Atomic shape factors 3.04 3.21 Search for helices and strands: 0 residues in 0 chains, 3203 seeds are put forward NCS extension: 22 residues added (1 deleted due to clashes), 3225 seeds are put forward Round 1: 248 peptides, 41 chains. Longest chain 14 peptides. Score 0.484 Round 2: 282 peptides, 40 chains. Longest chain 25 peptides. Score 0.597 Round 3: 291 peptides, 37 chains. Longest chain 27 peptides. Score 0.653 Round 4: 274 peptides, 35 chains. Longest chain 24 peptides. Score 0.634 Round 5: 279 peptides, 36 chains. Longest chain 35 peptides. Score 0.635 Taking the results from Round 3 Chains 38, Residues 254, Estimated correctness of the model 54.6 % 2 chains (18 residues) have been docked in sequence ------------------------------------------------------ 7616 reflections ( 99.75 % complete ) and 6846 restraints for refining 3198 atoms. 5797 conditional restraints added. Observations/parameters ratio is 0.60 ------------------------------------------------------ Cycle 6: After refmac, R = 0.2611 (Rfree = 0.000) for 3198 atoms. Found 24 (28 requested) and removed 35 (14 requested) atoms. Cycle 7: After refmac, R = 0.2397 (Rfree = 0.000) for 3172 atoms. Found 14 (28 requested) and removed 26 (14 requested) atoms. Cycle 8: After refmac, R = 0.2334 (Rfree = 0.000) for 3154 atoms. Found 5 (28 requested) and removed 16 (14 requested) atoms. Cycle 9: After refmac, R = 0.2278 (Rfree = 0.000) for 3131 atoms. Found 8 (28 requested) and removed 14 (14 requested) atoms. Cycle 10: After refmac, R = 0.2211 (Rfree = 0.000) for 3123 atoms. Found 7 (28 requested) and removed 14 (14 requested) atoms. ------------------------------------------------------ Building Cycle 3 Atomic shape factors 3.09 3.26 Search for helices and strands: 0 residues in 0 chains, 3218 seeds are put forward NCS extension: 39 residues added (2 deleted due to clashes), 3257 seeds are put forward Round 1: 261 peptides, 39 chains. Longest chain 29 peptides. Score 0.551 Round 2: 276 peptides, 33 chains. Longest chain 24 peptides. Score 0.660 Round 3: 275 peptides, 33 chains. Longest chain 35 peptides. Score 0.658 Round 4: 297 peptides, 31 chains. Longest chain 35 peptides. Score 0.725 Round 5: 288 peptides, 30 chains. Longest chain 33 peptides. Score 0.717 Taking the results from Round 4 Chains 35, Residues 266, Estimated correctness of the model 70.3 % 4 chains (57 residues) have been docked in sequence Building loops using Loopy2018 Built loop between residues 204 A and 208 A 34 chains (268 residues) following loop building 3 chains (60 residues) in sequence following loop building ------------------------------------------------------ 7616 reflections ( 99.75 % complete ) and 6283 restraints for refining 3199 atoms. 5036 conditional restraints added. Observations/parameters ratio is 0.60 ------------------------------------------------------ Cycle 11: After refmac, R = 0.2686 (Rfree = 0.000) for 3199 atoms. Found 28 (28 requested) and removed 49 (14 requested) atoms. Cycle 12: After refmac, R = 0.2404 (Rfree = 0.000) for 3166 atoms. Found 11 (27 requested) and removed 22 (14 requested) atoms. Cycle 13: After refmac, R = 0.2343 (Rfree = 0.000) for 3149 atoms. Found 11 (27 requested) and removed 17 (14 requested) atoms. Cycle 14: After refmac, R = 0.2316 (Rfree = 0.000) for 3140 atoms. Found 7 (26 requested) and removed 14 (14 requested) atoms. Cycle 15: After refmac, R = 0.2287 (Rfree = 0.000) for 3128 atoms. Found 13 (26 requested) and removed 16 (14 requested) atoms. ------------------------------------------------------ Building Cycle 4 Atomic shape factors 3.04 3.21 Search for helices and strands: 0 residues in 0 chains, 3222 seeds are put forward NCS extension: 16 residues added (7 deleted due to clashes), 3238 seeds are put forward Round 1: 266 peptides, 40 chains. Longest chain 25 peptides. Score 0.553 Round 2: 285 peptides, 34 chains. Longest chain 25 peptides. Score 0.671 Round 3: 271 peptides, 34 chains. Longest chain 26 peptides. Score 0.638 Round 4: 261 peptides, 34 chains. Longest chain 23 peptides. Score 0.612 Round 5: 271 peptides, 32 chains. Longest chain 27 peptides. Score 0.659 Taking the results from Round 2 Chains 35, Residues 251, Estimated correctness of the model 58.8 % 2 chains (34 residues) have been docked in sequence ------------------------------------------------------ 7616 reflections ( 99.75 % complete ) and 6689 restraints for refining 3199 atoms. 5574 conditional restraints added. Observations/parameters ratio is 0.60 ------------------------------------------------------ Cycle 16: After refmac, R = 0.2419 (Rfree = 0.000) for 3199 atoms. Found 17 (25 requested) and removed 24 (14 requested) atoms. Cycle 17: After refmac, R = 0.2282 (Rfree = 0.000) for 3186 atoms. Found 10 (25 requested) and removed 21 (14 requested) atoms. Cycle 18: After refmac, R = 0.2205 (Rfree = 0.000) for 3172 atoms. Found 6 (25 requested) and removed 16 (14 requested) atoms. Cycle 19: After refmac, R = 0.2173 (Rfree = 0.000) for 3161 atoms. Found 6 (25 requested) and removed 16 (14 requested) atoms. Cycle 20: After refmac, R = 0.2139 (Rfree = 0.000) for 3147 atoms. Found 7 (25 requested) and removed 16 (14 requested) atoms. ------------------------------------------------------ Building Cycle 5 Atomic shape factors 3.06 3.23 Search for helices and strands: 0 residues in 0 chains, 3208 seeds are put forward NCS extension: 35 residues added (2 deleted due to clashes), 3243 seeds are put forward Round 1: 227 peptides, 31 chains. Longest chain 32 peptides. Score 0.554 Round 2: 237 peptides, 30 chains. Longest chain 35 peptides. Score 0.596 Round 3: 251 peptides, 32 chains. Longest chain 18 peptides. Score 0.609 Round 4: 250 peptides, 33 chains. Longest chain 27 peptides. Score 0.594 Round 5: 237 peptides, 27 chains. Longest chain 28 peptides. Score 0.632 Taking the results from Round 5 Chains 30, Residues 210, Estimated correctness of the model 49.4 % 4 chains (40 residues) have been docked in sequence ------------------------------------------------------ 7616 reflections ( 99.75 % complete ) and 6946 restraints for refining 3198 atoms. 5983 conditional restraints added. Observations/parameters ratio is 0.60 ------------------------------------------------------ Cycle 21: After refmac, R = 0.2528 (Rfree = 0.000) for 3198 atoms. Found 25 (25 requested) and removed 33 (14 requested) atoms. Cycle 22: After refmac, R = 0.2359 (Rfree = 0.000) for 3178 atoms. Found 25 (25 requested) and removed 19 (14 requested) atoms. Cycle 23: After refmac, R = 0.2301 (Rfree = 0.000) for 3177 atoms. Found 14 (25 requested) and removed 19 (14 requested) atoms. Cycle 24: After refmac, R = 0.2223 (Rfree = 0.000) for 3164 atoms. Found 11 (25 requested) and removed 18 (14 requested) atoms. Cycle 25: After refmac, R = 0.2152 (Rfree = 0.000) for 3156 atoms. Found 7 (25 requested) and removed 14 (14 requested) atoms. ------------------------------------------------------ Building Cycle 6 Atomic shape factors 3.06 3.23 Search for helices and strands: 0 residues in 0 chains, 3231 seeds are put forward NCS extension: 20 residues added (4 deleted due to clashes), 3251 seeds are put forward Round 1: 216 peptides, 33 chains. Longest chain 24 peptides. Score 0.493 Round 2: 222 peptides, 27 chains. Longest chain 19 peptides. Score 0.592 Round 3: 236 peptides, 29 chains. Longest chain 24 peptides. Score 0.605 Round 4: 238 peptides, 31 chains. Longest chain 32 peptides. Score 0.586 Round 5: 245 peptides, 32 chains. Longest chain 19 peptides. Score 0.593 Taking the results from Round 3 Chains 30, Residues 207, Estimated correctness of the model 42.4 % 3 chains (38 residues) have been docked in sequence ------------------------------------------------------ 7616 reflections ( 99.75 % complete ) and 6841 restraints for refining 3199 atoms. 5901 conditional restraints added. Observations/parameters ratio is 0.60 ------------------------------------------------------ Cycle 26: After refmac, R = 0.2383 (Rfree = 0.000) for 3199 atoms. Found 23 (25 requested) and removed 32 (14 requested) atoms. Cycle 27: After refmac, R = 0.2222 (Rfree = 0.000) for 3184 atoms. Found 9 (25 requested) and removed 17 (14 requested) atoms. Cycle 28: After refmac, R = 0.2224 (Rfree = 0.000) for 3175 atoms. Found 7 (25 requested) and removed 14 (14 requested) atoms. Cycle 29: After refmac, R = 0.2118 (Rfree = 0.000) for 3165 atoms. Found 8 (25 requested) and removed 15 (14 requested) atoms. Cycle 30: After refmac, R = 0.2087 (Rfree = 0.000) for 3157 atoms. Found 9 (25 requested) and removed 16 (14 requested) atoms. ------------------------------------------------------ Building Cycle 7 Atomic shape factors 3.07 3.24 Search for helices and strands: 0 residues in 0 chains, 3240 seeds are put forward NCS extension: 36 residues added (5 deleted due to clashes), 3276 seeds are put forward Round 1: 215 peptides, 37 chains. Longest chain 22 peptides. Score 0.431 Round 2: 231 peptides, 32 chains. Longest chain 23 peptides. Score 0.553 Round 3: 233 peptides, 36 chains. Longest chain 17 peptides. Score 0.505 Round 4: 231 peptides, 34 chains. Longest chain 17 peptides. Score 0.526 Round 5: 231 peptides, 33 chains. Longest chain 17 peptides. Score 0.540 Taking the results from Round 2 Chains 32, Residues 199, Estimated correctness of the model 27.8 % 1 chains (13 residues) have been docked in sequence ------------------------------------------------------ 7616 reflections ( 99.75 % complete ) and 7065 restraints for refining 3199 atoms. 6256 conditional restraints added. Observations/parameters ratio is 0.60 ------------------------------------------------------ Cycle 31: After refmac, R = 0.2271 (Rfree = 0.000) for 3199 atoms. Found 11 (25 requested) and removed 19 (14 requested) atoms. Cycle 32: After refmac, R = 0.2243 (Rfree = 0.000) for 3183 atoms. Found 5 (25 requested) and removed 14 (14 requested) atoms. Cycle 33: After refmac, R = 0.2162 (Rfree = 0.000) for 3173 atoms. Found 3 (25 requested) and removed 15 (14 requested) atoms. Cycle 34: After refmac, R = 0.2125 (Rfree = 0.000) for 3159 atoms. Found 4 (25 requested) and removed 14 (14 requested) atoms. Cycle 35: After refmac, R = 0.2056 (Rfree = 0.000) for 3149 atoms. Found 4 (25 requested) and removed 14 (14 requested) atoms. ------------------------------------------------------ Building Cycle 8 Atomic shape factors 3.05 3.22 Search for helices and strands: 0 residues in 0 chains, 3234 seeds are put forward NCS extension: 27 residues added (1 deleted due to clashes), 3261 seeds are put forward Round 1: 188 peptides, 35 chains. Longest chain 17 peptides. Score 0.364 Round 2: 211 peptides, 31 chains. Longest chain 18 peptides. Score 0.505 Round 3: 218 peptides, 32 chains. Longest chain 15 peptides. Score 0.513 Round 4: 218 peptides, 30 chains. Longest chain 21 peptides. Score 0.541 Round 5: 222 peptides, 28 chains. Longest chain 23 peptides. Score 0.579 Taking the results from Round 5 Chains 28, Residues 194, Estimated correctness of the model 35.3 % 2 chains (26 residues) have been docked in sequence ------------------------------------------------------ 7616 reflections ( 99.75 % complete ) and 6755 restraints for refining 3199 atoms. 5887 conditional restraints added. Observations/parameters ratio is 0.60 ------------------------------------------------------ Cycle 36: After refmac, R = 0.2400 (Rfree = 0.000) for 3199 atoms. Found 25 (25 requested) and removed 37 (14 requested) atoms. Cycle 37: After refmac, R = 0.2203 (Rfree = 0.000) for 3179 atoms. Found 19 (25 requested) and removed 18 (14 requested) atoms. Cycle 38: After refmac, R = 0.2187 (Rfree = 0.000) for 3179 atoms. Found 12 (25 requested) and removed 14 (14 requested) atoms. Cycle 39: After refmac, R = 0.2152 (Rfree = 0.000) for 3174 atoms. Found 13 (25 requested) and removed 14 (14 requested) atoms. Cycle 40: After refmac, R = 0.2066 (Rfree = 0.000) for 3169 atoms. Found 9 (25 requested) and removed 14 (14 requested) atoms. ------------------------------------------------------ Building Cycle 9 Atomic shape factors 3.09 3.26 Search for helices and strands: 0 residues in 0 chains, 3235 seeds are put forward NCS extension: 33 residues added (4 deleted due to clashes), 3268 seeds are put forward Round 1: 173 peptides, 30 chains. Longest chain 14 peptides. Score 0.388 Round 2: 189 peptides, 29 chains. Longest chain 13 peptides. Score 0.461 Round 3: 195 peptides, 28 chains. Longest chain 14 peptides. Score 0.496 Round 4: 196 peptides, 32 chains. Longest chain 12 peptides. Score 0.440 Round 5: 198 peptides, 28 chains. Longest chain 18 peptides. Score 0.506 Taking the results from Round 5 Chains 28, Residues 170, Estimated correctness of the model 13.3 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 7616 reflections ( 99.75 % complete ) and 7261 restraints for refining 3199 atoms. 6609 conditional restraints added. Observations/parameters ratio is 0.60 ------------------------------------------------------ Cycle 41: After refmac, R = 0.2214 (Rfree = 0.000) for 3199 atoms. Found 22 (25 requested) and removed 29 (14 requested) atoms. Cycle 42: After refmac, R = 0.2102 (Rfree = 0.000) for 3190 atoms. Found 10 (25 requested) and removed 14 (14 requested) atoms. Cycle 43: After refmac, R = 0.2065 (Rfree = 0.000) for 3184 atoms. Found 10 (25 requested) and removed 15 (14 requested) atoms. Cycle 44: After refmac, R = 0.2062 (Rfree = 0.000) for 3179 atoms. Found 10 (25 requested) and removed 16 (14 requested) atoms. Cycle 45: After refmac, R = 0.2017 (Rfree = 0.000) for 3172 atoms. Found 18 (25 requested) and removed 18 (14 requested) atoms. ------------------------------------------------------ Building Cycle 10 Atomic shape factors 3.09 3.26 Search for helices and strands: 0 residues in 0 chains, 3228 seeds are put forward NCS extension: 25 residues added (1 deleted due to clashes), 3253 seeds are put forward Round 1: 167 peptides, 31 chains. Longest chain 11 peptides. Score 0.349 Round 2: 199 peptides, 30 chains. Longest chain 18 peptides. Score 0.480 Round 3: 210 peptides, 32 chains. Longest chain 16 peptides. Score 0.487 Round 4: 213 peptides, 32 chains. Longest chain 16 peptides. Score 0.497 Round 5: 197 peptides, 34 chains. Longest chain 16 peptides. Score 0.413 Taking the results from Round 4 Last building cycle: Chain fragments will be rearranged Chains 33, Residues 181, Estimated correctness of the model 10.4 % 5 chains (30 residues) have been docked in sequence Sequence coverage is 16 % Consider running further cycles of model building using 1vlm-3_warpNtrace.pdb as input Building loops using Loopy2018 33 chains (181 residues) following loop building 5 chains (30 residues) in sequence following loop building ------------------------------------------------------ ---> Final restrained refinement block. No atom update. 7616 reflections ( 99.75 % complete ) and 6950 restraints for refining 3199 atoms. 6135 conditional restraints added. Observations/parameters ratio is 0.60 ------------------------------------------------------ Cycle 46: After refmac, R = 0.2221 (Rfree = 0.000) for 3199 atoms. Found 0 (25 requested) and removed 8 (14 requested) atoms. Cycle 47: After refmac, R = 0.2162 (Rfree = 0.000) for 3187 atoms. Found 0 (25 requested) and removed 2 (14 requested) atoms. Cycle 48: After refmac, R = 0.2215 (Rfree = 0.000) for 3184 atoms. Found 0 (25 requested) and removed 0 (14 requested) atoms. Cycle 49: After refmac, R = 0.2216 (Rfree = 0.000) for 3182 atoms. Found 0 (25 requested) and removed 1 (14 requested) atoms. Writing output files ... Normal termination of warpNtrace Mon 24 Dec 08:46:01 GMT 2018 Job finished. TimeTaking 42.79 Used memory is bytes: 11294824