Mon 24 Dec 07:28:44 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 2opk-3.8-parrot-noncs X-ray data file /users/emra500/scratch/Dataset/noncsChltofom/2opk-3.8-parrot-noncs.mtz Sequence file /users/emra500/scratch/Dataset/noncsChltofom/2opk-3.8-parrot-noncs.fasta Tracing mode WARPNTRACEPHASES Creating directory /mnt/lustre/users/emra500/PipeliensFastaNoRFree/noncs/ArpWArp/wArpResults/WorkingDir/2opk-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/2opk-3.8-parrot-noncs/arp_warp_classic.par Job launched in /mnt/lustre/users/emra500/PipeliensFastaNoRFree/noncs/ArpWArp/wArpResults/WorkingDir/2opk-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 07:28:48 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/2opk-3.8-parrot-noncs ARP/wARP software version: 8.0 The parameter file: /mnt/lustre/users/emra500/PipeliensFastaNoRFree/noncs/ArpWArp/wArpResults/WorkingDir/2opk-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 400 and 0 Target number of residues in the AU: 400 Target solvent content: 0.6190 Checking the provided sequence file Detected sequence length: 112 Maximum limit of NCS related copies: 60 Number of NCS-related molecules: 4 Adjusted target number of residues: 448 Adjusted target solvent content: 0.57 Input MTZ file: 2opk-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: 96 Cell parameters: 75.570 75.570 198.970 90.000 90.000 90.000 Input sequence file: 2opk-3.8-parrot-noncs.fasta_lf Building free atoms model in initial map for 3584 target number of atoms Had to go as low as 0.85 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: 28.177 3.801 Wilson plot Bfac: 60.71 6142 reflections ( 99.53 % complete ) and 0 restraints for refining 3977 atoms. Observations/parameters ratio is 0.39 ------------------------------------------------------ Starting model: R = 0.3115 (Rfree = 0.000). ------------------------------------------------------ Cycle 0: After refmac, R = 0.2896 (Rfree = 0.000) for 3977 atoms. Found 21 (21 requested) and removed 40 (10 requested) atoms. ------------------------------------------------------ Building Cycle 1 Atomic shape factors 3.32 3.02 Search for helices and strands: 0 residues in 0 chains, 3999 seeds are put forward NCS extension: 0 residues added, 3999 seeds are put forward Round 1: 229 peptides, 39 chains. Longest chain 13 peptides. Score 0.400 Round 2: 278 peptides, 40 chains. Longest chain 19 peptides. Score 0.517 Round 3: 288 peptides, 36 chains. Longest chain 21 peptides. Score 0.581 Round 4: 312 peptides, 36 chains. Longest chain 27 peptides. Score 0.631 Round 5: 316 peptides, 35 chains. Longest chain 24 peptides. Score 0.648 Taking the results from Round 5 Chains 35, Residues 281, Estimated correctness of the model 19.9 % 2 chains (10 residues) have been docked in sequence ------------------------------------------------------ 6142 reflections ( 99.53 % complete ) and 6659 restraints for refining 3240 atoms. 5552 conditional restraints added. Observations/parameters ratio is 0.47 ------------------------------------------------------ Cycle 1: After refmac, R = 0.2476 (Rfree = 0.000) for 3240 atoms. Found 17 (17 requested) and removed 23 (8 requested) atoms. Cycle 2: After refmac, R = 0.2426 (Rfree = 0.000) for 3181 atoms. Found 17 (17 requested) and removed 21 (8 requested) atoms. Cycle 3: After refmac, R = 0.2278 (Rfree = 0.000) for 3155 atoms. Found 17 (17 requested) and removed 16 (8 requested) atoms. Cycle 4: After refmac, R = 0.2225 (Rfree = 0.000) for 3139 atoms. Found 17 (17 requested) and removed 25 (8 requested) atoms. Cycle 5: After refmac, R = 0.2244 (Rfree = 0.000) for 3115 atoms. Found 17 (17 requested) and removed 21 (8 requested) atoms. ------------------------------------------------------ Building Cycle 2 Atomic shape factors 3.35 3.05 Search for helices and strands: 0 residues in 0 chains, 3214 seeds are put forward NCS extension: 17 residues added (11 deleted due to clashes), 3231 seeds are put forward Round 1: 268 peptides, 39 chains. Longest chain 14 peptides. Score 0.503 Round 2: 296 peptides, 34 chains. Longest chain 21 peptides. Score 0.618 Round 3: 295 peptides, 32 chains. Longest chain 28 peptides. Score 0.634 Round 4: 294 peptides, 30 chains. Longest chain 23 peptides. Score 0.650 Round 5: 302 peptides, 33 chains. Longest chain 29 peptides. Score 0.639 Taking the results from Round 4 Chains 35, Residues 264, Estimated correctness of the model 20.7 % 5 chains (60 residues) have been docked in sequence ------------------------------------------------------ 6142 reflections ( 99.53 % complete ) and 6415 restraints for refining 3241 atoms. 5197 conditional restraints added. Observations/parameters ratio is 0.47 ------------------------------------------------------ Cycle 6: After refmac, R = 0.2703 (Rfree = 0.000) for 3241 atoms. Found 17 (17 requested) and removed 36 (8 requested) atoms. Cycle 7: After refmac, R = 0.2498 (Rfree = 0.000) for 3209 atoms. Found 17 (17 requested) and removed 24 (8 requested) atoms. Cycle 8: After refmac, R = 0.2380 (Rfree = 0.000) for 3190 atoms. Found 17 (17 requested) and removed 31 (8 requested) atoms. Cycle 9: After refmac, R = 0.2311 (Rfree = 0.000) for 3166 atoms. Found 17 (17 requested) and removed 17 (8 requested) atoms. Cycle 10: After refmac, R = 0.2062 (Rfree = 0.000) for 3157 atoms. Found 5 (17 requested) and removed 13 (8 requested) atoms. ------------------------------------------------------ Building Cycle 3 Atomic shape factors 3.40 3.10 Search for helices and strands: 0 residues in 0 chains, 3205 seeds are put forward NCS extension: 22 residues added (1 deleted due to clashes), 3227 seeds are put forward Round 1: 267 peptides, 42 chains. Longest chain 15 peptides. Score 0.467 Round 2: 287 peptides, 33 chains. Longest chain 17 peptides. Score 0.609 Round 3: 281 peptides, 36 chains. Longest chain 20 peptides. Score 0.566 Round 4: 284 peptides, 35 chains. Longest chain 23 peptides. Score 0.583 Round 5: 295 peptides, 36 chains. Longest chain 21 peptides. Score 0.597 Taking the results from Round 2 Chains 36, Residues 254, Estimated correctness of the model 2.9 % 2 chains (22 residues) have been docked in sequence ------------------------------------------------------ 6142 reflections ( 99.53 % complete ) and 6717 restraints for refining 3240 atoms. 5662 conditional restraints added. Observations/parameters ratio is 0.47 ------------------------------------------------------ Cycle 11: After refmac, R = 0.2295 (Rfree = 0.000) for 3240 atoms. Found 17 (17 requested) and removed 22 (8 requested) atoms. Cycle 12: After refmac, R = 0.2370 (Rfree = 0.000) for 3210 atoms. Found 17 (17 requested) and removed 22 (8 requested) atoms. Cycle 13: After refmac, R = 0.2177 (Rfree = 0.000) for 3193 atoms. Found 17 (17 requested) and removed 14 (8 requested) atoms. Cycle 14: After refmac, R = 0.2162 (Rfree = 0.000) for 3181 atoms. Found 17 (17 requested) and removed 19 (8 requested) atoms. Cycle 15: After refmac, R = 0.2142 (Rfree = 0.000) for 3169 atoms. Found 17 (17 requested) and removed 17 (8 requested) atoms. ------------------------------------------------------ Building Cycle 4 Atomic shape factors 3.35 3.05 Search for helices and strands: 0 residues in 0 chains, 3226 seeds are put forward NCS extension: 14 residues added (3 deleted due to clashes), 3240 seeds are put forward Round 1: 258 peptides, 41 chains. Longest chain 16 peptides. Score 0.455 Round 2: 290 peptides, 39 chains. Longest chain 23 peptides. Score 0.556 Round 3: 286 peptides, 37 chains. Longest chain 23 peptides. Score 0.567 Round 4: 296 peptides, 34 chains. Longest chain 20 peptides. Score 0.618 Round 5: 288 peptides, 35 chains. Longest chain 27 peptides. Score 0.591 Taking the results from Round 4 Chains 34, Residues 262, Estimated correctness of the model 7.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 6142 reflections ( 99.53 % complete ) and 6933 restraints for refining 3241 atoms. 5919 conditional restraints added. Observations/parameters ratio is 0.47 ------------------------------------------------------ Cycle 16: After refmac, R = 0.2332 (Rfree = 0.000) for 3241 atoms. Found 11 (17 requested) and removed 20 (8 requested) atoms. Cycle 17: After refmac, R = 0.2195 (Rfree = 0.000) for 3207 atoms. Found 11 (17 requested) and removed 13 (8 requested) atoms. Cycle 18: After refmac, R = 0.2253 (Rfree = 0.000) for 3189 atoms. Found 17 (17 requested) and removed 16 (8 requested) atoms. Cycle 19: After refmac, R = 0.2005 (Rfree = 0.000) for 3182 atoms. Found 6 (17 requested) and removed 14 (8 requested) atoms. Cycle 20: After refmac, R = 0.1990 (Rfree = 0.000) for 3161 atoms. Found 7 (17 requested) and removed 10 (8 requested) atoms. ------------------------------------------------------ Building Cycle 5 Atomic shape factors 3.33 3.03 Search for helices and strands: 0 residues in 0 chains, 3216 seeds are put forward NCS extension: 19 residues added (4 deleted due to clashes), 3235 seeds are put forward Round 1: 260 peptides, 44 chains. Longest chain 13 peptides. Score 0.426 Round 2: 288 peptides, 44 chains. Longest chain 21 peptides. Score 0.498 Round 3: 277 peptides, 39 chains. Longest chain 16 peptides. Score 0.525 Round 4: 279 peptides, 37 chains. Longest chain 21 peptides. Score 0.551 Round 5: 280 peptides, 38 chains. Longest chain 17 peptides. Score 0.543 Taking the results from Round 4 Chains 39, Residues 242, Estimated correctness of the model 0.0 % 1 chains (10 residues) have been docked in sequence ------------------------------------------------------ 6142 reflections ( 99.53 % complete ) and 6939 restraints for refining 3241 atoms. 5964 conditional restraints added. Observations/parameters ratio is 0.47 ------------------------------------------------------ Cycle 21: After refmac, R = 0.2341 (Rfree = 0.000) for 3241 atoms. Found 17 (17 requested) and removed 20 (8 requested) atoms. Failed to save intermediate PDB Cycle 22: After refmac, R = 0.2292 (Rfree = 0.000) for 3215 atoms. Found 17 (17 requested) and removed 15 (8 requested) atoms. Cycle 23: After refmac, R = 0.2307 (Rfree = 0.000) for 3199 atoms. Found 17 (17 requested) and removed 19 (8 requested) atoms. Cycle 24: After refmac, R = 0.2146 (Rfree = 0.000) for 3189 atoms. Found 17 (17 requested) and removed 12 (8 requested) atoms. Cycle 25: After refmac, R = 0.2214 (Rfree = 0.000) for 3188 atoms. Found 17 (17 requested) and removed 19 (8 requested) atoms. ------------------------------------------------------ Building Cycle 6 Atomic shape factors 3.27 2.98 Search for helices and strands: 0 residues in 0 chains, 3293 seeds are put forward NCS extension: 18 residues added (2 deleted due to clashes), 3311 seeds are put forward Round 1: 248 peptides, 45 chains. Longest chain 13 peptides. Score 0.380 Round 2: 272 peptides, 39 chains. Longest chain 32 peptides. Score 0.513 Round 3: 258 peptides, 35 chains. Longest chain 20 peptides. Score 0.522 Round 4: 267 peptides, 36 chains. Longest chain 20 peptides. Score 0.533 Round 5: 264 peptides, 34 chains. Longest chain 20 peptides. Score 0.548 Taking the results from Round 5 Chains 35, Residues 230, Estimated correctness of the model 0.0 % 1 chains (9 residues) have been docked in sequence ------------------------------------------------------ Failed to save intermediate PDB 6142 reflections ( 99.53 % complete ) and 7103 restraints for refining 3241 atoms. 6194 conditional restraints added. Observations/parameters ratio is 0.47 ------------------------------------------------------ Cycle 26: After refmac, R = 0.2490 (Rfree = 0.000) for 3241 atoms. Found 17 (17 requested) and removed 23 (8 requested) atoms. Cycle 27: After refmac, R = 0.2483 (Rfree = 0.000) for 3215 atoms. Found 17 (17 requested) and removed 23 (8 requested) atoms. Cycle 28: After refmac, R = 0.2374 (Rfree = 0.000) for 3194 atoms. Found 17 (17 requested) and removed 14 (8 requested) atoms. Cycle 29: After refmac, R = 0.2360 (Rfree = 0.000) for 3179 atoms. Found 17 (17 requested) and removed 16 (8 requested) atoms. Cycle 30: After refmac, R = 0.2337 (Rfree = 0.000) for 3174 atoms. Found 17 (17 requested) and removed 17 (8 requested) atoms. ------------------------------------------------------ Building Cycle 7 Atomic shape factors 3.25 2.96 Search for helices and strands: 0 residues in 0 chains, 3236 seeds are put forward NCS extension: 20 residues added (2 deleted due to clashes), 3256 seeds are put forward Round 1: 219 peptides, 40 chains. Longest chain 10 peptides. Score 0.358 Round 2: 248 peptides, 38 chains. Longest chain 17 peptides. Score 0.463 Round 3: 259 peptides, 38 chains. Longest chain 16 peptides. Score 0.492 Round 4: 260 peptides, 37 chains. Longest chain 16 peptides. Score 0.505 Round 5: 256 peptides, 36 chains. Longest chain 17 peptides. Score 0.507 Taking the results from Round 5 Chains 36, Residues 220, Estimated correctness of the model 0.0 % 3 chains (33 residues) have been docked in sequence ------------------------------------------------------ 6142 reflections ( 99.53 % complete ) and 6834 restraints for refining 3240 atoms. 5866 conditional restraints added. Observations/parameters ratio is 0.47 ------------------------------------------------------ Cycle 31: After refmac, R = 0.2488 (Rfree = 0.000) for 3240 atoms. Found 17 (17 requested) and removed 27 (8 requested) atoms. Cycle 32: After refmac, R = 0.2358 (Rfree = 0.000) for 3211 atoms. Found 17 (17 requested) and removed 24 (8 requested) atoms. Cycle 33: After refmac, R = 0.2332 (Rfree = 0.000) for 3191 atoms. Found 17 (17 requested) and removed 19 (8 requested) atoms. Cycle 34: After refmac, R = 0.2314 (Rfree = 0.000) for 3180 atoms. Found 17 (17 requested) and removed 14 (8 requested) atoms. Cycle 35: After refmac, R = 0.1985 (Rfree = 0.000) for 3175 atoms. Found 13 (17 requested) and removed 11 (8 requested) atoms. ------------------------------------------------------ Building Cycle 8 Atomic shape factors 3.28 2.99 Search for helices and strands: 0 residues in 0 chains, 3214 seeds are put forward NCS extension: 15 residues added (3 deleted due to clashes), 3229 seeds are put forward Round 1: 219 peptides, 42 chains. Longest chain 16 peptides. Score 0.333 Round 2: 260 peptides, 42 chains. Longest chain 18 peptides. Score 0.449 Round 3: 262 peptides, 38 chains. Longest chain 20 peptides. Score 0.499 Round 4: 256 peptides, 37 chains. Longest chain 19 peptides. Score 0.495 Round 5: 266 peptides, 42 chains. Longest chain 19 peptides. Score 0.465 Taking the results from Round 3 Chains 38, Residues 224, Estimated correctness of the model 0.0 % 2 chains (19 residues) have been docked in sequence ------------------------------------------------------ 6142 reflections ( 99.53 % complete ) and 6951 restraints for refining 3241 atoms. 6026 conditional restraints added. Observations/parameters ratio is 0.47 ------------------------------------------------------ Cycle 36: After refmac, R = 0.2517 (Rfree = 0.000) for 3241 atoms. Found 17 (17 requested) and removed 22 (8 requested) atoms. Cycle 37: After refmac, R = 0.2480 (Rfree = 0.000) for 3214 atoms. Found 17 (17 requested) and removed 22 (8 requested) atoms. Cycle 38: After refmac, R = 0.2445 (Rfree = 0.000) for 3193 atoms. Found 17 (17 requested) and removed 18 (8 requested) atoms. Cycle 39: After refmac, R = 0.2428 (Rfree = 0.000) for 3174 atoms. Found 17 (17 requested) and removed 16 (8 requested) atoms. Cycle 40: After refmac, R = 0.2418 (Rfree = 0.000) for 3161 atoms. Found 17 (17 requested) and removed 18 (8 requested) atoms. ------------------------------------------------------ Building Cycle 9 Atomic shape factors 3.15 2.87 Search for helices and strands: 0 residues in 0 chains, 3222 seeds are put forward NCS extension: 26 residues added (1 deleted due to clashes), 3248 seeds are put forward Round 1: 201 peptides, 43 chains. Longest chain 9 peptides. Score 0.264 Round 2: 233 peptides, 38 chains. Longest chain 14 peptides. Score 0.423 Round 3: 225 peptides, 37 chains. Longest chain 16 peptides. Score 0.413 Round 4: 229 peptides, 34 chains. Longest chain 14 peptides. Score 0.460 Round 5: 245 peptides, 38 chains. Longest chain 16 peptides. Score 0.456 Taking the results from Round 4 Chains 34, Residues 195, Estimated correctness of the model 0.0 % 2 chains (6 residues) have been docked in sequence ------------------------------------------------------ 6142 reflections ( 99.53 % complete ) and 7234 restraints for refining 3241 atoms. 6480 conditional restraints added. Observations/parameters ratio is 0.47 ------------------------------------------------------ Cycle 41: After refmac, R = 0.2711 (Rfree = 0.000) for 3241 atoms. Found 17 (17 requested) and removed 27 (8 requested) atoms. Cycle 42: After refmac, R = 0.2555 (Rfree = 0.000) for 3216 atoms. Found 17 (17 requested) and removed 25 (8 requested) atoms. Cycle 43: After refmac, R = 0.2427 (Rfree = 0.000) for 3194 atoms. Found 17 (17 requested) and removed 13 (8 requested) atoms. Cycle 44: After refmac, R = 0.2535 (Rfree = 0.000) for 3187 atoms. Found 17 (17 requested) and removed 29 (8 requested) atoms. Cycle 45: After refmac, R = 0.2652 (Rfree = 0.000) for 3171 atoms. Found 17 (17 requested) and removed 25 (8 requested) atoms. ------------------------------------------------------ Building Cycle 10 Atomic shape factors 3.12 2.84 Search for helices and strands: 0 residues in 0 chains, 3216 seeds are put forward NCS extension: 18 residues added (0 deleted due to clashes), 3234 seeds are put forward Round 1: 154 peptides, 33 chains. Longest chain 8 peptides. Score 0.246 Round 2: 205 peptides, 38 chains. Longest chain 11 peptides. Score 0.342 Round 3: 210 peptides, 37 chains. Longest chain 12 peptides. Score 0.370 Round 4: 240 peptides, 34 chains. Longest chain 13 peptides. Score 0.489 Round 5: 230 peptides, 38 chains. Longest chain 15 peptides. Score 0.415 Taking the results from Round 4 Last building cycle: Chain fragments will be rearranged Chains 34, Residues 206, Estimated correctness of the model 0.0 % 3 chains (12 residues) have been docked in sequence Sequence coverage is 5 % Consider running further cycles of model building using 2opk-3_warpNtrace.pdb as input Building loops using Loopy2018 34 chains (206 residues) following loop building 3 chains (12 residues) in sequence following loop building ------------------------------------------------------ ---> Final restrained refinement block. No atom update. 6142 reflections ( 99.53 % complete ) and 6832 restraints for refining 3139 atoms. 6008 conditional restraints added. Observations/parameters ratio is 0.49 ------------------------------------------------------ Cycle 46: After refmac, R = 0.2546 (Rfree = 0.000) for 3139 atoms. Found 0 (17 requested) and removed 8 (8 requested) atoms. Cycle 47: After refmac, R = 0.2583 (Rfree = 0.000) for 3115 atoms. Found 0 (17 requested) and removed 8 (8 requested) atoms. Cycle 48: After refmac, R = 0.2560 (Rfree = 0.000) for 3102 atoms. Found 0 (17 requested) and removed 8 (8 requested) atoms. Cycle 49: After refmac, R = 0.2546 (Rfree = 0.000) for 3083 atoms. TimeTaking 35.62