Sun 23 Dec 23:43:06 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 2od6-3.2-parrot-mrncs X-ray data file /users/emra500/scratch/Dataset/mrncsChltofom/2od6-3.2-parrot-mrncs.mtz Sequence file /users/emra500/scratch/Dataset/mrncsChltofom/2od6-3.2-parrot-mrncs.fasta Tracing mode WARPNTRACEPHASES Creating directory /mnt/lustre/users/emra500/PipeliensFastaNoRFree/mrncs/ArpWArp/wArpResults/WorkingDir/2od6-3.2-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/2od6-3.2-parrot-mrncs/arp_warp_classic.par Job launched in /mnt/lustre/users/emra500/PipeliensFastaNoRFree/mrncs/ArpWArp/wArpResults/WorkingDir/2od6-3.2-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 ============================================================ Sun 23 Dec 23:43:11 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/2od6-3.2-parrot-mrncs ARP/wARP software version: 8.0 The parameter file: /mnt/lustre/users/emra500/PipeliensFastaNoRFree/mrncs/ArpWArp/wArpResults/WorkingDir/2od6-3.2-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 333 and 0 Target number of residues in the AU: 333 Target solvent content: 0.6318 Checking the provided sequence file Detected sequence length: 110 Maximum limit of NCS related copies: 60 Number of NCS-related molecules: 4 Adjusted target number of residues: 440 Adjusted target solvent content: 0.51 Input MTZ file: 2od6-3.2-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: 36.403 92.834 144.837 90.000 90.000 90.000 Input sequence file: 2od6-3.2-parrot-mrncs.fasta_lf Building free atoms model in initial map for 3520 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: 29.066 3.200 Wilson plot Bfac: 67.36 8570 reflections ( 99.12 % complete ) and 0 restraints for refining 3880 atoms. Observations/parameters ratio is 0.55 ------------------------------------------------------ Starting model: R = 0.3307 (Rfree = 0.000). ------------------------------------------------------ Cycle 0: After refmac, R = 0.3163 (Rfree = 0.000) for 3880 atoms. Found 34 (34 requested) and removed 31 (17 requested) atoms. ------------------------------------------------------ Building Cycle 1 Atomic shape factors 3.23 3.19 Search for helices and strands: 0 residues in 0 chains, 3982 seeds are put forward NCS extension: 0 residues added, 3982 seeds are put forward Round 1: 225 peptides, 38 chains. Longest chain 11 peptides. Score 0.428 Round 2: 278 peptides, 38 chains. Longest chain 17 peptides. Score 0.578 Round 3: 304 peptides, 35 chains. Longest chain 27 peptides. Score 0.668 Round 4: 288 peptides, 33 chains. Longest chain 31 peptides. Score 0.654 Round 5: 308 peptides, 34 chains. Longest chain 32 peptides. Score 0.686 Taking the results from Round 5 Chains 36, Residues 274, Estimated correctness of the model 62.2 % 3 chains (58 residues) have been docked in sequence ------------------------------------------------------ 8570 reflections ( 99.12 % complete ) and 6160 restraints for refining 3213 atoms. 4848 conditional restraints added. Observations/parameters ratio is 0.67 ------------------------------------------------------ Cycle 1: After refmac, R = 0.2716 (Rfree = 0.000) for 3213 atoms. Found 23 (28 requested) and removed 31 (14 requested) atoms. Cycle 2: After refmac, R = 0.2507 (Rfree = 0.000) for 3171 atoms. Found 8 (28 requested) and removed 19 (14 requested) atoms. Cycle 3: After refmac, R = 0.2447 (Rfree = 0.000) for 3150 atoms. Found 9 (28 requested) and removed 18 (14 requested) atoms. Cycle 4: After refmac, R = 0.2289 (Rfree = 0.000) for 3130 atoms. Found 6 (28 requested) and removed 16 (14 requested) atoms. Cycle 5: After refmac, R = 0.2319 (Rfree = 0.000) for 3108 atoms. Found 8 (28 requested) and removed 17 (14 requested) atoms. ------------------------------------------------------ Building Cycle 2 Atomic shape factors 3.28 3.24 Search for helices and strands: 0 residues in 0 chains, 3212 seeds are put forward NCS extension: 34 residues added (7 deleted due to clashes), 3246 seeds are put forward Round 1: 272 peptides, 35 chains. Longest chain 18 peptides. Score 0.596 Round 2: 286 peptides, 34 chains. Longest chain 18 peptides. Score 0.639 Round 3: 293 peptides, 33 chains. Longest chain 31 peptides. Score 0.664 Round 4: 296 peptides, 32 chains. Longest chain 25 peptides. Score 0.680 Round 5: 314 peptides, 32 chains. Longest chain 30 peptides. Score 0.715 Taking the results from Round 5 Chains 32, Residues 282, Estimated correctness of the model 68.3 % 2 chains (32 residues) have been docked in sequence Building loops using Loopy2018 32 chains (282 residues) following loop building 2 chains (32 residues) in sequence following loop building ------------------------------------------------------ 8570 reflections ( 99.12 % complete ) and 6465 restraints for refining 3213 atoms. 5239 conditional restraints added. Observations/parameters ratio is 0.67 ------------------------------------------------------ Cycle 6: After refmac, R = 0.2691 (Rfree = 0.000) for 3213 atoms. Found 17 (28 requested) and removed 21 (14 requested) atoms. Cycle 7: After refmac, R = 0.2637 (Rfree = 0.000) for 3184 atoms. Found 6 (27 requested) and removed 21 (14 requested) atoms. Failed to save intermediate PDB Cycle 8: After refmac, R = 0.2517 (Rfree = 0.000) for 3153 atoms. Found 8 (27 requested) and removed 15 (14 requested) atoms. Cycle 9: After refmac, R = 0.2378 (Rfree = 0.000) for 3142 atoms. Found 8 (26 requested) and removed 16 (14 requested) atoms. Cycle 10: After refmac, R = 0.2802 (Rfree = 0.000) for 3130 atoms. Found 22 (26 requested) and removed 21 (14 requested) atoms. ------------------------------------------------------ Building Cycle 3 Atomic shape factors 3.27 3.23 Search for helices and strands: 0 residues in 0 chains, 3259 seeds are put forward NCS extension: 34 residues added (2 deleted due to clashes), 3293 seeds are put forward Round 1: 282 peptides, 39 chains. Longest chain 25 peptides. Score 0.577 Round 2: 309 peptides, 35 chains. Longest chain 33 peptides. Score 0.678 Round 3: 297 peptides, 32 chains. Longest chain 29 peptides. Score 0.682 Round 4: 294 peptides, 32 chains. Longest chain 28 peptides. Score 0.676 Round 5: 291 peptides, 35 chains. Longest chain 27 peptides. Score 0.640 Taking the results from Round 3 Chains 35, Residues 265, Estimated correctness of the model 61.3 % 2 chains (30 residues) have been docked in sequence ------------------------------------------------------ 8570 reflections ( 99.12 % complete ) and 6619 restraints for refining 3213 atoms. 5464 conditional restraints added. Observations/parameters ratio is 0.67 ------------------------------------------------------ Cycle 11: After refmac, R = 0.2631 (Rfree = 0.000) for 3213 atoms. Found 19 (25 requested) and removed 19 (14 requested) atoms. Cycle 12: After refmac, R = 0.2520 (Rfree = 0.000) for 3202 atoms. Found 7 (25 requested) and removed 15 (14 requested) atoms. Cycle 13: After refmac, R = 0.2384 (Rfree = 0.000) for 3190 atoms. Found 5 (25 requested) and removed 16 (14 requested) atoms. Cycle 14: After refmac, R = 0.2420 (Rfree = 0.000) for 3177 atoms. Found 8 (25 requested) and removed 17 (14 requested) atoms. Cycle 15: After refmac, R = 0.2475 (Rfree = 0.000) for 3161 atoms. Found 19 (25 requested) and removed 15 (14 requested) atoms. ------------------------------------------------------ Building Cycle 4 Atomic shape factors 3.28 3.24 Search for helices and strands: 0 residues in 0 chains, 3260 seeds are put forward NCS extension: 30 residues added (1 deleted due to clashes), 3290 seeds are put forward Round 1: 281 peptides, 33 chains. Longest chain 21 peptides. Score 0.638 Round 2: 298 peptides, 30 chains. Longest chain 36 peptides. Score 0.702 Round 3: 292 peptides, 33 chains. Longest chain 23 peptides. Score 0.662 Round 4: 287 peptides, 32 chains. Longest chain 37 peptides. Score 0.661 Round 5: 282 peptides, 33 chains. Longest chain 32 peptides. Score 0.641 Taking the results from Round 2 Chains 31, Residues 268, Estimated correctness of the model 65.6 % 1 chains (24 residues) have been docked in sequence ------------------------------------------------------ 8570 reflections ( 99.12 % complete ) and 6615 restraints for refining 3213 atoms. 5471 conditional restraints added. Observations/parameters ratio is 0.67 ------------------------------------------------------ Cycle 16: After refmac, R = 0.2503 (Rfree = 0.000) for 3213 atoms. Found 9 (25 requested) and removed 18 (14 requested) atoms. Cycle 17: After refmac, R = 0.2620 (Rfree = 0.000) for 3200 atoms. Found 12 (25 requested) and removed 19 (14 requested) atoms. Cycle 18: After refmac, R = 0.3134 (Rfree = 0.000) for 3189 atoms. Found 24 (24 requested) and removed 27 (14 requested) atoms. Failed to save intermediate PDB Cycle 19: After refmac, R = 0.2503 (Rfree = 0.000) for 3180 atoms. Found 16 (24 requested) and removed 20 (14 requested) atoms. Cycle 20: After refmac, R = 0.2284 (Rfree = 0.000) for 3170 atoms. Found 8 (23 requested) and removed 16 (14 requested) atoms. ------------------------------------------------------ Building Cycle 5 Atomic shape factors 3.28 3.24 Search for helices and strands: 0 residues in 0 chains, 3280 seeds are put forward NCS extension: 14 residues added (0 deleted due to clashes), 3294 seeds are put forward Round 1: 261 peptides, 33 chains. Longest chain 16 peptides. Score 0.591 Round 2: 281 peptides, 29 chains. Longest chain 28 peptides. Score 0.678 Round 3: 284 peptides, 30 chains. Longest chain 28 peptides. Score 0.675 Round 4: 297 peptides, 28 chains. Longest chain 36 peptides. Score 0.718 Round 5: 279 peptides, 32 chains. Longest chain 30 peptides. Score 0.644 Taking the results from Round 4 Chains 31, Residues 269, Estimated correctness of the model 68.9 % 2 chains (26 residues) have been docked in sequence Building loops using Loopy2018 31 chains (269 residues) following loop building 2 chains (26 residues) in sequence following loop building ------------------------------------------------------ 8570 reflections ( 99.12 % complete ) and 6585 restraints for refining 3213 atoms. 5432 conditional restraints added. Observations/parameters ratio is 0.67 ------------------------------------------------------ Cycle 21: After refmac, R = 0.2581 (Rfree = 0.000) for 3213 atoms. Found 18 (22 requested) and removed 25 (14 requested) atoms. Cycle 22: After refmac, R = 0.2422 (Rfree = 0.000) for 3197 atoms. Found 7 (22 requested) and removed 17 (14 requested) atoms. Cycle 23: After refmac, R = 0.2415 (Rfree = 0.000) for 3187 atoms. Found 6 (21 requested) and removed 16 (14 requested) atoms. Cycle 24: After refmac, R = 0.2550 (Rfree = 0.000) for 3174 atoms. Found 10 (21 requested) and removed 21 (14 requested) atoms. Failed to save intermediate PDB Cycle 25: After refmac, R = 0.2549 (Rfree = 0.000) for 3159 atoms. Found 14 (20 requested) and removed 19 (14 requested) atoms. ------------------------------------------------------ Building Cycle 6 Atomic shape factors 3.24 3.20 Search for helices and strands: 0 residues in 0 chains, 3262 seeds are put forward NCS extension: 48 residues added (3 deleted due to clashes), 3310 seeds are put forward Round 1: 258 peptides, 36 chains. Longest chain 14 peptides. Score 0.549 Round 2: 288 peptides, 32 chains. Longest chain 27 peptides. Score 0.664 Round 3: 283 peptides, 32 chains. Longest chain 23 peptides. Score 0.653 Round 4: 292 peptides, 30 chains. Longest chain 33 peptides. Score 0.691 Round 5: 276 peptides, 35 chains. Longest chain 22 peptides. Score 0.606 Taking the results from Round 4 Chains 30, Residues 262, Estimated correctness of the model 63.2 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 8570 reflections ( 99.12 % complete ) and 7107 restraints for refining 3213 atoms. 6089 conditional restraints added. Observations/parameters ratio is 0.67 ------------------------------------------------------ Cycle 26: After refmac, R = 0.2508 (Rfree = 0.000) for 3213 atoms. Found 20 (20 requested) and removed 19 (14 requested) atoms. Cycle 27: After refmac, R = 0.2743 (Rfree = 0.000) for 3209 atoms. Found 20 (20 requested) and removed 17 (14 requested) atoms. Cycle 28: After refmac, R = 0.2451 (Rfree = 0.000) for 3208 atoms. Found 18 (20 requested) and removed 15 (14 requested) atoms. Cycle 29: After refmac, R = 0.2192 (Rfree = 0.000) for 3209 atoms. Found 8 (20 requested) and removed 16 (14 requested) atoms. Cycle 30: After refmac, R = 0.2279 (Rfree = 0.000) for 3199 atoms. Found 14 (20 requested) and removed 14 (14 requested) atoms. ------------------------------------------------------ Building Cycle 7 Atomic shape factors 3.27 3.23 Search for helices and strands: 0 residues in 0 chains, 3294 seeds are put forward NCS extension: 23 residues added (10 deleted due to clashes), 3317 seeds are put forward Round 1: 244 peptides, 32 chains. Longest chain 22 peptides. Score 0.559 Round 2: 275 peptides, 32 chains. Longest chain 29 peptides. Score 0.635 Round 3: 275 peptides, 33 chains. Longest chain 27 peptides. Score 0.625 Round 4: 272 peptides, 29 chains. Longest chain 36 peptides. Score 0.659 Round 5: 280 peptides, 30 chains. Longest chain 28 peptides. Score 0.666 Taking the results from Round 5 Chains 30, Residues 250, Estimated correctness of the model 57.6 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 8570 reflections ( 99.12 % complete ) and 7170 restraints for refining 3213 atoms. 6200 conditional restraints added. Observations/parameters ratio is 0.67 ------------------------------------------------------ Cycle 31: After refmac, R = 0.2470 (Rfree = 0.000) for 3213 atoms. Found 19 (20 requested) and removed 14 (14 requested) atoms. Cycle 32: After refmac, R = 0.2358 (Rfree = 0.000) for 3209 atoms. Found 7 (20 requested) and removed 15 (14 requested) atoms. Cycle 33: After refmac, R = 0.2379 (Rfree = 0.000) for 3199 atoms. Found 10 (20 requested) and removed 15 (14 requested) atoms. Cycle 34: After refmac, R = 0.2190 (Rfree = 0.000) for 3187 atoms. Found 4 (20 requested) and removed 15 (14 requested) atoms. Cycle 35: After refmac, R = 0.2243 (Rfree = 0.000) for 3174 atoms. Found 6 (20 requested) and removed 14 (14 requested) atoms. ------------------------------------------------------ Building Cycle 8 Atomic shape factors 3.28 3.24 Search for helices and strands: 0 residues in 0 chains, 3264 seeds are put forward NCS extension: 19 residues added (5 deleted due to clashes), 3283 seeds are put forward Round 1: 233 peptides, 34 chains. Longest chain 13 peptides. Score 0.504 Round 2: 258 peptides, 33 chains. Longest chain 17 peptides. Score 0.584 Round 3: 270 peptides, 32 chains. Longest chain 18 peptides. Score 0.624 Round 4: 271 peptides, 32 chains. Longest chain 17 peptides. Score 0.626 Round 5: 257 peptides, 33 chains. Longest chain 18 peptides. Score 0.581 Taking the results from Round 4 Chains 34, Residues 239, Estimated correctness of the model 47.9 % 1 chains (10 residues) have been docked in sequence ------------------------------------------------------ 8570 reflections ( 99.12 % complete ) and 7076 restraints for refining 3213 atoms. 6107 conditional restraints added. Observations/parameters ratio is 0.67 ------------------------------------------------------ Cycle 36: After refmac, R = 0.2413 (Rfree = 0.000) for 3213 atoms. Found 15 (20 requested) and removed 14 (14 requested) atoms. Cycle 37: After refmac, R = 0.2274 (Rfree = 0.000) for 3207 atoms. Found 11 (20 requested) and removed 14 (14 requested) atoms. Cycle 38: After refmac, R = 0.2222 (Rfree = 0.000) for 3199 atoms. Found 7 (20 requested) and removed 14 (14 requested) atoms. Cycle 39: After refmac, R = 0.2223 (Rfree = 0.000) for 3189 atoms. Found 2 (20 requested) and removed 14 (14 requested) atoms. Cycle 40: After refmac, R = 0.2223 (Rfree = 0.000) for 3176 atoms. Found 2 (20 requested) and removed 14 (14 requested) atoms. ------------------------------------------------------ Building Cycle 9 Atomic shape factors 3.29 3.25 Search for helices and strands: 0 residues in 0 chains, 3240 seeds are put forward NCS extension: 14 residues added (0 deleted due to clashes), 3254 seeds are put forward Round 1: 251 peptides, 35 chains. Longest chain 16 peptides. Score 0.542 Round 2: 281 peptides, 34 chains. Longest chain 22 peptides. Score 0.628 Round 3: 278 peptides, 35 chains. Longest chain 18 peptides. Score 0.611 Round 4: 267 peptides, 35 chains. Longest chain 16 peptides. Score 0.584 Round 5: 272 peptides, 35 chains. Longest chain 16 peptides. Score 0.596 Taking the results from Round 2 Chains 35, Residues 247, Estimated correctness of the model 48.4 % 1 chains (10 residues) have been docked in sequence ------------------------------------------------------ 8570 reflections ( 99.12 % complete ) and 6999 restraints for refining 3212 atoms. 6000 conditional restraints added. Observations/parameters ratio is 0.67 ------------------------------------------------------ Cycle 41: After refmac, R = 0.2448 (Rfree = 0.000) for 3212 atoms. Found 13 (20 requested) and removed 15 (14 requested) atoms. Cycle 42: After refmac, R = 0.2413 (Rfree = 0.000) for 3209 atoms. Found 5 (20 requested) and removed 15 (14 requested) atoms. Cycle 43: After refmac, R = 0.2313 (Rfree = 0.000) for 3195 atoms. Found 8 (20 requested) and removed 15 (14 requested) atoms. Cycle 44: After refmac, R = 0.2209 (Rfree = 0.000) for 3184 atoms. Found 4 (20 requested) and removed 14 (14 requested) atoms. Cycle 45: After refmac, R = 0.2184 (Rfree = 0.000) for 3173 atoms. Found 5 (20 requested) and removed 14 (14 requested) atoms. ------------------------------------------------------ Building Cycle 10 Atomic shape factors 3.27 3.23 Search for helices and strands: 0 residues in 0 chains, 3265 seeds are put forward NCS extension: 20 residues added (4 deleted due to clashes), 3285 seeds are put forward Round 1: 229 peptides, 35 chains. Longest chain 17 peptides. Score 0.480 Round 2: 260 peptides, 33 chains. Longest chain 23 peptides. Score 0.589 Round 3: 274 peptides, 35 chains. Longest chain 26 peptides. Score 0.601 Round 4: 265 peptides, 36 chains. Longest chain 19 peptides. Score 0.567 Round 5: 259 peptides, 34 chains. Longest chain 25 peptides. Score 0.575 Taking the results from Round 3 Last building cycle: Chain fragments will be rearranged Chains 37, Residues 239, Estimated correctness of the model 41.3 % 2 chains (27 residues) have been docked in sequence Sequence coverage is 11 % Consider running further cycles of model building using 2od6-3_warpNtrace.pdb as input Building loops using Loopy2018 37 chains (239 residues) following loop building 2 chains (27 residues) in sequence following loop building ------------------------------------------------------ ---> Final restrained refinement block. No atom update. 8570 reflections ( 99.12 % complete ) and 6704 restraints for refining 3212 atoms. 5650 conditional restraints added. Observations/parameters ratio is 0.67 ------------------------------------------------------ Cycle 46: After refmac, R = 0.2369 (Rfree = 0.000) for 3212 atoms. Found 0 (20 requested) and removed 14 (14 requested) atoms. Cycle 47: After refmac, R = 0.2335 (Rfree = 0.000) for 3191 atoms. Found 0 (20 requested) and removed 8 (14 requested) atoms. Cycle 48: After refmac, R = 0.2269 (Rfree = 0.000) for 3180 atoms. Found 0 (20 requested) and removed 7 (14 requested) atoms. Cycle 49: After refmac, R = 0.2303 (Rfree = 0.000) for 3169 atoms. TimeTaking 45.32