Mon 24 Dec 00:05:40 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 2a6a-3.2-parrot-mrncs X-ray data file /users/emra500/scratch/Dataset/mrncsChltofom/2a6a-3.2-parrot-mrncs.mtz Sequence file /users/emra500/scratch/Dataset/mrncsChltofom/2a6a-3.2-parrot-mrncs.fasta Tracing mode WARPNTRACEPHASES Creating directory /mnt/lustre/users/emra500/PipeliensFastaNoRFree/mrncs/ArpWArp/wArpResults/WorkingDir/2a6a-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/2a6a-3.2-parrot-mrncs/arp_warp_classic.par Job launched in /mnt/lustre/users/emra500/PipeliensFastaNoRFree/mrncs/ArpWArp/wArpResults/WorkingDir/2a6a-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 ============================================================ Mon 24 Dec 00:05:44 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/2a6a-3.2-parrot-mrncs ARP/wARP software version: 8.0 The parameter file: /mnt/lustre/users/emra500/PipeliensFastaNoRFree/mrncs/ArpWArp/wArpResults/WorkingDir/2a6a-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 339 and 0 Target number of residues in the AU: 339 Target solvent content: 0.6516 Checking the provided sequence file Detected sequence length: 218 Maximum limit of NCS related copies: 60 Number of NCS-related molecules: 2 Adjusted target number of residues: 436 Adjusted target solvent content: 0.55 Input MTZ file: 2a6a-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: 21 Cell parameters: 93.313 217.176 51.977 90.000 90.000 90.000 Input sequence file: 2a6a-3.2-parrot-mrncs.fasta_lf Building free atoms model in initial map for 3488 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: 108.588 3.200 Wilson plot Bfac: 79.01 9055 reflections ( 99.15 % complete ) and 0 restraints for refining 3838 atoms. Observations/parameters ratio is 0.59 ------------------------------------------------------ Starting model: R = 0.3362 (Rfree = 0.000). ------------------------------------------------------ Cycle 0: After refmac, R = 0.3439 (Rfree = 0.000) for 3838 atoms. Found 34 (34 requested) and removed 58 (17 requested) atoms. ------------------------------------------------------ Building Cycle 1 Atomic shape factors 3.44 3.22 Search for helices and strands: 0 residues in 0 chains, 3892 seeds are put forward NCS extension: 0 residues added, 3892 seeds are put forward Round 1: 196 peptides, 34 chains. Longest chain 13 peptides. Score 0.378 Round 2: 254 peptides, 36 chains. Longest chain 24 peptides. Score 0.520 Round 3: 245 peptides, 32 chains. Longest chain 24 peptides. Score 0.542 Round 4: 261 peptides, 31 chains. Longest chain 24 peptides. Score 0.592 Round 5: 279 peptides, 31 chains. Longest chain 23 peptides. Score 0.633 Taking the results from Round 5 Chains 35, Residues 248, Estimated correctness of the model 49.7 % 4 chains (48 residues) have been docked in sequence ------------------------------------------------------ 9055 reflections ( 99.15 % complete ) and 6543 restraints for refining 3184 atoms. 5410 conditional restraints added. Observations/parameters ratio is 0.71 ------------------------------------------------------ Cycle 1: After refmac, R = 0.3079 (Rfree = 0.000) for 3184 atoms. Found 22 (28 requested) and removed 52 (14 requested) atoms. Cycle 2: After refmac, R = 0.2640 (Rfree = 0.000) for 3090 atoms. Found 28 (28 requested) and removed 23 (14 requested) atoms. Cycle 3: After refmac, R = 0.2618 (Rfree = 0.000) for 3050 atoms. Found 19 (27 requested) and removed 21 (13 requested) atoms. Cycle 4: After refmac, R = 0.2856 (Rfree = 0.000) for 3017 atoms. Found 27 (27 requested) and removed 31 (13 requested) atoms. Cycle 5: After refmac, R = 0.2691 (Rfree = 0.000) for 2998 atoms. Found 27 (27 requested) and removed 27 (13 requested) atoms. ------------------------------------------------------ Building Cycle 2 Atomic shape factors 3.33 3.11 Search for helices and strands: 0 residues in 0 chains, 3125 seeds are put forward NCS extension: 27 residues added (5 deleted due to clashes), 3152 seeds are put forward Round 1: 248 peptides, 29 chains. Longest chain 22 peptides. Score 0.583 Round 2: 280 peptides, 29 chains. Longest chain 24 peptides. Score 0.654 Round 3: 283 peptides, 24 chains. Longest chain 39 peptides. Score 0.705 Round 4: 294 peptides, 21 chains. Longest chain 44 peptides. Score 0.749 Round 5: 287 peptides, 23 chains. Longest chain 42 peptides. Score 0.721 Taking the results from Round 4 Chains 25, Residues 273, Estimated correctness of the model 74.9 % 4 chains (86 residues) have been docked in sequence Building loops using Loopy2018 Built loop between residues 60 A and 70 A 24 chains (276 residues) following loop building 3 chains (95 residues) in sequence following loop building ------------------------------------------------------ 9055 reflections ( 99.15 % complete ) and 5637 restraints for refining 3144 atoms. 4288 conditional restraints added. Observations/parameters ratio is 0.72 ------------------------------------------------------ Cycle 6: After refmac, R = 0.2909 (Rfree = 0.000) for 3144 atoms. Found 28 (28 requested) and removed 39 (14 requested) atoms. Cycle 7: After refmac, R = 0.2693 (Rfree = 0.000) for 3091 atoms. Found 26 (27 requested) and removed 31 (14 requested) atoms. Cycle 8: After refmac, R = 0.2752 (Rfree = 0.000) for 3055 atoms. Found 26 (26 requested) and removed 35 (13 requested) atoms. Cycle 9: After refmac, R = 0.2300 (Rfree = 0.000) for 3010 atoms. Found 18 (25 requested) and removed 25 (13 requested) atoms. Cycle 10: After refmac, R = 0.2229 (Rfree = 0.000) for 2986 atoms. Found 7 (24 requested) and removed 21 (13 requested) atoms. ------------------------------------------------------ Building Cycle 3 Atomic shape factors 3.36 3.14 Search for helices and strands: 0 residues in 0 chains, 3092 seeds are put forward NCS extension: 33 residues added (3 deleted due to clashes), 3125 seeds are put forward Round 1: 272 peptides, 32 chains. Longest chain 31 peptides. Score 0.607 Round 2: 291 peptides, 31 chains. Longest chain 31 peptides. Score 0.657 Round 3: 283 peptides, 26 chains. Longest chain 23 peptides. Score 0.688 Round 4: 282 peptides, 29 chains. Longest chain 25 peptides. Score 0.658 Round 5: 281 peptides, 25 chains. Longest chain 23 peptides. Score 0.693 Taking the results from Round 5 Chains 27, Residues 256, Estimated correctness of the model 63.7 % 3 chains (50 residues) have been docked in sequence ------------------------------------------------------ 9055 reflections ( 99.15 % complete ) and 6364 restraints for refining 3185 atoms. 5185 conditional restraints added. Observations/parameters ratio is 0.71 ------------------------------------------------------ Cycle 11: After refmac, R = 0.2652 (Rfree = 0.000) for 3185 atoms. Found 25 (25 requested) and removed 43 (14 requested) atoms. Cycle 12: After refmac, R = 0.2698 (Rfree = 0.000) for 3156 atoms. Found 25 (25 requested) and removed 25 (14 requested) atoms. Cycle 13: After refmac, R = 0.2325 (Rfree = 0.000) for 3148 atoms. Found 15 (25 requested) and removed 21 (14 requested) atoms. Cycle 14: After refmac, R = 0.2671 (Rfree = 0.000) for 3124 atoms. Found 25 (25 requested) and removed 25 (14 requested) atoms. Cycle 15: After refmac, R = 0.2270 (Rfree = 0.000) for 3118 atoms. Found 19 (25 requested) and removed 15 (14 requested) atoms. ------------------------------------------------------ Building Cycle 4 Atomic shape factors 3.36 3.14 Search for helices and strands: 0 residues in 0 chains, 3202 seeds are put forward NCS extension: 14 residues added (3 deleted due to clashes), 3216 seeds are put forward Round 1: 244 peptides, 29 chains. Longest chain 22 peptides. Score 0.574 Round 2: 262 peptides, 28 chains. Longest chain 39 peptides. Score 0.626 Round 3: 253 peptides, 25 chains. Longest chain 21 peptides. Score 0.637 Round 4: 255 peptides, 30 chains. Longest chain 20 peptides. Score 0.589 Round 5: 254 peptides, 30 chains. Longest chain 20 peptides. Score 0.587 Taking the results from Round 3 Chains 26, Residues 228, Estimated correctness of the model 50.7 % 3 chains (42 residues) have been docked in sequence ------------------------------------------------------ 9055 reflections ( 99.15 % complete ) and 6471 restraints for refining 3185 atoms. 5431 conditional restraints added. Observations/parameters ratio is 0.71 ------------------------------------------------------ Cycle 16: After refmac, R = 0.2854 (Rfree = 0.000) for 3185 atoms. Found 25 (25 requested) and removed 41 (14 requested) atoms. Cycle 17: After refmac, R = 0.2447 (Rfree = 0.000) for 3157 atoms. Found 25 (25 requested) and removed 21 (14 requested) atoms. Cycle 18: After refmac, R = 0.2711 (Rfree = 0.000) for 3153 atoms. Found 25 (25 requested) and removed 24 (14 requested) atoms. Cycle 19: After refmac, R = 0.2630 (Rfree = 0.000) for 3135 atoms. Found 25 (25 requested) and removed 20 (14 requested) atoms. Cycle 20: After refmac, R = 0.2323 (Rfree = 0.000) for 3131 atoms. Found 21 (25 requested) and removed 15 (14 requested) atoms. ------------------------------------------------------ Building Cycle 5 Atomic shape factors 3.33 3.11 Search for helices and strands: 0 residues in 0 chains, 3222 seeds are put forward NCS extension: 18 residues added (5 deleted due to clashes), 3240 seeds are put forward Round 1: 249 peptides, 32 chains. Longest chain 20 peptides. Score 0.553 Round 2: 269 peptides, 27 chains. Longest chain 32 peptides. Score 0.651 Round 3: 270 peptides, 30 chains. Longest chain 20 peptides. Score 0.623 Round 4: 253 peptides, 25 chains. Longest chain 30 peptides. Score 0.637 Round 5: 251 peptides, 28 chains. Longest chain 25 peptides. Score 0.601 Taking the results from Round 2 Chains 27, Residues 242, Estimated correctness of the model 54.1 % 1 chains (31 residues) have been docked in sequence ------------------------------------------------------ 9055 reflections ( 99.15 % complete ) and 6186 restraints for refining 3140 atoms. 5114 conditional restraints added. Observations/parameters ratio is 0.72 ------------------------------------------------------ Cycle 21: After refmac, R = 0.2912 (Rfree = 0.000) for 3140 atoms. Found 25 (25 requested) and removed 41 (14 requested) atoms. Cycle 22: After refmac, R = 0.2673 (Rfree = 0.000) for 3105 atoms. Found 25 (25 requested) and removed 31 (14 requested) atoms. Cycle 23: After refmac, R = 0.2673 (Rfree = 0.000) for 3085 atoms. Found 24 (24 requested) and removed 24 (13 requested) atoms. Cycle 24: After refmac, R = 0.2338 (Rfree = 0.000) for 3074 atoms. Found 16 (24 requested) and removed 32 (13 requested) atoms. Cycle 25: After refmac, R = 0.2843 (Rfree = 0.000) for 3049 atoms. Found 24 (24 requested) and removed 70 (13 requested) atoms. ------------------------------------------------------ Building Cycle 6 Atomic shape factors 3.37 3.15 Search for helices and strands: 0 residues in 0 chains, 3138 seeds are put forward NCS extension: 29 residues added (8 deleted due to clashes), 3167 seeds are put forward Round 1: 213 peptides, 32 chains. Longest chain 19 peptides. Score 0.456 Round 2: 248 peptides, 33 chains. Longest chain 25 peptides. Score 0.539 Round 3: 249 peptides, 31 chains. Longest chain 31 peptides. Score 0.564 Round 4: 249 peptides, 24 chains. Longest chain 30 peptides. Score 0.639 Round 5: 251 peptides, 27 chains. Longest chain 42 peptides. Score 0.612 Taking the results from Round 4 Chains 26, Residues 225, Estimated correctness of the model 51.1 % 1 chains (10 residues) have been docked in sequence ------------------------------------------------------ 9055 reflections ( 99.15 % complete ) and 6286 restraints for refining 3049 atoms. 5387 conditional restraints added. Observations/parameters ratio is 0.74 ------------------------------------------------------ Cycle 26: After refmac, R = 0.2434 (Rfree = 0.000) for 3049 atoms. Found 23 (24 requested) and removed 40 (13 requested) atoms. Cycle 27: After refmac, R = 0.2426 (Rfree = 0.000) for 3016 atoms. Found 24 (24 requested) and removed 24 (13 requested) atoms. Cycle 28: After refmac, R = 0.2765 (Rfree = 0.000) for 2994 atoms. Found 24 (24 requested) and removed 25 (13 requested) atoms. Cycle 29: After refmac, R = 0.2359 (Rfree = 0.000) for 2980 atoms. Found 23 (23 requested) and removed 18 (13 requested) atoms. Cycle 30: After refmac, R = 0.2806 (Rfree = 0.000) for 2975 atoms. Found 23 (23 requested) and removed 20 (13 requested) atoms. ------------------------------------------------------ Building Cycle 7 Atomic shape factors 3.36 3.14 Search for helices and strands: 0 residues in 0 chains, 3097 seeds are put forward NCS extension: 23 residues added (6 deleted due to clashes), 3120 seeds are put forward Round 1: 223 peptides, 32 chains. Longest chain 20 peptides. Score 0.484 Round 2: 257 peptides, 27 chains. Longest chain 31 peptides. Score 0.625 Round 3: 253 peptides, 28 chains. Longest chain 27 peptides. Score 0.606 Round 4: 247 peptides, 25 chains. Longest chain 37 peptides. Score 0.624 Round 5: 262 peptides, 29 chains. Longest chain 31 peptides. Score 0.616 Taking the results from Round 2 Chains 31, Residues 230, Estimated correctness of the model 47.6 % 3 chains (67 residues) have been docked in sequence ------------------------------------------------------ 9055 reflections ( 99.15 % complete ) and 5659 restraints for refining 3110 atoms. 4497 conditional restraints added. Observations/parameters ratio is 0.73 ------------------------------------------------------ Cycle 31: After refmac, R = 0.2935 (Rfree = 0.000) for 3110 atoms. Found 24 (24 requested) and removed 142 (13 requested) atoms. Cycle 32: After refmac, R = 0.2282 (Rfree = 0.000) for 2972 atoms. Found 23 (23 requested) and removed 16 (13 requested) atoms. Cycle 33: After refmac, R = 0.2480 (Rfree = 0.000) for 2965 atoms. Found 23 (23 requested) and removed 21 (13 requested) atoms. Cycle 34: After refmac, R = 0.2242 (Rfree = 0.000) for 2956 atoms. Found 23 (23 requested) and removed 16 (13 requested) atoms. Cycle 35: After refmac, R = 0.2184 (Rfree = 0.000) for 2954 atoms. Found 19 (23 requested) and removed 15 (13 requested) atoms. ------------------------------------------------------ Building Cycle 8 Atomic shape factors 3.36 3.14 Search for helices and strands: 0 residues in 0 chains, 3055 seeds are put forward NCS extension: 47 residues added (5 deleted due to clashes), 3102 seeds are put forward Round 1: 229 peptides, 32 chains. Longest chain 18 peptides. Score 0.500 Round 2: 258 peptides, 30 chains. Longest chain 33 peptides. Score 0.596 Round 3: 272 peptides, 33 chains. Longest chain 19 peptides. Score 0.597 Round 4: 260 peptides, 27 chains. Longest chain 36 peptides. Score 0.632 Round 5: 263 peptides, 27 chains. Longest chain 39 peptides. Score 0.638 Taking the results from Round 5 Chains 28, Residues 236, Estimated correctness of the model 50.9 % 1 chains (36 residues) have been docked in sequence ------------------------------------------------------ 9055 reflections ( 99.15 % complete ) and 5900 restraints for refining 3094 atoms. 4814 conditional restraints added. Observations/parameters ratio is 0.73 ------------------------------------------------------ Cycle 36: After refmac, R = 0.2609 (Rfree = 0.000) for 3094 atoms. Found 24 (24 requested) and removed 34 (13 requested) atoms. Cycle 37: After refmac, R = 0.2431 (Rfree = 0.000) for 3066 atoms. Found 24 (24 requested) and removed 38 (13 requested) atoms. Cycle 38: After refmac, R = 0.2813 (Rfree = 0.000) for 3036 atoms. Found 24 (24 requested) and removed 25 (13 requested) atoms. Cycle 39: After refmac, R = 0.2611 (Rfree = 0.000) for 3032 atoms. Found 24 (24 requested) and removed 21 (13 requested) atoms. Cycle 40: After refmac, R = 0.2192 (Rfree = 0.000) for 3021 atoms. Found 20 (24 requested) and removed 15 (13 requested) atoms. ------------------------------------------------------ Building Cycle 9 Atomic shape factors 3.38 3.16 Search for helices and strands: 0 residues in 0 chains, 3095 seeds are put forward NCS extension: 31 residues added (13 deleted due to clashes), 3126 seeds are put forward Round 1: 221 peptides, 31 chains. Longest chain 17 peptides. Score 0.491 Round 2: 247 peptides, 27 chains. Longest chain 29 peptides. Score 0.603 Round 3: 242 peptides, 24 chains. Longest chain 32 peptides. Score 0.623 Round 4: 235 peptides, 28 chains. Longest chain 20 peptides. Score 0.563 Round 5: 238 peptides, 26 chains. Longest chain 16 peptides. Score 0.593 Taking the results from Round 3 Chains 27, Residues 218, Estimated correctness of the model 47.1 % 2 chains (44 residues) have been docked in sequence ------------------------------------------------------ 9055 reflections ( 99.15 % complete ) and 6158 restraints for refining 3151 atoms. 5124 conditional restraints added. Observations/parameters ratio is 0.72 ------------------------------------------------------ Cycle 41: After refmac, R = 0.2421 (Rfree = 0.000) for 3151 atoms. Found 23 (25 requested) and removed 42 (14 requested) atoms. Failed to save intermediate PDB Cycle 42: After refmac, R = 0.2418 (Rfree = 0.000) for 3125 atoms. Found 25 (25 requested) and removed 28 (14 requested) atoms. Cycle 43: After refmac, R = 0.2266 (Rfree = 0.000) for 3110 atoms. Found 21 (25 requested) and removed 23 (14 requested) atoms. Cycle 44: After refmac, R = 0.2279 (Rfree = 0.000) for 3090 atoms. Found 21 (24 requested) and removed 18 (13 requested) atoms. Cycle 45: After refmac, R = 0.2202 (Rfree = 0.000) for 3087 atoms. Found 19 (24 requested) and removed 20 (13 requested) atoms. ------------------------------------------------------ Building Cycle 10 Atomic shape factors 3.35 3.13 Search for helices and strands: 0 residues in 0 chains, 3167 seeds are put forward NCS extension: 23 residues added (5 deleted due to clashes), 3190 seeds are put forward Round 1: 221 peptides, 35 chains. Longest chain 18 peptides. Score 0.440 Round 2: 244 peptides, 30 chains. Longest chain 27 peptides. Score 0.563 Round 3: 255 peptides, 31 chains. Longest chain 31 peptides. Score 0.578 Round 4: 256 peptides, 30 chains. Longest chain 33 peptides. Score 0.591 Round 5: 245 peptides, 28 chains. Longest chain 20 peptides. Score 0.587 Taking the results from Round 4 Last building cycle: Chain fragments will be rearranged Chains 30, Residues 226, Estimated correctness of the model 38.6 % 0 chains (0 residues) have been docked in sequence Sequence coverage is 0 % Consider running further cycles of model building using 2a6a-3_warpNtrace.pdb as input ------------------------------------------------------ ---> Final restrained refinement block. No atom update. 9055 reflections ( 99.15 % complete ) and 6620 restraints for refining 3149 atoms. 5746 conditional restraints added. Observations/parameters ratio is 0.72 ------------------------------------------------------ Cycle 46: After refmac, R = 0.2262 (Rfree = 0.000) for 3149 atoms. Found 0 (25 requested) and removed 14 (14 requested) atoms. Cycle 47: After refmac, R = 0.2346 (Rfree = 0.000) for 3118 atoms. Found 0 (25 requested) and removed 14 (14 requested) atoms. Cycle 48: After refmac, R = 0.2693 (Rfree = 0.000) for 3096 atoms. Found 0 (24 requested) and removed 13 (13 requested) atoms. Cycle 49: After refmac, R = 0.2293 (Rfree = 0.000) for 3078 atoms. TimeTaking 48.3