Mon 24 Dec 07:53:17 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 2nyh-1.7-parrot-noncs X-ray data file /users/emra500/scratch/Dataset/noncsChltofom/2nyh-1.7-parrot-noncs.mtz Sequence file /users/emra500/scratch/Dataset/noncsChltofom/2nyh-1.7-parrot-noncs.fasta Tracing mode WARPNTRACEPHASES Creating directory /mnt/lustre/users/emra500/PipeliensFastaNoRFree/noncs/ArpWArp/wArpResults/WorkingDir/2nyh-1.7-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/2nyh-1.7-parrot-noncs/arp_warp_classic.par Job launched in /mnt/lustre/users/emra500/PipeliensFastaNoRFree/noncs/ArpWArp/wArpResults/WorkingDir/2nyh-1.7-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 07:53:22 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/2nyh-1.7-parrot-noncs ARP/wARP software version: 8.0 The parameter file: /mnt/lustre/users/emra500/PipeliensFastaNoRFree/noncs/ArpWArp/wArpResults/WorkingDir/2nyh-1.7-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 293 and 0 Target number of residues in the AU: 293 Target solvent content: 0.4292 Checking the provided sequence file Detected sequence length: 117 Maximum limit of NCS related copies: 60 Number of NCS-related molecules: 2 Adjusted target number of residues: 234 Adjusted target solvent content: 0.54 Input MTZ file: 2nyh-1.7-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: 20 Cell parameters: 70.985 88.344 88.592 90.000 90.000 90.000 Input sequence file: 2nyh-1.7-parrot-noncs.fasta_lf Building free atoms model in initial map for 1872 target number of atoms Had to go as low as 0.55 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 1 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: 55.335 1.699 Wilson plot Bfac: 11.46 30388 reflections ( 97.99 % complete ) and 0 restraints for refining 2081 atoms. Observations/parameters ratio is 3.65 ------------------------------------------------------ Starting model: R = 0.4048 (Rfree = 0.000). ------------------------------------------------------ Cycle 0: After refmac, R = 0.3711 (Rfree = 0.000) for 2081 atoms. Found 105 (113 requested) and removed 58 (56 requested) atoms. ------------------------------------------------------ Building Cycle 1 Atomic shape factors 1.71 1.62 NCS extension: 0 residues added, 2128 seeds are put forward Round 1: 119 peptides, 25 chains. Longest chain 9 peptides. Score 0.291 Round 2: 117 peptides, 22 chains. Longest chain 10 peptides. Score 0.355 Round 3: 121 peptides, 23 chains. Longest chain 7 peptides. Score 0.354 Round 4: 131 peptides, 23 chains. Longest chain 11 peptides. Score 0.412 Round 5: 112 peptides, 19 chains. Longest chain 10 peptides. Score 0.402 Taking the results from Round 4 Chains 23, Residues 108, Estimated correctness of the model 84.2 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 30388 reflections ( 97.99 % complete ) and 4012 restraints for refining 1961 atoms. 3603 conditional restraints added. Observations/parameters ratio is 3.87 ------------------------------------------------------ Cycle 1: After refmac, R = 0.3912 (Rfree = 0.000) for 1961 atoms. Found 101 (106 requested) and removed 58 (53 requested) atoms. Cycle 2: After refmac, R = 0.3769 (Rfree = 0.000) for 2003 atoms. Found 79 (109 requested) and removed 28 (54 requested) atoms. Cycle 3: After refmac, R = 0.3672 (Rfree = 0.000) for 2050 atoms. Found 70 (112 requested) and removed 20 (56 requested) atoms. Cycle 4: After refmac, R = 0.3567 (Rfree = 0.000) for 2097 atoms. Found 61 (114 requested) and removed 4 (57 requested) atoms. Cycle 5: After refmac, R = 0.3416 (Rfree = 0.000) for 2151 atoms. Found 55 (117 requested) and removed 6 (58 requested) atoms. ------------------------------------------------------ Building Cycle 2 Atomic shape factors 1.64 1.55 NCS extension: 0 residues added, 2236 seeds are put forward Round 1: 100 peptides, 19 chains. Longest chain 9 peptides. Score 0.329 Round 2: 110 peptides, 19 chains. Longest chain 12 peptides. Score 0.390 Round 3: 121 peptides, 21 chains. Longest chain 11 peptides. Score 0.404 Round 4: 119 peptides, 20 chains. Longest chain 10 peptides. Score 0.417 Round 5: 116 peptides, 21 chains. Longest chain 10 peptides. Score 0.375 Taking the results from Round 4 Chains 20, Residues 99, Estimated correctness of the model 84.4 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 30388 reflections ( 97.99 % complete ) and 4621 restraints for refining 2163 atoms. 4245 conditional restraints added. Observations/parameters ratio is 3.51 ------------------------------------------------------ Cycle 6: After refmac, R = 0.3577 (Rfree = 0.000) for 2163 atoms. Found 90 (117 requested) and removed 21 (58 requested) atoms. Cycle 7: After refmac, R = 0.3408 (Rfree = 0.000) for 2230 atoms. Found 59 (121 requested) and removed 8 (60 requested) atoms. Cycle 8: After refmac, R = 0.3319 (Rfree = 0.000) for 2279 atoms. Found 53 (124 requested) and removed 4 (62 requested) atoms. Cycle 9: After refmac, R = 0.3249 (Rfree = 0.000) for 2326 atoms. Found 41 (126 requested) and removed 2 (63 requested) atoms. Cycle 10: After refmac, R = 0.3177 (Rfree = 0.000) for 2363 atoms. Found 32 (128 requested) and removed 7 (64 requested) atoms. ------------------------------------------------------ Building Cycle 3 Atomic shape factors 1.63 1.55 NCS extension: 0 residues added, 2409 seeds are put forward Round 1: 101 peptides, 20 chains. Longest chain 9 peptides. Score 0.309 Round 2: 111 peptides, 19 chains. Longest chain 13 peptides. Score 0.396 Round 3: 102 peptides, 18 chains. Longest chain 9 peptides. Score 0.368 Round 4: 102 peptides, 16 chains. Longest chain 9 peptides. Score 0.420 Round 5: 111 peptides, 20 chains. Longest chain 9 peptides. Score 0.370 Taking the results from Round 4 Chains 16, Residues 86, Estimated correctness of the model 84.6 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 30388 reflections ( 97.99 % complete ) and 5078 restraints for refining 2331 atoms. 4750 conditional restraints added. Observations/parameters ratio is 3.26 ------------------------------------------------------ Cycle 11: After refmac, R = 0.3285 (Rfree = 0.000) for 2331 atoms. Found 96 (127 requested) and removed 12 (63 requested) atoms. Cycle 12: After refmac, R = 0.3175 (Rfree = 0.000) for 2415 atoms. Found 73 (131 requested) and removed 5 (65 requested) atoms. Cycle 13: After refmac, R = 0.3096 (Rfree = 0.000) for 2482 atoms. Found 49 (135 requested) and removed 6 (67 requested) atoms. Cycle 14: After refmac, R = 0.3039 (Rfree = 0.000) for 2524 atoms. Found 43 (137 requested) and removed 3 (68 requested) atoms. Cycle 15: After refmac, R = 0.2985 (Rfree = 0.000) for 2563 atoms. Found 50 (139 requested) and removed 3 (69 requested) atoms. ------------------------------------------------------ Building Cycle 4 Atomic shape factors 1.61 1.53 NCS extension: 0 residues added, 2625 seeds are put forward Round 1: 105 peptides, 20 chains. Longest chain 8 peptides. Score 0.334 Round 2: 118 peptides, 22 chains. Longest chain 9 peptides. Score 0.361 Round 3: 109 peptides, 20 chains. Longest chain 9 peptides. Score 0.358 Round 4: 118 peptides, 19 chains. Longest chain 9 peptides. Score 0.436 Round 5: 103 peptides, 19 chains. Longest chain 9 peptides. Score 0.348 Taking the results from Round 4 Chains 19, Residues 99, Estimated correctness of the model 85.3 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 30388 reflections ( 97.99 % complete ) and 5609 restraints for refining 2520 atoms. 5232 conditional restraints added. Observations/parameters ratio is 3.01 ------------------------------------------------------ Cycle 16: After refmac, R = 0.3155 (Rfree = 0.000) for 2520 atoms. Found 101 (137 requested) and removed 16 (68 requested) atoms. Cycle 17: After refmac, R = 0.3044 (Rfree = 0.000) for 2605 atoms. Found 73 (141 requested) and removed 2 (70 requested) atoms. Cycle 18: After refmac, R = 0.2966 (Rfree = 0.000) for 2674 atoms. Found 55 (145 requested) and removed 1 (72 requested) atoms. Cycle 19: After refmac, R = 0.2893 (Rfree = 0.000) for 2727 atoms. Found 39 (148 requested) and removed 1 (74 requested) atoms. Cycle 20: After refmac, R = 0.2835 (Rfree = 0.000) for 2763 atoms. Found 29 (150 requested) and removed 1 (75 requested) atoms. ------------------------------------------------------ Building Cycle 5 Atomic shape factors 1.58 1.50 NCS extension: 0 residues added, 2806 seeds are put forward Round 1: 123 peptides, 24 chains. Longest chain 9 peptides. Score 0.341 Round 2: 116 peptides, 21 chains. Longest chain 10 peptides. Score 0.375 Round 3: 123 peptides, 24 chains. Longest chain 9 peptides. Score 0.341 Round 4: 126 peptides, 22 chains. Longest chain 10 peptides. Score 0.408 Round 5: 127 peptides, 23 chains. Longest chain 9 peptides. Score 0.389 Taking the results from Round 4 Chains 22, Residues 104, Estimated correctness of the model 84.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 30388 reflections ( 97.99 % complete ) and 5987 restraints for refining 2674 atoms. 5593 conditional restraints added. Observations/parameters ratio is 2.84 ------------------------------------------------------ Cycle 21: After refmac, R = 0.3126 (Rfree = 0.000) for 2674 atoms. Found 134 (145 requested) and removed 16 (72 requested) atoms. Cycle 22: After refmac, R = 0.2968 (Rfree = 0.000) for 2790 atoms. Found 59 (151 requested) and removed 7 (75 requested) atoms. Cycle 23: After refmac, R = 0.2885 (Rfree = 0.000) for 2838 atoms. Found 45 (154 requested) and removed 5 (77 requested) atoms. Cycle 24: After refmac, R = 0.2825 (Rfree = 0.000) for 2872 atoms. Found 45 (156 requested) and removed 5 (78 requested) atoms. Cycle 25: After refmac, R = 0.2779 (Rfree = 0.000) for 2908 atoms. Found 34 (158 requested) and removed 6 (79 requested) atoms. ------------------------------------------------------ Building Cycle 6 Atomic shape factors 1.61 1.53 NCS extension: 0 residues added, 2948 seeds are put forward Round 1: 117 peptides, 22 chains. Longest chain 9 peptides. Score 0.355 Round 2: 117 peptides, 20 chains. Longest chain 9 peptides. Score 0.405 Round 3: 122 peptides, 20 chains. Longest chain 9 peptides. Score 0.434 Round 4: 120 peptides, 19 chains. Longest chain 10 peptides. Score 0.447 Round 5: 114 peptides, 19 chains. Longest chain 12 peptides. Score 0.413 Taking the results from Round 4 Chains 19, Residues 101, Estimated correctness of the model 85.8 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 30388 reflections ( 97.99 % complete ) and 6388 restraints for refining 2816 atoms. 6003 conditional restraints added. Observations/parameters ratio is 2.70 ------------------------------------------------------ Cycle 26: After refmac, R = 0.2968 (Rfree = 0.000) for 2816 atoms. Found 117 (153 requested) and removed 12 (76 requested) atoms. Cycle 27: After refmac, R = 0.2855 (Rfree = 0.000) for 2918 atoms. Found 56 (159 requested) and removed 7 (79 requested) atoms. Cycle 28: After refmac, R = 0.2779 (Rfree = 0.000) for 2966 atoms. Found 41 (161 requested) and removed 1 (80 requested) atoms. Cycle 29: After refmac, R = 0.2717 (Rfree = 0.000) for 3003 atoms. Found 47 (163 requested) and removed 1 (81 requested) atoms. Cycle 30: After refmac, R = 0.2674 (Rfree = 0.000) for 3048 atoms. Found 22 (166 requested) and removed 2 (83 requested) atoms. ------------------------------------------------------ Building Cycle 7 Atomic shape factors 1.59 1.51 NCS extension: 0 residues added, 3079 seeds are put forward Round 1: 100 peptides, 19 chains. Longest chain 9 peptides. Score 0.329 Round 2: 101 peptides, 16 chains. Longest chain 12 peptides. Score 0.414 Round 3: 105 peptides, 17 chains. Longest chain 12 peptides. Score 0.412 Round 4: 103 peptides, 17 chains. Longest chain 12 peptides. Score 0.400 Round 5: 118 peptides, 18 chains. Longest chain 12 peptides. Score 0.460 Taking the results from Round 5 Chains 18, Residues 100, Estimated correctness of the model 86.4 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 30388 reflections ( 97.99 % complete ) and 6892 restraints for refining 2947 atoms. 6510 conditional restraints added. Observations/parameters ratio is 2.58 ------------------------------------------------------ Cycle 31: After refmac, R = 0.2849 (Rfree = 0.000) for 2947 atoms. Found 121 (160 requested) and removed 19 (80 requested) atoms. Cycle 32: After refmac, R = 0.2761 (Rfree = 0.000) for 3049 atoms. Found 74 (166 requested) and removed 11 (83 requested) atoms. Cycle 33: After refmac, R = 0.2683 (Rfree = 0.000) for 3110 atoms. Found 52 (169 requested) and removed 4 (84 requested) atoms. Cycle 34: After refmac, R = 0.2656 (Rfree = 0.000) for 3154 atoms. Found 54 (172 requested) and removed 4 (86 requested) atoms. Cycle 35: After refmac, R = 0.2637 (Rfree = 0.000) for 3202 atoms. Found 47 (174 requested) and removed 3 (87 requested) atoms. ------------------------------------------------------ Building Cycle 8 Atomic shape factors 1.58 1.50 NCS extension: 0 residues added, 3254 seeds are put forward Round 1: 105 peptides, 21 chains. Longest chain 10 peptides. Score 0.308 Round 2: 90 peptides, 16 chains. Longest chain 11 peptides. Score 0.347 Round 3: 89 peptides, 17 chains. Longest chain 9 peptides. Score 0.314 Round 4: 98 peptides, 18 chains. Longest chain 9 peptides. Score 0.343 Round 5: 80 peptides, 13 chains. Longest chain 8 peptides. Score 0.367 Taking the results from Round 5 Chains 13, Residues 67, Estimated correctness of the model 81.9 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 30388 reflections ( 97.99 % complete ) and 7386 restraints for refining 3060 atoms. 7131 conditional restraints added. Observations/parameters ratio is 2.48 ------------------------------------------------------ Cycle 36: After refmac, R = 0.2848 (Rfree = 0.000) for 3060 atoms. Found 123 (166 requested) and removed 12 (83 requested) atoms. Failed to save intermediate PDB Cycle 37: After refmac, R = 0.2784 (Rfree = 0.000) for 3169 atoms. Found 68 (172 requested) and removed 5 (86 requested) atoms. Cycle 38: After refmac, R = 0.2694 (Rfree = 0.000) for 3227 atoms. Found 60 (176 requested) and removed 5 (88 requested) atoms. Cycle 39: After refmac, R = 0.2647 (Rfree = 0.000) for 3279 atoms. Found 61 (178 requested) and removed 7 (89 requested) atoms. Cycle 40: After refmac, R = 0.2629 (Rfree = 0.000) for 3330 atoms. Found 44 (181 requested) and removed 6 (90 requested) atoms. ------------------------------------------------------ Building Cycle 9 Atomic shape factors 1.58 1.50 NCS extension: 0 residues added, 3379 seeds are put forward Round 1: 83 peptides, 15 chains. Longest chain 11 peptides. Score 0.330 Round 2: 80 peptides, 13 chains. Longest chain 11 peptides. Score 0.367 Round 3: 81 peptides, 14 chains. Longest chain 11 peptides. Score 0.346 Round 4: 87 peptides, 13 chains. Longest chain 16 peptides. Score 0.410 Round 5: 82 peptides, 13 chains. Longest chain 11 peptides. Score 0.380 Taking the results from Round 4 Chains 13, Residues 74, Estimated correctness of the model 84.1 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 30388 reflections ( 97.99 % complete ) and 7908 restraints for refining 3207 atoms. 7625 conditional restraints added. Observations/parameters ratio is 2.37 ------------------------------------------------------ Cycle 41: After refmac, R = 0.2779 (Rfree = 0.000) for 3207 atoms. Found 142 (174 requested) and removed 9 (87 requested) atoms. Cycle 42: After refmac, R = 0.2721 (Rfree = 0.000) for 3340 atoms. Found 71 (181 requested) and removed 9 (90 requested) atoms. Cycle 43: After refmac, R = 0.2611 (Rfree = 0.000) for 3401 atoms. Found 36 (185 requested) and removed 3 (92 requested) atoms. Cycle 44: After refmac, R = 0.2556 (Rfree = 0.000) for 3431 atoms. Found 23 (186 requested) and removed 6 (93 requested) atoms. Cycle 45: After refmac, R = 0.2497 (Rfree = 0.000) for 3445 atoms. Found 29 (187 requested) and removed 1 (93 requested) atoms. ------------------------------------------------------ Building Cycle 10 Atomic shape factors 1.58 1.50 NCS extension: 0 residues added, 3478 seeds are put forward Round 1: 82 peptides, 14 chains. Longest chain 12 peptides. Score 0.352 Round 2: 84 peptides, 13 chains. Longest chain 12 peptides. Score 0.392 Round 3: 93 peptides, 16 chains. Longest chain 12 peptides. Score 0.366 Round 4: 87 peptides, 14 chains. Longest chain 11 peptides. Score 0.383 Round 5: 81 peptides, 13 chains. Longest chain 11 peptides. Score 0.374 Taking the results from Round 2 Last building cycle: Chain fragments will be rearranged Chains 13, Residues 71, Estimated correctness of the model 83.2 % 0 chains (0 residues) have been docked in sequence Sequence coverage is 0 % Consider running further cycles of model building using 2nyh-1_warpNtrace.pdb as input ------------------------------------------------------ ---> Final restrained refinement block. No atom update. 30388 reflections ( 97.99 % complete ) and 8362 restraints for refining 3339 atoms. 8091 conditional restraints added. Observations/parameters ratio is 2.28 ------------------------------------------------------ Cycle 46: After refmac, R = 0.2643 (Rfree = 0.000) for 3339 atoms. Found 0 (182 requested) and removed 2 (91 requested) atoms. Cycle 47: After refmac, R = 0.2578 (Rfree = 0.000) for 3337 atoms. Found 0 (181 requested) and removed 0 (90 requested) atoms. Cycle 48: After refmac, R = 0.2548 (Rfree = 0.000) for 3337 atoms. Found 0 (181 requested) and removed 0 (90 requested) atoms. Cycle 49: After refmac, R = 0.2544 (Rfree = 0.000) for 3337 atoms. TimeTaking 41.77